CH 3 Click Chemistry

The Molecular Probes Handbook
A GUIDE TO FLUORESCENT PROBES AND LABELING TECHNOLOGIES

11th Edition (2010)
Molecular Probes Handbook

A Guide to Fluorescent Probes and Labeling Technologies
11th Edition (2010)
CHAPTER 1
Fluorophores
CHAPTER
3
and
Their
Amine-Reactive
Cli ck
Chemistry
and
Derivatives
Other
Fu nctional
Group Modifications
Molecular Probes Resources
Molecular Probes Handbook (online version)
Comprehensive guide to fluorescent probes and labeling technologies
thermo isher.com/handbook
Molecular
ProbesSpectraViewer
Resources
Molecular
Probes Fluorescence
Identify compatible sets of fluorescent dyes and cell structure probes
Molecular Probes Handbook (online version)
thermofisher.com/spectraviewer
Comprehensive guide to fluorescent probes and labeling technologies
lifetechnologies.com/handbook
BioProbes Journal
of Cell Biology Applications
Award-winning magazine highlighting cell biology products and applications
Fluorescence SpectraViewer
thermofisher.com/bioprobes
Identify compatible sets of fluorescent dyes and cell structure probes
Access all Molecular
Probes educational resources at thermofisher.com/probes
lifetechnologies.com/spectraviewer
BioProbes Journal of Cell Biology Applications

Award-winning magazine highlighting cell biology products and applications
lifetechnologies.com/bioprobes
Access all Molecular Probes educational resources at lifetechnologies.com/mpeducat
THREE
CHAPTER 3
Click Chemistry and

Other Functional Group Modifications
3.1 Click Chemistry
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Principles of Bioorthogonal Labeling and Click Chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

Click-iT Azide and Alkyne Labeling Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Azide- and Alkyne-Derivatized Dyes and Biotinylation Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Azide- and Alkyne-Modified Nucleosides and Amino Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Azide- and Alkyne-Modified Monosaccharides, Fatty Acids and Isoprenoids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
Heterobifunctional Reagents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
Click-iT Reaction Buffers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Click-iT Tools for Cell Proliferation Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129

Click-iT EdU Flow Cytometry Assay Kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Click-iT EdU Imaging Kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Click-iT EdU HCS Assay Kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Click-iT EdU Microplate Assay Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Click-iT TUNEL Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130

Click-iT Tools for Detecting RNA and Protein Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Click-iT RNA Kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Click-iT Nascent Protein Synthesis Detection Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
Data Table 3.1 Click Chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132

Product List 3.1 Click Chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
3.2 Reagents for Modifying Alcohols
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
Alcohols in Proteins: Serine, Threonine and Tyrosine Residues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134

Serine and Threonine Residues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
Tyrosine Residues. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Alcohols in Carbohydrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135

Dichlorotriazines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
N-Methylisatoic Anhydride . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Dansyl Aminophenylboronic Acid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Alcohol Modification in Organic Solvents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136

Isocyanates Prepared from Acyl Azides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Acyl Nitriles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
Data Table 3.2 Reagents for Modifying Alcohols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

Product List 3.2 Reagents for Modifying Alcohols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
3.3 Reagents for Modifying Aldehydes and Ketones .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Introducing Aldehydes and Ketones into Biomolecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138

Periodate Oxidation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Galactose OxidaseMediated Oxidation and Other Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Coupling Hydrazines and Amines to Amine-Containing Biomolecules without Introducing Aldehydes and Ketones . . . . . . . . . . . . . . . . . . 139
TheMolecular
Molecular
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
The
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT NOTICE: The products described in this manual are covered by one or more Limited Use Label License(s). Please refer to the Appendix on
IMPORTANT NOTICE
: The
products
inon
this
manual
are covered
one or more
Limited
Use Label
License(s).
to the or
Appendix
onuse.
page
971 and
Masterdescribed
Product List
page
975. Products
are ForbyResearch
Use Only.
Not intended
for any
animal orPlease
humanrefer
therapeutic
diagnostic
page 971 and Master Product List on page 975. Products are For Research Use Only. Not intended for any animal
or human therapeutic or diagnostic use.
www.invitrogen.com/probes
thermofisher.com/probes
123
Chapter 3 Click Chemistry and Other Functional Group Modifications
Introducing a Hydroxylamine into a Biomolecule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139

Hydrazines and Hydroxylamines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Reactivity of Hydrazine and Hydroxylamine Derivatives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Fluorescent Hydrazine and Hydroxylamine Derivatives Excited with Visible Light . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Fluorescent Hydrazine and Hydroxylamine Derivatives Excited with UV Light . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Polar Fluorescent Hydrazides and Hydroxylamines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
NBD Methylhydrazine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Biotin Hydrazides and Biotin Hydroxylamine. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Aliphatic and Aromatic Amines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142

Data Table 3.3 Reagents for Modifying Aldehydes and Ketones . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Product List 3.3 Reagents for Modifying Aldehydes and Ketones . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
3.4 Derivatization Reagents for Carboxylic Acids and Carboxamides
. . . . . . . . . . . . . . . . . . . . . . 145
Coupling Hydrazines, Hydroxylamines and Amines to Carboxylic Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145

Modification in Aqueous Solutions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Modification in Organic Solvents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Hydrazine, Hydroxylamine and Aliphatic Amine Derivatives. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Enzyme-Catalyzed Transamidation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Esterification of Carboxylic Acids with Fluorescent Diazoalkanes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

Fluorescent Alkyl Halides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Fluorescent Trifluoromethanesulfonate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
4-Sulfo-2,3,5,6-Tetrafluorophenol (STP) and N-Hydroxysulfosuccinimide (NHSS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
Data Table 3.4 Derivatization Reagents for Carboxylic Acids and Carboxamides. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Product List 3.4 Derivatization Reagents for Carboxylic Acids and Carboxamides . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
The
Molecular
Guide to
to Fluorescent
Fluorescent Probes
The
MolecularProbes
Probes Handbook:
Handbook: AA Guide
Probesand
andLabeling
LabelingTechnologies
Technologies
124
page
971 and Master
Product
List on
page 975.
Products in
arethis
For Research
Usecovered
Only. Notby
intended
anyLimited
animal orUse
human
therapeutic
or diagnostic
use.to
IMPORTANT
NOTICE
: The
products
described
manual are
one or for
more
Label
License(s).
Please refer
the Appendix on
page 971 and Master Product List on page 975. Products are For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.
Section 3.1
Click Chemistry
3.1 Click Chemistry

Principles of Bioorthogonal Labeling and Click Chemistry
The amine and thiol-reactive labeling chemistries described in
Chapter 1 and Chapter 2 are generally used in one of two ways: (1)
labeling of purified proteins or other biopolymers yielding conjugates
that are subsequently applied to cell or tissue specimens, or (2) nonselective in situ labeling of total cellular thiol or amine content. In
situ labeling of specific molecular populationssuch as proteins and
nucleic acids that have been newly synthesized in some experimental
time window of interestis not feasible due to the ubiquitous distribution of amines and thiols in cells, as well as in the media in which they
are maintained. Click-iT labeling technology overcomes this obstacle
O
CH
SO 3
SO 3
C
HN
NH2
SO 3
NH2
NH2
NH2
C O
C O
O
O
N N N
OH
SO 3
O
Cu
HOCH2 O
by employing bioorthogonal reactive chemistry, in which the reaction

partners have no endogenous representation in biological molecules,
cells, tissues or model organisms.13 In addition to reaction selectivity,
in situ labeling methods should allow reactivity under mild conditions
and in predominantly aqueous solvent conditions.
Although several known chemistries fulfill the requirements described above,1,3 Click-iT labeling technology is founded upon one of
the most successful and versatile bioorthogonal labeling reactions currently availablethe copper-catalyzed azidealkyne cyloaddition 4,5
(Figure 3.1.1). Application of this reaction to in situ labeling of cells
(CH 2) 6NH C
N N
N
HN
(CH 2) 6NH C
O
O
HOCH2 O
OH
SO 3
SO 3
NH2
O
HO C
CH CH2CH2C CH
NH2
N N N
C O
C O
SO 3
NH2
HO C
HO
CH CH2CH2
SO 3
NH2
NH
OH
HO
CCH2N N N
CH CCH2NH C
NH2
C O
O
CH2
C O
O
NH
OH
N N
CCH2 N
CH2NH C
SO 3
NH2
HO C (CH 2) 14N N N
SO 3
NH2
NH2
SO 3
O
NH2
OH
HO
SO 3
SO 3
Cu
O
(CH 2) 6NH C
NH2
OH
CH2
N N
(CH 2) 6NH C
O
NH2
Cu
NH2
HO
SO 3
SO 3
NH2
SO 3
NH2
Cu
C O
C O
O
O
CH CCH2NH C
O
N N
HO C (CH) 14 N
CH2NH C
O
Figure 3.1.1 Click-iT copper-catalyzed azidealkyne cycloaddition chemistry applied to detection of A) nucleic acids, B) proteins, C) carbohydrates and D) lipids. The reaction partners are
A) 5-ethynyl-2-deoxyuridine (EdU) and Alexa Fluor 488 azide, B) L-homopropargylglycine (HPG) and Alexa Fluor 488 azide, C) N-azidoacetylgalactosamine and Alexa Fluor 488 alkyne and
D) 15-azidopentadecanoic acid and Alexa Fluor 488 alkyne (D). In each case, the left-hand partner is a metabolic precursor that can be incorporated into proteins and nucleic acids via de novo
synthesis or post-translational modification pathways.
The
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
TheMolecular
Molecular
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT
NOTICE:described
The products
described
thiscovered
manual are
by oneLimited
or moreUse
Limited
Use
Label License(s).
to the
Appendix
IMPORTANT NOTICE
: The products
in this
manualinare
by covered
one or more
Label
License(s).
PleasePlease
referrefer
to the
Appendix
on on
125
is a two-step process. First, one reaction partnereither an azide or

alkyne linked to a building block such as a nucleotide, nucleoside,
amino acid, monosaccharide or fatty acidis biosynthetically incorporated. Subsequently, the other reaction partnerthe complementary
alkyne or azide linked to a fluorescent dye, biotin or other detection
reagentis clicked into place in the presence of catalytic copper (I).
One reaction partner must be an azide derivative and the other an
alkyne derivative, but either functional moiety can serve as the biosynthetically incorporated molecule or the detection molecule 6 (e.g.,
L-azidohomoalanine (AHA) + Alexa Fluor 488 alkyne is the inverse
of the reaction scheme shown in Figure 3.1.1B).
Another important aspect of the azide and alkyne reaction partners is their small size (Figure 3.1.2). Expression tags such as Green
Fluorescent Protein (GFP) provide the ultimate in labeling specificity because their linkage to proteins of interest is genetically prescribed. Once
the GFP transgene has been inserted into a cell (BacMam Gene Delivery
and Expression TechnologyNote 11.1), in situ labeling is obtained

without any outside intervention using the cellular transcription and
translation machinery. However, the finite size of GFP (~27,000 daltons) sometimes causes functional perturbations and has spurred the
development of alternative, smaller-sized expression tags such as the
TC-FlAsH tetracysteine tag and biarsenical ligand system (T34561,
T34562, T34563; Section 2.2). Furthermore, nucleic acids, lipids, glycans and post-translational protein modifications can only be detected
indirectly by genetically encoded protein reporters. The small size of
alkyne and azide tags allows the biosynthetic building blocks to which
they are attached to be processed by enzymes, such as nucleotide polymerases and aminoacyl tRNA synthetases, that have poor tolerance for
substrates with larger modifications such as fluorescent organic dyes.7
The 1,2,3-triazole linkage between the azide and alkyne reaction partners (Figure 3.1.1) is extremely stable. It is not susceptible to
hydrolysis, oxidation or reduction, and it survives ionization in mass
SO
3
H N
2
SO
3 +
NH
R1
MW
Click Chemistry
Section 3.1
R1
R2 O C
R2
Isotope(s)
Click-iT alkyne
Click-iT azide
Biotin
Alexa Fluor 488
Streptavidin
IgG antibody
25
42
~300
500
~68,000
~150,000
Both required for detection
Both required for detection
Figure 3.1.2 Relative size of detection molecules commonly used in cellular analysis. Because the azide and alkyne moieties can be used interchangeably to optimize labeling configurations,
R1 can be either the biomolecule of interest or the detection reagent. For biotin and Alexa Fluor 488, R2 represents the biomolecule of interest.
Table 3.1 Molecular Probes azide and alkyne derivatives.

Compound or Fluorophore
Azide or Alkyne
Cat. No.
Application
Monitor nascent protein synthesis or inhibition
Azide- or Alkyne-Modified Biomolecules for Metabolic or Enzymatic Labeling

Click-iT AHA (L-azidohomoalanine)
azide
C10102
Click-iT HPG (L-homopropargylglycine)
alkyne
C10186
Click-iT farnesyl alcohol, azide
azide
C10248
Click-iT geranylgeranyl alcohol, azide
azide
C10249
Click-iT fucose alkyne (tetraacetylfucose alkyne)
alkyne
C10264
Identification of fucoslyated proteins
Click-iT palmitic acid, azide
azide
C10265
Identification of protein fatty acylation
Click-iT myristic acid, azide
azide
C10268
Identification of isoprenylated proteins
Click-iT GalNAz (tetraacetylated N-azidoacetylgalactosamine)
azide
C33365
Identification of O-linked glycoproteins, including O-GlcNAc
Click-iT ManNAz (tetraacetylated N-azidoacetylmannosamine)
azide
C33366
Identification of sialic acidmodified glycoproteins
Click-iT ManNAz (tetraacetylated N-azidoacetylglucosamine)
azide
C33367
Identification of O-GlcNAcmodified glycoproteins
Azide- or Alkyne-Modified Fluorophores and Haptens for Detection (Ex/Em)*

Alexa Fluor 488 (495/519)
azide
alkyne
A10266
A10267
Fluorescent dye or hapten
azide
alkyne
A20012
A20013
Fluorescent dye
azide
alkyne
A10270
A10275
Fluorescent dye
azide
A10277
Fluorescent dye
Biotin (NA)
azide
alkyne
B10184
B10185
Hapten
Oregon Green 488 (496/524)
azide
alkyne
O10180
O10181
Tetramethylrhodamine (TAMRA) (555/580)
azide
alkyne
T10182
T10183
*Absorption and fluorescence emission maxima, in nm. As hapten, use with anti-dye antibody; see Section 7.4. Requires streptavidin for detection; see Section 7.6.
The
MolecularProbes
Probes Handbook:
Handbook: A
Probesand
andLabeling
Technologies
The
Molecular
A Guide
Guide to
to Fluorescent
Fluorescent Probes
126
IMPORTANT
NOTICE:
The products
described
in this manual
aremanual
coveredare
by one
or more
Use Label
License(s).
Please
refer to thePlease
Appendix
on to
IMPORTANT
NOTICE
: The products
described
in this
covered
by Limited
one or more
Limited
Use Label
License(s).
refer
the Appendix on
Section 3.1
spectrometry (MS) analysis. The reaction is also regiospecific, yielding exclusively 1,4-disubstituted-1,2,3-triazole linkages (Figure 3.1.1). The copper (I) catalyst is both an essential feature of
the reaction and its most problematic aspect in terms of applications.1,3,8 Without the copper (I)
catalyst, which accelerates the rate of the reaction by a factor of >106, the reaction is impractically
slow. For convenience, copper (I) is usually prepared in situ by reduction of extraneously added
copper (II) using ascorbate or TCEP (T2556, Section 2.1). Insufficient reductive capacity can result
in attenuation of in situ reactions in highly oxidizing environments.9 Copper is cytotoxic, due at
least in part to its capacity for sensitizing oxidative damage to proteins and nucleic acids, and limiting applications of the azidealkyne cyloaddition reaction in live cells. Copper/ascorbate treatment
also causes extinction of R-phycoerythrin (R-PE) and GFP fluorescence.10 An excellent analysis of
these considerations, together with a list of practical recommendations for their management with
respect to bioconjugation applications of copper-catalyzed azidealkyne cyloaddition chemistry,
has been published by Finn and co-workers.8 Our Click-iT product portfolio, consisting of individual azide and alkyne labeling reagents and application-specific kits, is described in detail below.
Click Chemistry
H
N
H
S
NH
(CH 2) 4
O C
NH(CH 2CH2O) 4CH2CH2
Although in situ labeling of biomolecules for cytochemical and proteomic analysis is perhaps
the most notable application of Click-iT technology, it is by no means the only one. This specific
and direct labeling methodology can also be applied to bioconjugate preparation, 8 surface and
particle functionalization and molecular ligations. Our Click-iT azide and alkyne labeling reagents support these applications and also provide foundational tools for developing new in situ
labeling applications (Table 3.1).
C NH(CH 2) 6 N N N
Figure 3.1.3 Biotin azide (PEG4 carboxamide-6-azidohexanyl biotin, B10184).
Click-iT Azide and Alkyne Labeling Reagents
H
N
O
NH
(CH 2) 4
O C
H
O
NH(CH 2CH2O) 4CH2CH2 C NHCH2C CH

Figure 3.1.4 Biotin alkyne (PEG4 carboxamide-propargyl
biotin, B10185).
Azide- and Alkyne-Derivatized Dyes and Biotinylation Reagents
We offer a rich selection of azide- and alkyne-derivatized fluorescent dyes for coupling to
complementary azide- and alkyne-functionalized biomolecules:
Alexa Fluor 488 azide (A10266, Figure 3.1.1) and alkyne (A10267, Figure 3.1.1)
Alexa Fluor 555 azide (A20012) and alkyne (A20013)
Oregon Green 488 azide (O10180) and alkyne (O10181)
Tetramethylrhodamine (TAMRA) azide (T10182) and alkyne (T10183)
Biotin azide (B10184, Figure 3.1.3) and alkyne (B10185, Figure 3.1.4)
Antibodies to Oregon Green 488, tetramethylrhodamine and Alexa Fluor 488 dyes (Section
7.4) and Tyramide Signal Amplification (TSA) Kits (Section 6.2) are available to provide signal
amplification if necessary.11 The biotin azide and alkyne reagents facilitate western blotting applications and streptavidin enrichment in combination with our streptavidin or CaptAvidin
agarose 1214 (S951, C21386; Section 7.6).
Azide- and Alkyne-Modified Nucleosides and Amino Acids
We offer the following azide- and alkyne-modified nucleosides and amino acids for
Click-iT labeling protocols:
5-ethynyl uridine (EU, E10345)

5-ethynyl-2-deoxyuridine (EdU; A10044, E10187, E10415; Figure 3.1.1A)
Click-iT AHA (L-azidohomoalanine for nascent protein synthesis, C10102)
Click-iT HPG (L-homopropargylglycine for nascent protein synthesis, C10186; Figure
3.1.1B)
The alkyne-modified nucleosides EdU and EU form the basis of our Click-iT cell proliferation and nascent RNA assays described below. The individual packagings of these reagents
provide the larger quantities required for in vivo labeling applications.6,15 AHA and HPG are
methionine surrogates providing nonradioactive alternatives to 35S-methionine for pulse-chase
detection of protein synthesis and degradation.1619
The
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
TheMolecular
Molecular
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT
NOTICE:described
The products
described
this covered
manual are
by oneLimited
or moreUse
Limited
Use
Label License(s).
to the
Appendix
IMPORTANT NOTICE
: The products
in this
manualinare
by covered
one or more
Label
License(s).
PleasePlease
referrefer
to the
Appendix
on on
127
Section 3.1
Click Chemistry
Azide- and Alkyne-Modified Monosaccharides, Fatty Acids and Isoprenoids
The Click-iT metabolic glycoprotein labeling reagents provide biosynthetic precursors for
detecting and characterizing post-translational glycosylation of proteins:14,2022
CH3CO OCCH3
CH2 O
O
OCCH
CH3CO
3
NH
O
CCH2N N N
O
Figure 3.1.5 Click-iT GalNAz metabolic glycoprotein labeling reagent (tetraacetylated N-azidoacetylgalactosamine,
C33365).
O
OCCH3
O
CH3CO
CH3CO
CH2
O
NH
O
OCCH3
CCH2N N N
O
Figure 3.17 Click-iT GlcNAz metabolic glycoprotein labeling reagent (tetraacetylated N-azidoacetylglucosamine for
labeling O-linked N-acetylglucosamine (O-GlcNAc)modified glycoproteins; C33367).
OCCH3
OCCH3
OCCH3 O
OCCH3
O
O
Figure 3.1.8 Click-iT fucose alkyne (tetraacetylfucose
alkyne, C10264).
O
H3CCO
H2C
O
H3CCO
Cultured cells are simply incubated with the modified sugars for 23 days or until cells
reach the appropriate density. The acetyl groups improve cell permeability of the modified sugars and are removed by nonspecific intracellular esterases (Figure 3.1.8). The resulting azide- or
alkyne-modified sugar is then metabolically incorporated through the permissive nature of the
oligosaccharide biosynthesis pathway, yielding functionalized glycoproteins that can be chemoselectively coupled to complementary alkyne- or azide-functionalized fluorophores and biotinylation reagents for detection or affinity capture. We also offer the the Click-iT O-GlcNAc
Enzymatic Labeling System for in vitro enzyme-mediated N-azidoacetylgalactosamine labeling
of O-GlcNAcmodified glycoproteins 26,27 (C33368, Section 9.4) and Click-iT Protein Analysis
Detection Kits (C33370, C33371, C33372; Section 9.4) for detection of azide-functionalized glycoproteins in 1D or 2D electrophoresis gels or western blots.
Similarly, our azide-functionalized isoprenoids and fatty acids enable detection of posttranslational lipidation of proteins by in-gel fluorescence scanning, fluorescence microscopy and
flow cytometry.2325 We offer the following azide-modified fatty acids and isoprenoids:
O
CH C
Click-iT GalNAz metabolic glycoprotein labeling reagent (tetraacetylated N-azidoacetylgalactosamine for labeling O-linked glycoproteins, C33365; Figure 3.1.1C, Figure 3.1.5)
Click-iT ManNAz metabolic glycoprotein labeling reagent (tetraacetylated N-azidoacetylmannosamine for labeling sialic acidmodified glycoproteins, C33366; Figure 3.1.6)
Click-iT GlcNAz metabolic glycoprotein labeling reagent (tetraacetylated
N-azidoacetylglucosamine for labeling O-linked N-acetylglucosamine
(O-GlcNAc)modified glycoproteins, C33367; Figure 3.1.7)
Click-iT fucose alkyne (tetraacetylfucose alkyne, C10264; Figure 3.1.8)
Click-iT farnesyl alcohol, azide (C10248, Figure 3.1.9)

Click-iT geranylgeranyl alcohol, azide (C10249, Figure 3.1.10)
Click-iT palmitic acid, azide (15-azidopentadecanoic acid, C10265; Figure 3.1.1D)
Click-iT myristic acid, azide (12-azidododecanoic acid, C10268)
Heterobifunctional Reagents
Our collection of heterobifunctional reagents provide a means for adapting the amine- and
thiol-reactive labeling chemistries described in Chapters 1 and 2 with the azidealkyne Click-iT
labeling protocols:
Azide succinimidyl ester (A10280, Figure 3.1.11)

Alkyne succinimidyl ester (A10279, Figure 3.1.12)
Azide iodoacetamide (I10188, Figure 3.1.13)
Alkyne iodoacetamide (I10189, Figure 3.1.14)
HN C CH2 N3
HO
H2C
HO
O
OCCH3
H3CCO
HO
HN C CH2 N3
O
HO
OH
Tetraacetylated azido sugar

(ManNAz)
Nonspecific esterases
cleave acetates, leaving
hydroxyls
HO
Metabolic
incorporation
Cell membrane
Figure 3.1.6 Metabolic incorporation of tetraacetylated azido sugars.
The
MolecularProbes
Probes Handbook:
Handbook: A
Probesand
andLabeling
Technologies
The
Molecular
A Guide
Guide to
to Fluorescent
Fluorescent Probes
128
HO
H2C
Protein
IMPORTANT
NOTICE:
The products
described
in this manual
coveredare
by one
or more
Limited
Use Label
License(s).
Please
refer to thePlease
Appendix
onto
IMPORTANT
NOTICE
: The products
described
in thisaremanual
covered
by one
or more
Limited
Use Label
License(s).
refer
the Appendix on
HN C CH2 N3
O
Protein
Section 3.1
The succinimidyl ester reagents can be used for azide or alkyne functionalization of aminecontaining molecules and molecular assemblies including terminally or internally modified oligonucleotides and nanoparticles.8,28
Click-iT Reaction Buffers
For added convenience, we offer Click-iT Reaction Buffer Kits for protein or cell samples
labeled with an azide- or alkyne-tagged biomolecule. The Click-iT Cell Reaction Buffer Kit
(C10269) includes sufficient reagents to perform 50 reactions based on a 0.5 mL reaction volume
for subsequent analyses by flow cytometry, fluorescence microscopy or high-content screening
(HCS). The Click-iT Protein Reaction Buffer Kit (C10276) includes everything required for click
coupling to functionalized proteins for subsequent standard protein biochemical analyses (e.g.,
western blots or mass spectrometry).
Click-iT Tools for Cell Proliferation Analysis

The Click-iT EdU cell proliferation assay provides a superior alternative to bromodeoxyuridine (BrdU) or 3H-thymidine incorporation methods for measuring new DNA synthesis.29,30 The
alkynyl nucleoside analog EdU (5-ethynyl-2-deoxyuridine; A10044, E10187, E10415) is incorporated into DNA during the synthesis phase (S phase) of the cell cycle and is subsequently detected
by copper (I)catalyzed click coupling to an azide-derivatized fluorophore 6 (Figure 3.1.2). The
small size of the click-coupled fluorophore compared to that of antibodies required for immunodetection of BrdU (Figure 3.31) enables efficient penetration of complex samples without the need
for harsh cell treatment, simplifying the assay considerably. The Click-iT EdU assay protocol is
compatible with both adherent cells and cell suspensions. From start to finish, the EdU detection
assay is complete in as little as 90 minutes, as compared with the antibody-based BrdU method,
which takes 624 hours to complete. In addition, the Click-iT EdU cell proliferation assay can
be multiplexed with surface and intracellular marker detection using Alexa Fluor dyelabeled
secondary antibodies 15,3133 (Section 7.2) (Figure 3.1.15). Although the majority of applications
are in cultured mammalian cells, Click-iT EdU reagents and methods have also been successfully applied to a wide range of model organisms including:
Escherichia coli 34
Caenorhabditis elegans 32
Drosophila 35
Zebrafish 36
Mouse 15
Plants 37,38 (alfalfa, Arabidopsis, grape, maize, rice and tobacco)
Click Chemistry
CH3
CH3
N N NCH2(C CHCH2CH2) 2C CHCH2OH
Figure 3.1.9 Click-iT farnesyl alcohol, azide (C10248).
CH3
CH3
N N NCH2(C CHCH2CH2) 3C CHCH2OH
Figure 3.1.10 Click-iT geranylgeranyl alcohol, azide
(C10249).
O
N N N
(CH 2CH2O) 4CH2CH2 C O N

O
Figure 3.1.11 Azido (PEO)4 propionic acid, succinimidyl

ester (3-(azidotetra(ethyleneoxy))propionic acid, succinimidyl ester, A10280).
CH CCH2OCH2CH2 C O N
O
Figure 3.1.12 Alkyne, succinimidyl ester (3-propargyloxypropanoic acid, succinimidyl ester, A10279).
O
ICH2 C NH(CH 2) 6 N N N
Figure 3.1.13 Iodoacetamide azide (I10188).
Figure 3.1.15 Multicolor imaging with the Click-iT EdU Imaging Kits. Muntjac cells were treated with 10 M EdU for
45 minutes. Cells were then fixed and permeabilized, and EdU that had been incorporated into newly synthesized DNA was
detected by the far-redfluorescent Click-iT EdU Alexa Fluor 647 HCS Assay Kit (C10356, C10357). Tubulin was labeled with
an anti-tubulin antibody and visualized with an Alexa Fluor 350 goat antimouse IgG antibody (A21049). The Golgi complex
was stained with the green-fluorescent Alexa Fluor 488 conjugate of lectin HPA from Helix pomatia (edible snail) (L11271),
and peroxisomes were labeled with an anti-peroxisome antibody and visualized with an orange-fluorescent Alexa Fluor 555
donkey antirabbit IgG antibody (A31572).
O
ICH2 C NHCH2C CH
Figure 3.1.14 Iodoacetamide alkyne (I10189).
The
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
TheMolecular
Molecular
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT
NOTICE:described
The products
described
thiscovered
manual are
by one
or moreUse
Limited
Label License(s).
to Appendix
the Appendix
IMPORTANT NOTICE
: The products
in this
manualinare
by covered
one or more
Limited
LabelUse
License(s).
PleasePlease
referrefer
to the
on on
129
Section 3.1
Click Chemistry
Click-iT EdU Flow Cytometry Assay Kits
O
C
HN
O
HO P O P O P OCH2
O
3 (CH3CH2)3NH
CH
OH
Figure 3.1.16 EdUTP nucleotide, provided in the Click-iT

TUNEL Imaging Assay Kits.
O
C
HN
CH
HOCH2 O
OH
Click-iT EdU Alexa Fluor 488 Flow Cytometry Assay Kit (C35002)
Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit (A10202)
Click-iT EdU Pacific Blue Flow Cytometry Assay Kit (A10034)
Additionally, two cell-cycle stains compatible with the fluorescence excitation and emission
characteristics of the fluorescent azide detection reagents are included.
Click-iT EdU Imaging Kits
The Click-iT EdU Imaging Kits contain all of the components needed to label and detect
incorporated EdU on 50 coverslips using 0.5 mL reaction buffer per test, as well as the bluefluorescent Hoechst 33342 nuclear stain for identification of cells irrespective of EdU incorporation status:
The Click-iT EdU Flow Cytometry Assay Kits provide all the reagents needed to perform
50 assays using 0.5 mL reaction buffer per assay, including the nucleoside analog EdU and all
components for fixation, permeabilization and labeling whole blood samples, adherent cells or
suspension cells.:30,39
OH
Figure 3.1.17 5-Ethynyl uridine (EU, E10345).
Click-iT EdU Alexa Fluor 488 Imaging Kit (C10337)

Click-iT EdU HCS Assay Kits
The Click-iT EdU HCS Assay Kits contain all of the materials needed to label and detect
incorporated EdU in adherent cells in 96-well microplates and 100 L reaction buffer per assay:
Click-iT EdU Alexa Fluor 488 HCS Assay Kit (2-plate size, C10350; 10-plate size, C10351)
Click-iT EdU Alexa Fluor 647 HCS Assay Kit (2-plate size, C10356; 10-plate size, C10357;
Figure 3.1.15)
For cell registration or DNA profiling, these kits also include the blue-fluorescent HCS
NuclearMask Blue stain.
Click-iT EdU Microplate Assay Kit
The Click-iT EdU Microplate Assay Kit provides a simple and rapid workflow with fewer
wash steps resulting in a substantial time-savings advantage over traditional BrdU colorimetric
or fluorescent cell proliferation assays. This assay uses Oregon Green 488 azide for click coupling to synthetically incorporated EdU. The signal is amplified using immunodetection of the
Oregon Green 488 fluorophore by a rabbit antiOregon Green horseradish peroxidase (HRP)
conjugate followed by fluorogenic or chromogenic detection with our Amplex UltraRed HRP
substrate. The Click-iT EdU microplate assay has been successfully tested in HeLa, A549, U2OS
and A541 cells with a variety of reagents that modulate DNA synthesis, including the DNA synthesis inhibitor aphidicolin and the mitotic inhibitor paclitaxel. The Click-iT EdU Microplate
Assay Kit (C10214) contains sufficient reagents for performing 400 individual assays in a 96-well
plate format.
Click-iT TUNEL Assay

The terminal deoxynucleotidyl transferase-dUTP nick end labeling (TUNEL) assaybased
on the incorporation of modified dUTPs by terminal deoxynucleotidyl transferase (TdT) at
the 3-OH ends of fragmented DNAis probably the most widely used in situ test for studying apoptotic DNA fragmentation. For a sensitive and reliable TUNEL imaging assay, it is vital
that the modified nucleotide is an efficient substrate for TdT. The minimally modified EdUTP
The
MolecularProbes
Probes Handbook:
Handbook: AA Guide
Probesand
andLabeling
Technologies
The
Molecular
Guide to
to Fluorescent
Fluorescent Probes
130
IMPORTANT
NOTICE:
The products
described
in this manual
coveredare
by covered
one or more
Limited
Use Label
License(s).
Please
refer to thePlease
Appendix
onto
IMPORTANT
NOTICE
: The products
described
in thisaremanual
by one
or more
Limited
Use Label
License(s).
refer
the Appendix on
Section 3.1
nucleotide (Figure 3.1.16) used in the Click-iT TUNEL imaging assay is rapidly incorporated by
TdT, allowing samples to be rapidly fixed in order to preserve late-stage apoptotic cells, thereby
lessening the possibility of false-negative results due to cell detachment and subsequent loss. The
enzymatically incorporated nucleotide is detected by copper (I)catalyzed click coupling to an
azide-derivatized fluorophore. Compared with assays that use one-step incorporation of dyemodified nucleotides, the fast and sensitive Click-iT TUNEL imaging assay can detect a higher
percentage of apoptotic cells under identical conditions in 2 hours or less.
The Click-iT TUNEL Imaging Assay Kits are available with a choice of azide-derivatized
Alexa Fluor dyes, providing flexibility for combination with other apoptosis detection reagents
(Section 15.5):
Click Chemistry
O
N N NCH2CH2 CH C OH
NH2
CF 3COOH
Figure 3.1.18 Click-iT AHA (L-azidohomoalanine, C10102).
Click-iT TUNEL Alexa Fluor 488 Imaging Assay (C10245)

The Click-iT TUNEL assay has been tested in HeLa, A549 and CHO K1 cells with a variety of
reagents that induce apoptosis, including staurosporine, and multiplexed with antibody-based detection of other apoptosis biomarkers such as cleaved poly(ADP-ribose) polymerase (PARP), cleaved
caspase-3 and phosphohistone 2B. It has also proven effective for detection of apoptosis induced by
siRNA knockdown of the DEC2 transcription factor in human MCF-7 breast cancer cells.40
Click-iT Tools for Detecting RNA and Protein Synthesis

Click-iT RNA Kits
Click-iT RNA Imaging and Click-iT RNA HCS Assay Kits provide everything needed to
detect newly synthesized RNA in adherent cells.:
Click-iT RNA Alexa Fluor 488 Imaging Kit (C10329)

Click-iT RNA Alexa Fluor 594 Imaging Kit (C10330)
Click-iT RNA Alexa Fluor 488 HCS Assay (C10327)
Click-iT RNA Alexa Fluor 594 HCS Assay (C10328)
Click-iT RNA assays are ideal for imaging global RNA synthesis in multiplex analyses using traditional fluorescence microscopy or high-content screening (HCS). The Click-iT RNA
assays employ the alkyne-modified nucleoside EU (5-ethynyl uridine, E10345; Figure 3.1.17),
which is supplied to cells and incorporated into nascent RNA.41 The small size of the alkyne tag
enables efficient incorporation by RNA polymerases without any apparent changes to the RNA
levels of several housekeeping genes. Detection of incorporated EU is accomplished by copper
(I)catalyzed click coupling to an azide-derivatized fluorophore. The multiplexing capability of
the assays makes them ideal for toxicological profiling or interrogation of disease models using
high-content imaging platforms.
The Click-iT RNA HCS Assay Kits (C10329, C10330) contain sufficient reagents to label and
detect newly synthesized RNA in whole cells using two 96-well microplates and 50 L reaction
volumes per well. These kits also supply the blue-fluorescent HCS NuclearMask blue stain as
a nuclear counterstain for cell demarcation or for DNA profiling. The Click-iT RNA Imaging
Kits (C10327, C10328) contain sufficient reagents to label and detect newly synthesized RNA in
whole cells using 25 coverslips and 500 L reaction volume per well. These kits also supply the
blue-fluorescent Hoechst 33342 dye as a nuclear counterstain or for DNA profiling.
The Click-iT Nascent RNA Capture Kit (C10365) enables RNA synthesized during a time window defined by administration of EU to be selectively biotinylated via click coupling of EU to biotin
azide. Biotinylated RNA is then captured using streptavidin-functionalized magnetic beads for reverse transcription and subsequent analysis by DNA sequencing, PCR or microarray hybridization.
Click-iT Nascent Protein Synthesis Detection Kit
Detecting newly synthesized protein is key for researchers studying protein biosynthesis, trafficking and degradation. Click-iT AHA (L-azidohomoalanine, Figure 3.1.18) incorporation provides a fast, sensitive and nonradioactive alternative to the traditional radioactive 35S-methionine
The
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
TheMolecular
MolecularProbes
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT
NOTICE: described
The products
described
in this
oneLimited
or moreUse
Limited
UseLicense(s).
Label License(s).
Please
to the
Appendix
IMPORTANT NOTICE
: The products
in this
manual
are manual
coveredare
bycovered
one or by
more
Label
Please
referrefer
to the
Appendix
onon
131
technique for the detection of nascent protein.19,42L-azidohomoalanine,

an analog of L-methionine, is supplied to cultured cells and is biosynthetically incorporated into proteins. The incorporated amino acid
is then detected by copper (I)catalyzed click coupling to an alkynederivatized fluorophore. This two-step labeling and detection method
provides detection sensitivity comparable with that obtained using
the radioactive 35S-methionine method and is compatible with downstream LC-MS/MS and MALDI-MS analysis. Click-iT AHA is available as a stand-alone reagent (C10102) or in the Click-iT AHA Alexa
Section 3.1
Click Chemistry
Fluor 488 Protein Synthesis HCS Assay Kit (C10289), which contains
Alexa Fluor 488 alkyne for detection. Click-iT AHA has proven to
be a successful substitute for methionine in many cell types, including
COS-7, 3T3-L1, HeLa, HEK 293 and Jurkat cells. Cellular incorporation
of Click-iT AHA should be carried out in methionine-free media, as
methionine is the preferred substrate for methionyl tRNA transferase,
and supplemented media (i.e., methionine-free DMEM) should be used
in place of HBSS to achieve greater Click-iT AHA incorporation at
lower concentrations.
REFERENCES
1. Angew Chem Int Ed Engl (2009) 48:6974; 2. Biochemistry (2009) 48:6571; 3. ACS
Chem Biol (2006) 1:644; 4. Chem Rev (2009) 109:4207; 5. Chem Rev (2008) 108:2952;
6. Proc Natl Acad Sci U S A (2008) 105:2415; 7. Protein Sci (2004) 13:2693; 8. Angew
Chem Int Ed Engl (2009) 48:9879; 9. Bioconjug Chem (2009) 20:728; 10. Methods
Enzymol (1990) 186:161; 11. J Histochem Cytochem (2010) 58:207; 12. J Am Chem
Soc (2010) 132:2504; 13. Chem Res Toxicol (2008) 21:432; 14. Nat Cell Biol (2008)
10:1224; 15. J Neurosci Methods (2009) 177:122; 16. Yeast (2008) 25:775; 17. Bioorg
Med Chem Lett (2008) 18:5995; 18. Proc Natl Acad Sci U S A (2006) 103:9482; 19. Nat
Protoc (2007) 2:532; 20. J Virol (2009) 83:13042; 21. Methods Enzymol (2006) 415:230;
22. Proc Natl Acad Sci U S A (2007) 104:2614; 23. J Am Chem Soc (2009) 131:4967;
24. J Am Chem Soc (2007) 129:2744; 25. Proc Natl Acad Sci U S A (2004) 101:12479;
26. J Biol Chem (2009) 284:21327; 27. J Am Chem Soc (2008) 130:11576; 28. Bioconjug
Chem (2008) 19:1570; 29. J Immunol Methods (2009) 350:29; 30. Biotechniques (2008)
44:927; 31. J Biol Chem (2010) 285:1544; 32. Genetics (2009) 183:233; 33. Nucleic Acids
Res (2009) 37:e31; 34. Methods (2009) 48:8; 35. Science (2009) 325:340; 36. Proc Natl
Acad Sci U S A (2009) 106:14896; 37. Plant Methods (2010) 6:5; 38. Proc Natl Acad Sci
U S A (2009) 106:11806; 39. Cytometry A (2009) 75:862; 40. Genes Cells (2010) 15:315;
41. Proc Natl Acad Sci U S A (2008) 105:15779; 42. J Neurosci (2009) 29:638.
DATA TABLE 3.1 CLICK CHEMISTRY

Cat. No.
MW
Storage
Soluble
Abs
EC
Em
Solvent
Notes
A10044
252.23
F,D
DMSO, H2O
<300
none
1
A10266
861.04
F,D,L
DMSO
493
76,000
516
pH 7
A10267
773.91
F,D,L
DMSO
494
76,000
520
pH 7
A10270
948.16
F,D,L
DMSO
590
105,000
617
pH 7
A10275
962.23
F,D,L
DMSO
588
100,000
616
pH 7
A10277
~850
F,D,L
DMSO
646
270,000
668
MeOH
A10278
~800
F,D,L
DMSO
646
250,000
661
pH 7
A10279
225.20
F,D
DMSO
<300
none
A10280
388.38
F,D,L
DMSO
<300
none
A20012
~850
F,D,L
DMSO
554
151,000
568
pH 7
A20013
~750
F,D,L
DMSO
554
150,000
567
pH 7
B10184
615.79
F,D,L
DMSO
<300
none
B10185
528.66
F,D
DMSO
<300
none
C10102
258.16
F,DD
DMSO
<300
none
C10186
127.14
F,D
DMSO
<300
none
C10248
263.38
F,D,LL
DMSO
<300
none
C10249
331.50
F,D,LL
DMSO
<300
none
C10264
342.30
F,D
DMSO
<300
none
2
C10265
283.41
F,D,L
DMSO
<300
none
C10268
241.33
F,D,L
DMSO
<300
none
C33365
430.37
F,D
DMSO
<300
none
3
C33366
430.37
F,D
DMSO
<300
none
3
C33367
430.37
F,D
DMSO
<300
none
3
E10345
268.23
F,D
DMSO
<300
none
I10188
310.14
F,D,L
DMSO
<300
none
4
I10189
223.01
F,D,L
DMSO
<300
none
4
O10180
637.68
F,D,L
DMSO
494
80,000
521
pH 9
5
O10181
449.37
F,D,L
DMSO
494
80,000
521
pH 9
5
T10182
554.65
F,D,L
DMSO
546
95,000
571
MeOH
6
T10183
467.52
F,D,L
DMSO
543
95,000
572
MeOH
6
For definitions of the contents of this data table, see Using The Molecular Probes Handbook in the introductory pages.
Notes
1. E10187 and E10415 are an alternative packaging sof A10044 but are otherwise identical.
2. C10264 is deacetylated in vivo yielding the 6-ethynyl analog of fucose (MW = 174.15).
3. C33365, C33366 and C33367 are deacetylated in vivo yielding N-azidoacetylgalactosamine, N-azidoacetylmannosamine and N-azidoacetylglucosamine (all MW = 262.22), respectively.
4. Iodoacetamides in solution undergo rapid photodecomposition to unreactive products. Minimize exposure to light prior to reaction.
5. Absorption and fluorescence of Oregon Green 488 dyes are pH dependent only in moderately acidic solutions (pH <5).
6. Abs and Em for tetramethylrhodamine dyes in pH 8 buffer are red-shifted approximately 8 nm compared to MeOH, with EC lower by ~10%.
The
MolecularProbes
Probes Handbook:
Handbook: A
Probesand
andLabeling
Technologies
The
Molecular
A Guide
Guide to
to Fluorescent
Fluorescent Probes
132
IMPORTANT
NOTICE:
The products
described
in this manual
coveredare
by one
or more
Limited
Use Label
License(s).
Please
refer to thePlease
Appendix
onto
IMPORTANT
NOTICE
: The products
described
in thisaremanual
covered
by one
or more
Limited
Use Label
License(s).
refer
the Appendix on
Section 3.1
Click Chemistry
PRODUCT LIST 3.1 CLICK CHEMISTRY

Cat. No.
Product
A10267
A20013
A10275
A10278
A10266
A20012
A10270
A10277
A10279
A10280
B10185
B10184
C10102
C10289
C10269
C35002
A10202
A10034
C10350
C10351
C10352
C10353
C10354
C10355
C10356
C10357
C10337
C10338
C10339
C10340
C10214
C10248
C10264
C33365
C10249
C33367
C10186
C33366
C10268
C10365
C10265
C10276
C10327
C10328
C10329
C10330
C10245
C10246
C10247
A10044
E10187
E10415
E10345
I10189
I10188
O10181
O10180
T10183
T10182
Alexa Fluor 488 alkyne (Alexa Fluor 488 5-carboxamido-(propargyl), bis(triethylammonium salt)) *5-isomer*
Alexa Fluor 555 alkyne, triethylammonium salt
Alexa Fluor 594 alkyne (Alexa Fluor 594 carboxamido-(5-(and 6-)propargyl), bis(triethylammonium salt)) *mixed isomers*
Alexa Fluor 647 alkyne, triethylammonium salt
Alexa Fluor 488 azide (Alexa Fluor 488 5-carboxamido-(6-azidohexanyl), bis(triethylammonium salt)) *5-isomer*
Alexa Fluor 555 azide, triethylammonium salt
Alexa Fluor 594 azide (Alexa Fluor 594 carboxamido-(6-azidohexanyl), triethylammonium salt) *mixed isomers*
Alexa Fluor 647 azide, triethylammonium salt
alkyne, succinimidyl ester (3-propargyloxypropanoic acid, succinimidyl ester)
azido (PEO)4 propionic acid, succinimidyl ester (3-(azidotetra(ethyleneoxy))propionic acid, succinimidyl ester)
biotin alkyne (PEG4 carboxamide-propargyl biotin)
biotin azide (PEG4 carboxamide-6-azidohexanyl biotin)
Click-iT AHA (L-azidohomoalanine) *for nascent protein synthesis*
Click-iT AHA Alexa Fluor 488 Protein Synthesis HCS Assay *2-plate size*
Click-iT Cell Reaction Buffer Kit
Click-iT EdU Alexa Fluor 488 Flow Cytometry Assay Kit *50 assays*
Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit *50 assays*
Click-iT EdU Pacific Blue Flow Cytometry Assay Kit *50 assays*
Click-iT EdU Alexa Fluor 488 HCS Assay *2-plate size*
Click-iT EdU Alexa Fluor 488 Imaging Kit *for 50 coverslips*
Click-iT EdU Microplate Assay *400 assays*
Click-iT farnesyl alcohol, azide *mixed isomers*
Click-iT fucose alkyne (tetraacetylfucose alkyne)
Click-iT GalNAz metabolic glycoprotein labeling reagent (tetraacetylated N-azidoacetylgalactosamine) *for O-linked glycoproteins* *5.2 mg*
Click-iT geranylgeranyl alcohol, azide *mixed isomers*
Click-iT GlcNAz metabolic glycoprotein labeling reagent (tetraacetylated N-azidoacetylglucosamine) *for O-GlcNAc-modified proteins* *5.2 mg*
Click-iT HPG (L-homopropargylglycine) *for nascent protein synthesis*
Click-iT ManNAz metabolic glycoprotein labeling reagent (tetraacetylated N-azidoacetyl-d-mannosamine) *for sialic acid glycoproteins* *5.2 mg*
Click-iT myristic acid, azide (12-azidododecanoic acid)
Click-iT Nascent RNA Capture Kit *for gene expression analysis*
Click-iT palmitic acid, azide (15-azidopentadecanoic acid)
Click-iT Protein Reaction Buffer Kit
Click-iT RNA Alexa Fluor 488 HCS Assay *2-plate size*
Click-iT RNA Alexa Fluor 594 HCS Assay *2-plate size*
Click-iT RNA Alexa Fluor 488 Imaging Kit *for 25 coverslips*
Click-iT RNA Alexa Fluor 594 Imaging Kit *for 25 coverslips*
Click-iT TUNEL Alexa Fluor 488 Imaging Assay *for microscopy and HCS* *50100 assays*
EdU (5-ethynyl-2-deoxyuridine)
5-ethynyl uridine (EU)
iodoacetamide alkyne
iodoacetamide azide
Oregon Green 488 alkyne *6-isomer*
Oregon Green 488 azide (Oregon Green 6-carboxamido-(6-azidohexanyl), triethylammonium salt) *6-isomer*
tetramethylrhodamine (TAMRA) alkyne (5-carboxytetramethylrhodamine, propargylamide) *5-isomer*
tetramethylrhodamine (TAMRA) azide (tetramethylrhodamine 5-carboxamido-(6-azidohexanyl)) *5-isomer*
Quantity
0.5 mg
0.5 mg
0.5 mg
0.5 mg
0.5 mg
0.5 mg
0.5 mg
0.5 mg
1 mg
1 mg
1 mg
1 mg
5 mg
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 mg
5 mg
each
1 mg
each
5 mg
each
1 mg
1 kit
1 mg
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
1 kit
50 mg
500 mg
5g
5 mg
1 mg
1 mg
0.5 mg
0.5 mg
0.5 mg
0.5 mg
TheMolecular
MolecularProbes
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
The
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
page: 971
Master described
Product Listinonthis
page
975. Products
are Forby
Research
Only.
Not intended
for any
animal or Please
human therapeutic
diagnosticon
use.
IMPORTANT NOTICE
Theand
products
manual
are covered
one orUse
more
Limited
Use Label
License(s).
refer to theorAppendix
page 971 and Master Product List on page 975. Products are For Research Use Only. Not intended for any animal
or human therapeutic or diagnostic use.
133
Section 3.2
Reagents for Modifying Alcohols
3.2 Reagents for Modifying Alcohols

Alcohols in Proteins: Serine, Threonine
and Tyrosine Residues
Although alcohols (including phenols such as tyrosine and the hydroxyl groups in serine,
threonine, sterols and carbohydrates) are abundant in biomolecules, their chemical reactivity in
aqueous solution is extremely low. Few reagents are selective for alcohols in aqueous solution,
especially in the presence of more reactive nucleophiles such as thiols and amines. It is therefore
difficult to selectively modify serine, threonine and tyrosine residues in proteins except when
they exhibit unusual reactivity, such as by residing at an enzymes active site.
Serine and Threonine Residues
Nonacylated N-terminal serine and threonine residues in peptides and proteins can be oxidized with periodate to yield aldehydes 1,2 (Figure 3.2.1) that can be subsequently modified with
a variety of hydrazine, hydroxylamine or amine derivatives (Section 3.3, Table 3.2). In addition,
peptides containing serine, threonine or tyrosine residues separated from a histidine residue by
a single amino acid can be selectively acylated by the succinimidyl ester or sulfosuccinimidyl
ester of biotin-X 3 (B1582, B6353; Section 4.2; Figure 3.2.2). This property may also permit selective modification of these sequences (Ser-x-His, Thr-x-His and Tyr-x-His, where x refers to any
amino acid) in peptides and proteins with fluorescent succinimidyl esters (Chapter 1). O-acylation
versus N-acylation can be detected by treatment with hydroxylamine, which cleaves esters but
usually not amides.4
Figure 3.2.3 4-Chloro-7-nitrobenz-2-oxa-1,3-diazole (NBD

chloride; 4-chloro-7-nitrobenzofurazan, C20260).
OH
CH
NH
NaIO4
CH
HC
O
+
HC H
Terminal serine
Figure 3.2.1 Sodium periodate oxidation of an N-terminal serine residue to an aldehyde, with the release of formaldehyde. The aldehyde thus formed from the protein can be subsequently modified with a variety of hydrazine, hydroxylamine or
amine derivatives.
H
N
O
CH2
R1
CH2
C R2
NH
( CH2) 4
H O
NH( CH2) 5
NH(CH2) 5
H
O
R1
) CH2) 4
SO3
NH
H
( CH2) 5NH
CH2
C C
( CH2) 5NH
CH2
R2
Figure 3.2.2 Nucleophilic attack of serine on the carbonyl group (C=O) of biotin-X, SSE (B6353) results in the stable
O-acylated derivative. In addition to histidine-x-serine, this stable intermediate can be formed in the presence of linear sequences of histidine-x-tyrosine and histidine-x-threonine, where x refers to any amino acid.
The
MolecularProbes
Probes Handbook:
Handbook: AAGuide
Probesand
andLabeling
Technologies
The
Molecular
Guide to
to Fluorescent
Fluorescent Probes
134
IMPORTANT
NOTICE:
The products
described
in this manual
coveredare
by covered
one or more
Limited
Use Label
License(s).
Please
refer to thePlease
Appendix
onto
IMPORTANT
NOTICE
: The products
described
in thisaremanual
by one
or more
Limited
Use Label
License(s).
refer
the Appendix on
Section 3.2
Tyrosine Residues
Modification of tyrosine residues is sometimes a side reaction when proteins are reacted with
sulfonyl chlorides, iodoacetamides or other reactive dyes described in Chapter 1 and Chapter
2. For example, NBD chloride (C20260, Section 1.8, Figure 3.2.3) reacts with an active-site tyrosine in Escherichia coli F1-ATPase, causing strong inhibition.5
Tyrosine residues in some proteins can be selectively modified by initial nitration of the
ortho position of its phenol using tetranitromethane, and then reduction of the o-nitrotyrosine
with sodium dithionite (Na 2S2O4) to form an o-aminotyrosine (Figure 3.2.4). Although much
less reactive than aliphatic amines, the aromatic amine of o-aminotyrosine can react with most
amine-reactive reagents (Chapter 1) between pH 5 and pH 7.6 To obtain selective derivatization in complex samples, it is of course critical to block all aliphatic primary amines, typically
by acetylation with acetic anhydride, prior to reduction of nitrotyrosine. Nitration of tyrosine
residues by nitric oxide occurs naturally in cells through peroxynitrite radical intermediates
(Section 18.3, Table 18.1), yielding derivatives that can be reduced to o-aminotyrosine and subsequently detected using amine-reactive reagents.6,7 Tyrosine residues of peptides and proteins can
be selectively coupled to aniline derivatives in the presence of formaldehyde.8 Chemoselective
derivatization of tyrosine has also been accomplished using a fluorescent diazodicarboxamide
reagent prepared from carboxy-X-rhodamine (ROX) succinimidyl ester 9 (C1309, Section 1.6).
Another method for modifying tyrosine groups in peptides is to convert the phenol group in
tyrosine residues to a salicylaldehyde derivative, and then to react the salicylaldehyde with 1,2-diamino-4,5-dimethoxybenzene (D1463, Section 3.3) to form a fluorescent benzimidazole.1012
The tyramide signal amplification (TSA) technology (Section 6.2), which was developed by
NEN (now a part of PerkinElmer Corporation) and licensed for in-cell and in-tissue applications,
permits significant amplification of the detectability of targets by a horseradish peroxidasemediated scheme. In the TSA method, the labeled tyramide becomes covalently linked to tyrosine
residues in or near the target. We have introduced an extensive selection of TSA Kits that utilize
an Alexa Fluor tyramide, Oregon Green 488 tyramide or biotin-XX tyramide as the amplification reagents (Section 6.2).
OH
O2 N
NO2
C NO2
NO2
CH2
CH
NH
OH
NO2
R1
CH2
NH
CH
R2
Na2S2O4
OH
NH2
R1
CH2
NH
CH
R2
Alcohols in Carbohydrates
As with derivatization of alcohols in proteins, it is difficult to selectively modify most carbohydrates in aqueous solution because of their low reactivity and the competing hydrolysis of the
reactive reagents. However, several reagents are available for derivatizing reducing sugars (which
contain a low equilibrium concentration of the reactive aldehyde function), as well as for modifying aldehydes and ketones obtained by periodate oxidation of various carbohydrates. To pursue
this labeling approach, see Section 3.3 for a description of aldehyde- and ketone-reactive reagents.
Figure 3.2.4 Reaction scheme for the conversion of tyrosine to o-aminotyrosine. Tyrosine undergoes nitration by reaction with tetranitromethane, followed by reduction with
sodium dithionite, to yield an o-aminotyrosine.
Dichlorotriazines
Dichlorotriazines readily modify amines in proteins, and they are among the few reactive
groups that are reported to react directly with polysaccharides and other alcohols in aqueous solution, provided that the pH is >9 and that other nucleophiles are absent. We offer the
5-isomer of fluorescein dichlorotriazine (5-DTAF, D16), with absorption/emission maxima of
~492/516 nm, as well as Texas Red C2-dichlorotriazine (T30200, Figure 3.2.5), with absorption/
emission maxima of ~588/601 nm. 5-DTAF has been used to label a wide range of hydroxylated
biopolymers including collagen,13 cellulose,14 cyclodextrins 15 and soluble beta-glucan,16 as well
as functionalized carbon nanotubes.17
N-Methylisatoic Anhydride
In the absence of other reactive functional groups, N-methylisatoic anhydride (M25) will
convert ribonucleotides and certain other carbohydrates 18,19 to fluorescent esters with excitation/emission maxima of ~350/446 nm in mildly basic aqueous solution.2024 The compactness
and moderate environmental sensitivity of this fluorophore, which is a synthetic precursor to
blue-fluorescent N-methylanthraniloyl (MANT) amides and esters,23 may be advantageous for
preparing site-selective probes. Low molecular weight alcohols are better derivatized by this
reagent in aprotic organic solvents 2527 (Figure 3.2.6).
Cl
SO 3
SO 2NHCH2CH2NH
N
N
Cl
Figure 3.2.5 Texas Red C2-dichlorotriazine (T30200).
O
N
OH
CH3
NH
CH3
Figure 3.2.6 Reaction of N-methylisatoic anhydride (M25)

with an alcohol to produce a blue-fluorescent (~350/446 nm)
N-methylanthraniloyl (MANT) ester.
The
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
TheMolecular
Molecular
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT NOTICE
: The products described in this manual are covered by one or more Limited Use Label License(s). Please refer to the Appendix on
135
Section 3.2
Dansyl Aminophenylboronic Acid
Figure 3.2.7 m-Dansylaminophenylboronic acid (D2281).
m-Dansylaminophenylboronic acid (D2281, Figure 3.2.7) reacts with vicinal diols (hydroxyl groups on adjacent carbon atoms) and certain amino alcohols 28 to form cyclic complexes 29 (Figure 3.2.8) that have a fluorescence intensity and peak emission dependent on the
environment of the dansyl fluorophore. This interesting reagent binds reversibly to cell-wall
carbohydrates, 30 as well as to glycosylated (but not deglycosylated) human serum albumin. 31
Dansylaminophenylboronic acid is also used as an HPLC derivatization reagent for vicinal diols 32 and as a detection reagent for glycolipids analyzed by thin-layer chromatography.33
Alcohol Modification in Organic Solvents

N( CH3) 2
+
SO2NH
R1
OH
OH
CH
CH
R2
B(OH2)
Two functional groupsacyl azides and acyl nitrilesreact directly with aliphatic amines
to yield the same products as do the corresponding succinimidyl esters. When reacted in organic
solvents, however, these reagents can also form derivatives of alcohols and phenols, making them
extremely useful for sensitive analysis of alcohols by HPLC or capillary electrophoresis.
Isocyanates Prepared from Acyl Azides
N( CH3) 2
O
SO2NH
H 1
R
B
O
H
R2
Figure 3.2.8 Reaction of m-dansylaminophenylboronic

acid (D2281) with a vicinal diol to form a reversible fluorescent cyclic complex.
Alcohols are much easier to modify in anhydrous organic solvents than in aqueous solution. Perhaps the most effective reagents are isocyanates, which are much more reactive with
alcohols (and amines) than are isothiocyanates but are not sufficiently stable to permit their
sale. Fortunately, isocyanates can often be prepared by Curtius rearrangement of acyl azides
(Figure 3.2.9). When an acyl azide and alcohol are heated together in an organic solvent such as
toluene, dioxane or DMF at 80C, the acyl azide will rearrange to form an isocyanate that then
reacts with the alcohol to form a stable urethane. As little as 50 femtograms of the urethane conjugates prepared from coumarin derivatives 7-methoxycoumarin-3-carbonyl azide (M1445) and
7-diethylaminocoumarin-3-carbonyl azide (D1446) can be detected using an HPLC fluorescence
detector.34,35 Alcohol conjugates (urethanes) prepared from the single-isomer carbonyl azides of
fluorescein diacetate (F6218) and tetramethylrhodamine (T6219) may provide even higher sensitivity, particularly with instruments that employ the argon-ion laser. Following rearrangement
and alcohol conjugation, the acetates of the fluorescein derivative can be removed by hydrolysis at
pH 910. The diacetate of fluorescein-5-carbonyl azide has been used to synthesize a fluorogenic
substrate for the anandamide transmembrane carrier.36 Tetramethylrhodamine-5-carbonyl azide
has been successfully conjugated to the hydrophobic poly(-caprolactone) (PCL) block of a diblock
copolymer micelle in order to follow its cellular internalization 37,38 and has also been used to prepare riboflavin conjugates for the same purpose.39,40
Acyl Nitriles
9-Anthroylnitrile (A1440) reacts with alcohols, such as steroids and acylglycerols, in organic
solvents to yield carboxylate esters that are useful for HPLC.41,42 To optimize solid-phase organic
synthesis, 9-anthroylnitrile has been used to quantitate the absolute amount of resin-bound hydroxyl groups directly on solid support.43 In addition, 9-anthroylnitrile has been reported to be
useful for the selective labeling of certain serine and threonine residues in myosin.4448 The lipophilicity of 9-anthroylnitrile may make it useful for modifying hydroxyl groups of proteins and
hydroxylated fatty acids that are buried within cell membranes.
Figure 3.2.9 Derivatization of an alcohol using the diacetate of fluorescein-5-carbonyl azide (F6218). This process consists of three steps: 1) rearrangement of the
acyl azide to an isocyanate, 2) reaction of the isocyanate with an alcohol to form a urethane and 3) deprotection of the nonfluorescent urethane derivative using
hydroxylamine.
The
MolecularProbes
Probes Handbook:
Handbook: AAGuide
Probes and
andLabeling
Technologies
The
Molecular
Guide to
toFluorescent
Fluorescent Probes
136
IMPORTANT
NOTICE:
The products
described
in this manual
coveredare
by covered
one or more
Limited
Use Label
License(s).
Please
refer to thePlease
Appendix
onto
IMPORTANT
NOTICE
: The products
described
in thisaremanual
by one
or more
Limited
Use Label
License(s).
refer
the Appendix on
REFERENCES
1. Bioconjug Chem (2003) 14:205; 2. Bioconjug Chem (1992) 3:138; 3. Anal Biochem
(2010) 398:123; 4. J Biol Chem (1992) 267:5060; 5. J Biol Chem (2004) 279:31505;
6. J Proteome Res (2007) 6:2257; 7. Anal Biochem (1998) 259:127; 8. Bioconjug Chem
(2008) 19:153; 9. J Am Chem Soc (2010) 132:1523; 10. J Chromatogr (1988) 430:271;
11. J Chromatogr (1986) 356:171; 12. J Chromatogr (1985) 344:267; 13. J Biomech
(2009) 42:2279; 14. Biomacromolecules (2003) 4:481; 15. Biomacromolecules
(2009) 10:505; 16. J Immunol (2006) 177:1661; 17. Langmuir (2009) 25:7573;
18. Electrophoresis (2007) 28:1221; 19. Anal Biochem (2000) 284:167; 20. Biochemistry
(1991) 30:422; 21. Biochemistry (1990) 29:3309; 22. Biochim Biophys Acta (1983)
742:496; 23. J Biol Chem (1982) 257:13354; 24. Arch Biochem Biophys (1973) 155:70;
Section 3.2
25. Anal Biochem (1996) 234:31; 26. Synthesis (1982) 39:266; 27. J Org Chem (1959)
24:1214; 28. Anal Bioanal Chem (2006) 386:506; 29. Med Res Rev (2010) 30:171;
30. Biochem Biophys Res Commun (1980) 96:157; 31. Clin Chim Acta (1985) 149:13;
32. Anal Chim Acta (1990) 228:101; 33. J Lipid Res (1995) 36:1848; 34. Chem Pharm
Bull (1985) 33:1164; 35. J Lipid Res (1997) 38:429; 36. J Pharmacol Exp Ther (2000)
293:289; 37. Science (2003) 300:615; 38. Bioconjug Chem (2002) 13:1259; 39. Mol
Pharm (2004) 1:257; 40. J Pharmacol Exp Ther (2003) 306:681; 41. Anal Chim Acta
(1983) 147:397; 42. J Chromatogr (1983) 276:289; 43. Anal Chem (1999) 71:4564;
44. Biochemistry (1996) 35:16061; 45. Biochemistry (1994) 33:6867; 46. J Biol Chem
(1990) 265:18791; 47. J Biol Chem (1990) 265:18786; 48. J Biol Chem (1989) 264:18188.
DATA TABLE 3.2 REAGENTS FOR MODIFYING ALCOHOLS

Cat. No.
MW
Storage
Soluble
Abs
EC
Em
Solvent
Notes
A1440
231.25
F,D,L
DMF, MeCN
361
7500
470
MeOH
1
D16
495.28
F,D,L
pH >6, DMF
492
83,000
516
pH 9
2, 3
D1446
286.29
F,D,L
DMF, MeCN
436
57,000
478
MeOH
D2281
370.23
D,L
DMF, DMSO
337
4600
517
MeOH
4
F6218
485.41
FF,D
DMF, MeCN
<300
none
M25
177.16
D
DMF, DMSO
316
3500
386
MeOH
5
M1445
245.19
FF,D,L
DMF, MeCN
360
25,000
415
MeOH
T6219
455.47
FF,D,L
DMF, MeCN
545
90,000
578
MeOH
T30200
796.74
F,D,L
DMF, DMSO
583
87,000
604
MeOH
Notes
1. The absorption spectrum of A1440 has subsidiary peaks at 380 nm and 344 nm. Emission spectrum is unstructured. Ester derivatives formed by reaction with alcohols have essentially similar
spectra.
2. Unstable in water. Use immediately.
3. Absorption and fluorescence of fluorescein derivatives are pH dependent. Extinction coefficients and fluorescence quantum yields decrease markedly at pH <7.
4. Fluorescence of D2281 when bound to proteins is typically blue shifted (Em ~490 nm).
5. The amide reaction product of M25 with butylamine has Abs = 353 nm (EC = 5900 cm1M1), Em = 426 nm in MeOH. Ester reaction products with alcohols have Abs = 350 nm
(EC = 5700 cm1M1), Em = 446 nm in water (pH 8).
PRODUCT LIST 3.2 REAGENTS FOR MODIFYING ALCOHOLS

Cat. No.
Product
A1440
D2281
D16
D1446
F6218
M1445
M25
T6219
T30200
9-anthroylnitrile
m-dansylaminophenylboronic acid
5-(4,6-dichlorotriazinyl)aminofluorescein (5-DTAF) *single isomer*
7-diethylaminocoumarin-3-carbonyl azide
fluorescein-5-carbonyl azide, diacetate
7-methoxycoumarin-3-carbonyl azide
N-methylisatoic anhydride *high purity*
tetramethylrhodamine-5-carbonyl azide
Texas Red C2-dichlorotriazine
Quantity
25 mg
100 mg
100 mg
25 mg
10 mg
25 mg
1g
5 mg
5 mg
The
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
TheMolecular
MolecularProbes
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT
NOTICE: described
The products
described
in are
this covered
manual are
by oneLimited
or moreUse
Limited
UseLicense(s).
Label License(s).
Please
to the
Appendix
IMPORTANT NOTICE
: The products
in this
manual
bycovered
one or more
Label
Please
referrefer
to the
Appendix
onon
137
Section 3.3
Reagents for Modifying Aldehydes and Ketones
3.3 Reagents for Modifying Aldehydes and Ketones

Aldehydes and ketones are present in a number of low molecular
weight molecules such as drugs, steroid hormones, reducing sugars and
metabolic intermediates (e.g., pyruvate and -ketoglutarate). Except for
polysaccharides containing free reducing sugars, however, biopolymers
generally lack aldehyde and ketone groups. Even those aldehydes and
ketones that are found in the open-ring form of simple carbohydrates
are usually in equilibrium with the closed-ring form of the sugar.
The infrequent occurrence of aldehydes and ketones in biomolecules has stimulated the development of techniques to selectively introduce these functional groups, thus providing unique sites for chemical
modification and greatly extending the applications of the probes found
in this section. Fluorescent modification of aldehyde or carboxylic acid
groups in carbohydrates is also frequently utilized for their analysis by
HPLC, capillary electrophoresis 1 and other methods.
Introducing Aldehydes and

Ketones into Biomolecules
Periodate Oxidation
The most common method for introducing aldehydes and ketones

into polysaccharides and glycoproteins (including antibodies) is by
periodate-mediated oxidation of vicinal diols. These introduced aldehydes and ketones can then be modified with fluorescent or biotinylated
hydrazine, hydroxylamine or amine derivatives to label the polysaccharide or glycoprotein. For example, some of the hydrazine derivatives
described in this section have been used to detect periodate-oxidized
glycoproteins in gels.2 The Pro-Q Emerald 300 and Pro-Q Emerald
488 Glycoprotein Gel and Blot Stain Kits (P21855, P21857, M33307;
OH
CH
NH
CH
NaIO4
2
C
HC
O
+
HC H
Terminal serine
Figure 3.3.1 Sodium periodate oxidation of an N-terminal serine residue to an aldehyde,
with the release of formaldehyde. The aldehyde thus formed from the protein can be subsequently modified with a variety of hydrazine, hydroxylamine or amine derivatives.
O
2
H O
2 2
O
CH OH
2
HO
O
OH
O
OH
R
CH
HO
OH
R
R
Galactose Oxidase
O
O
OH
Section 9.4) are based on periodate oxidation of glycoproteins and subsequent labeling with a Pro-Q Emerald dye.3
Periodate oxidation of the 3-terminal ribose provides one of the
few methods of selectively modifying RNA; periodate-oxidized ribonucleotides can subsequently be converted to fluorescent nucleic acid
probes by reaction with fluorescent hydrazines, hydroxylamines and
amines.46 Alkenes from unsaturated fatty acids and ceramides can also
be converted to glycols by osmium tetroxide and then oxidized by periodate to aldehydes, and periodate will oxidize certain -aminoethanol
derivatives such as the hydroxylysine residues in collagen, as well as methionine (to its sulfoxide) and certain thiols (usually to disulfides). These
other reactions, however, usually occur at a slower rate than oxidation
of vicinal diols.
In addition to vicinal diols, N-terminal serine and threonine residues of peptides and proteins can be selectively oxidized by periodate
to aldehyde groups 79 (Figure 3.3.1). Moreover, because antibodies are
glycosylated at sites distant from the antigen-binding region, modification of periodate-oxidized antibodies by hydrazines 10 and hydroxylamines usually does not inactivate the antibody, as sometimes occurs
with amine-reactive labeling.
Galactose OxidaseMediated
Oxidation and Other Methods
Galactose oxidase oxidizes terminal galactose residues to aldehydes,

particularly in glycoproteins.1115 The introduction of galactose residues
can be especially advantageous for structural studies because it provides a means of selectively labeling specific sites on biomolecules. For
example, 2-keto-galactose has been specifically inserted into the Fc glycans of therapeutic antibodies, including Herceptin and Avastin, enabling site-specific labeling with Alexa Fluor 488 hydroxylamine 16,17
(A30629). Galactose oxidasemodified lipopolysaccharides (LPS) have
been modified with Alexa Fluor 488 hydrazide (A10436) to probe for
LPS-binding sites on cells.18 Because galactose oxidasemediated oxidation liberates a molecule of hydrogen peroxide for each molecule of aldehyde that is formed (Figure 3.3.2), horseradish peroxidasecatalyzed
oxidation of the Amplex Red reagent to red-fluorescent resorufin by
hydrogen peroxide provides a ready means by which the number of aldehyde residues introduced into a biomolecule, including on a cell surface, can be quantitated. The Amplex Red Galactose/Galactose Oxidase
Assay Kit (A22179, Section 10.5) provides the reagents and a general
protocol for this assay of introduced aldehyde residues. Other methods for aldehyde and ketone introduction include selective N-terminal
transamination in the presence of pyridoxal-5-phosphate,19 ligation
of a ketone analog of biotin to proteins with a biotin acceptor peptide
(BAP) fusion tag by biotin ligase (BirA) 20 and co-translational modification of recombinantly tagged proteins by formylglycine-generating
enzyme 21 (FGE).
= glycolipid, polysaccharide or glycoprotein
Figure 3.3.2 Oxidation of the terminal galactose residue of a glycoprotein, glycolipid or

polysaccharide resultvs in the generation of an aldehyde, which can react with hydrazines,
hydroxylamines or primary aminecontaining compounds.
(CH 3) 3CO C NHOCH2 C O
Figure 3.3.3 N-(t-BOC)-aminooxyacetic acid, tetrafluorophenyl ester (B30300).
The
MolecularProbes
Probes Handbook:
Handbook: AA Guide
Probesand
andLabeling
Technologies
The
Molecular
Guide to
to Fluorescent
Fluorescent Probes
138
F
O
IMPORTANT
NOTICE:
The products
described
in this manual
coveredare
by covered
one or more
Limited
Use Label
License(s).
Please
refer to thePlease
Appendix
onto
IMPORTANT
NOTICE
: The products
described
in thisaremanual
by one
or more
Limited
Use Label
License(s).
refer
the Appendix on
Section 3.3
Coupling Hydrazines and Amines to Amine-Containing

Biomolecules without Introducing Aldehydes and Ketones
Common tissue fixatives such as formaldehyde and glutaraldehyde can be used to couple
hydrazine and amine derivatives to proteins and other amine-containing polymers. For example, lucifer yellow CH (L453) can be conjugated to surrounding biomolecules by common
aldehyde-based fixatives in order to preserve the dyes staining pattern during subsequent tissue
manipulations.22
Introducing a Hydroxylamine into a Biomolecule
Figure 3.3.4 8-Aminopyrene-1,3,6-trisulfonic acid, trisodium salt (APTS, A6257).
The tetrafluorophenyl (TFP) ester of N-(t-BOC)-aminooxyacetic acid (B30300, Figure 3.3.3)

is an amine-reactive protected hydroxylamine that is useful for synthesizing new aldehyde- and
ketone-reactive probes in an organic solvent. Following coupling to aliphatic amines, the t-BOC
group can be quantitatively removed with trifluoroacetic acid. The resultant hydroxylamine
probe can then spontaneously react with aldehydes, the reducing ends of saccharides and oligosaccharides, and abasic sites in oligonucleotides to form stable adducts.
Hydrazines and Hydroxylamines
O
R C NHNH2
Hydrazide
Reactivity of Hydrazine and Hydroxylamine Derivatives
Although certain aromatic amines such as 8-aminonaphthalene-1,3,6-trisulfonic acid

(ANTS, A350), 2-aminoacridone (A6289) and 8-aminopyrene-1,3,6-trisulfonic acid (APTS,
A6257; Figure 3.3.4) have been extensively utilized to modify reducing sugars for analysis and
sequencing, the most reactive reagents for forming stable conjugates of aldehydes and ketones
are usually hydrazine derivatives, including hydrazides, semicarbazides and carbohydrazides
(Figure 3.3.5), as well as hydroxylamine derivatives. Hydrazine derivatives react with ketones to
yield relatively stable hydrazones (Figure 3.3.6), and with aldehydes to yield hydrazones that are
somewhat less stable, though they may be formed faster. Hydroxylamine derivatives (aminooxy
compounds) react with aldehydes and ketones to yield oximes. Oximes are superior to hydrazones with respect to hydrolytic stability.23 Both hydrazones and oximes can be reduced with
sodium borohydride (NaBH4) to further increase the stability of the linkage. Rates and yields of
aldehyde reactions with hydrazine and hydroxylamine derivatives are substantially enhanced by
aniline catalysis.24 This chemistry is sufficiently mild and efficient to be applicable for labeling
periodate-oxidized sialylated glycoproteins on the surface of live cells.25
CNHNH2
Semicarbazide
O
NHNH
CNHNH2
Carbohydrazide
Figure 3.3.5 Structures of A) a hydrazide, B) a semicarbazide and C) a carbohydrazide.
Fluorescent Hydrazine and Hydroxylamine

Derivatives Excited with Visible Light
We offer a large number of fluorescent hydrazine and hydroxylamine derivatives for reaction with aldehydes or ketones (Table 3.2). Because they are more photostable than the fluorescein
derivatives, the Alexa Fluor, BODIPY and Texas Red hydrazides should be among the most
sensitive reagents for detecting aldehydes and ketones in laser-excited chromatographic methods.26
However, with the exception of the Alexa Fluor 555 and Alexa Fluor 647 hydrazides and the Alexa
Fluor 647 hydroxylamine, the Alexa Fluor reagents are mixed isomers and may resolve into multiple peaks when analyzed with high-resolution separation techniques. Fluorescent hydrazides and
hydroxylamines are extensively used for labeling glycans via derivatization of aldehydes generated
after periodate oxidation or via coupling to the reducing terminus.27,28 Alexa Fluor 488 hydroxylamine (A30629, Figure 3.3.7) is particularly useful for detecting aldehyde groups at abasic DNA
lesions,29,30 similar to the biotinylated hydroxylamine ARP described later in this section.
NH
R1 C O
R2
R3NHNH2
R1 C NNHR3
R2
Figure 3.3.6 Modifying aldehydes and ketones with hydrazine derivatives.
SO 3
SO 3
H2N
Fluorescent Hydrazine and Hydroxylamine Derivatives Excited with UV Light
Dansyl hydrazine (D100) has been by far the most widely used UV lightexcitable hydrazine
probe for derivatizing aldehydes and ketones for chromatographic analysis and mass spectrometry.31,32 A unique application that has been reported for dansyl hydrazine, but that is likely a general reaction of hydrazine derivatives, is the detection of N-acetylated or N-formylated proteins
through transfer of the acyl group to the fluorescent hydrazide.33,34 Although dansyl hydrazine
has been widely used as a UV lightexcitable derivatization reagent, our 7-diethylaminocoumarin
NH2
C O
O
NH2OCH2 C NH(CH 2) 5NH C

O
2 (CH 3CH2) 3NH

5
Figure 3.3.7 Alexa Fluor 488 C5-aminooxyacetamide,

bis(triethylammonium) salt (Alexa Fluor 488 hydroxylamine,
A30629).
The
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
TheMolecular
Molecular
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT
NOTICE:described
The products
described
thiscovered
manual are
by one
or moreUse
Limited
Label License(s).
to Appendix
the Appendix
IMPORTANT NOTICE
: The products
in this
manualinare
by covered
one or more
Limited
LabelUse
License(s).
PleasePlease
refer refer
to the
on on
139
Section 3.3
and pyrene hydrazides (D355, P101) have much higher absorptivity and fluorescence, which
should make their conjugates more detectable than those of dansyl hydrazine.
Polar Fluorescent Hydrazides and Hydroxylamines
Figure 3.3.8 Absorption and fluorescence emission spectra

of lucifer yellow CH in water.
Lucifer yellow CH (L453) is most commonly used as an aldehyde-fixable neuronal tracer

with visible absorption and emission (Figure 3.3.8). This membrane-impermeant hydrazide also
reacts with periodate-oxidized cell-surface glycoproteins, 35,36 oxidized ribonucleotides 37 and
gangliosides.38 Cascade Blue hydrazide (C687) exhibits high absorptivity (EC >28,000 cm1M1),
fluorescence quantum yield (0.54) and water solubility 39 (~1%). Like Cascade Blue hydrazide,
Alexa Fluor 350 hydrazide (A10439) and Alexa Fluor 350 hydroxylamine (A30627) also have
high water solubility and bright blue fluorescence. These sulfonated pyrene and coumarin derivatives have applications similar to those of lucifer yellow CH, including as aldehyde-fixable polar
tracers; 40 see Section 14.3 for a more complete discussion of this application.
Cell membraneimpermeant aldehyde- and ketone-reactive reagents are also important probes
for assessing the topology of peptide and protein exposure on the surface of live cells. Periodate- or
galactose oxidasemediated oxidation of cell-surface glycoproteins and polysaccharides can be
used to selectively introduce aldehyde residues on the cell surface, and these aldehydes can then be
reacted with a membrane-impermeant hydrazide. The high polarity of our Alexa Fluor hydrazides
(A10436, A10437, A10438, A10439, A20501MP, A20502, A30634), Alexa Fluor hydroxylamines
Table 3.2 Molecular Probes hydrazine, hydroxylamine and amine derivatives.

Derivative
Hydrazines*
Hydroxylamines*
Cadaverines*
Acridone
Other Amines*
A6289
Alexa Fluor 350
A10439
A30627
Alexa Fluor 488
A10436
A30629
Alexa Fluor 555
A20501MP
A30677
Alexa Fluor 568
A10437
A30680
Alexa Fluor 594
A10438
A30678
Alexa Fluor 633
A30634
Alexa Fluor 647
A20502
A30632
A30679
B1603, B2600, D20653
A10550
A1594, B1596
Alexa Fluor 405
A30674
A30675
A30676
Bimane
B30633
Biotin and DSB-X biotin

t-BOC
B30300**
BODIPY FL
M6248
D2371
BODIPY TR
A1593, B1592, N6356

D2390
D6251
Cascade Blue
C687
Coumarin
D355
Dansyl
D100
C621
A191
D113
Dapoxyl
D112
D10460
2,3-Diaminonaphthalene
D7918
Dimethoxybenzene
D1463
Dinitrophenyl
D1552*
Fluorescein
C356, F121
A10466
Lucifer yellow
L453
A1340
Naphthalene
M20490
Oregon Green 488
O10465
P101
A6257
QSY 7
Q10464
Rhodamine
Texas Red
A1339
A91, A350
NBD
Pyrene
A1351, A1353, A1363
A1318
T6256
L2424
T2425
*Hydrazine, hydroxylamine and aromatic amine derivatives are discussed in Section 3.3, and aliphatic amine derivatives are discussed in Section 3.4, except for D1552, which appears
in Section 12.3. Aromatic amines used extensively for modifying aldehydes and ketones. Biotin and desthiobiotin (DSB-X biotin) derivatives are listed in Section 4.2. ARP is the
abbreviation for N-(aminooxyacetyl)-N-(D-biotinoyl)hydrazine. **B30300 requires t-BOC deprotection by trifluoroacetic acid to generate free hydroxylamine. More information on reactive
dyes is available at www.invitrogen.com/handbook/labelingchemistry.
TheMolecular
MolecularProbes
Probes Handbook:
Handbook: AAGuide
and Labeling
Technologies
The
Guideto
toFluorescent
Fluorescent Probes
Probes and
140
IMPORTANT
NOTICE:
The products
described
in this manual
covered
bycovered
one or more
Limited
Use Label
License(s).
Please
refer to thePlease
Appendix
IMPORTANT
NOTICE
: The products
described
in thisare
manual
are
by one
or more
Limited
Use Label
License(s).
referonto
the Appendix on
(A30627, A30629, A30632), lucifer yellow CH (L453) and Cascade Blue

hydrazide (C687) make them the preferred labeling reagents.
NBD Methylhydrazine
NBD
methylhydrazine
(N-methyl-4-hydrazino-7nitrobenzofurazan, M20490) has been used to monitor aldehydes and
ketones in tobacco smoke 41 and automobile exhaust 42 and also to measure nitrite in water 43 (Section 21.2). NBD methylhydrazine reacts with
carbonyl compounds in acidic media, forming the corresponding hydrazones (Figure 3.3.9). Following separation by HPLC, the hydrazones
can be detected either by spectrophotometry (using wavelengths corresponding to the absorption maxima of the relevant hydrazone) or by
fluorescence spectroscopy using excitation/emission at ~470/560 nm.
Section 3.3
of abasic sites in live cells.47,48 Once the aldehyde groups in abasic sites
are modified by ARP and the cells are fixed and permeabilized, the resulting biotinylated DNA can be detected with fluorescent dye, Qdot
nanocrystal or enzyme-conjugated streptavidin conjugates (Section
7.6, Table 7.9). Likewise, ARP can be used to detect and capture 4-hydroxynonenal (HNE)modified proteins.49 ARP has also been used to
immobilize IgG antibodies on streptavidin-coated monolayer surfaces
with their binding sites oriented toward the solution phase.50 An alternative to ARP for detection of protein carbonyls is dinitrophenylhydrazine derivatization followed by immunolabeling with our Alexa Fluor
488 dyelabeled anti-dinitrophenyl antibody 51 (A11097, Section 7.4).
Biotin Hydrazides and Biotin Hydroxylamine
In addition to the fluorescent hydrazine and hydroxylamine derivatives, we offer several nonfluorescent biotin and DSB-X biotin
hydrazides (B1603, B2600, D20653; Section 4.2) and the biotin hydroxylamine derivative ARP (A10550, Section 4.2), each of which can be
detected using fluorescent dye or enzyme-labeled avidin or streptavidin (Section 7.6, Table 7.9). DSB-X biotin hydrazide, which has
moderate affinity for avidin and streptavidin that is rapidly reversed
by low concentrations of free biotin, can be used to produce a DSB-X
biotinlabeled molecule that reversibly binds avidin or streptavidin affinity matrices (Section 7.6).
We recommend the biotin hydroxylamine derivative ARP (aldehyde-reactive probe, A10550; Figure 3.3.10) as our most efficient reagent for incorporating biotins into aldehyde- or ketone-containing
cell surfaces. ARP has been used extensively to modify the exposed
aldehyde group at abasic lesions in DNA 44,45 (Figure 3.3.11). A quick
and sensitive microplate assay for abasic sites can be performed using
ARP.46 In addition, ARP is membrane permeant, permitting detection
5
O
O
P
O
CH
NH
N
3
Reactive Oxygen Species (ROS)
or Radiation
H C
3
NH
2
O C
N
O
H C N
3
NH OCH
2
2
CH O
O
NH
(CH )
24
C O
OH
ARP
C NHNH
O
N
NO
+
2
P
CH
H
N
O
O
N
1 2
R , R = H, alkyl, aryl
NO
5
Figure 3.3.9 Reaction scheme illustrating the principle of ketone and aldehyde detection by
NBD methylhydrazine (M20490).
H
N
P
O
CH
(CH )
24
C O
OH
CH
NOCH
O
NH
NHNH
O
O
Figure 3.3.10 N-(aminooxyacetyl)-N-(D-biotinoyl) hydrazine, trifluoroacetic acid salt (ARP,

A10550).
Figure 3.3.11 Aldehyde-reactive probe (ARP) used to detect DNA damage. The biotin hydroxylamine ARP (A10550) reacts with aldehyde groups formed when reactive oxygen species depurinate DNA. This reaction forms a covalent bond linking the DNA to biotin. The biotin can then be detected using fluorophore- or enzyme-linked streptavidin.
The
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
TheMolecular
MolecularProbes
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT
NOTICE: described
The products
described
in this
oneLimited
or more Use
Limited
UseLicense(s).
Label License(s).
Please
to the
Appendix
IMPORTANT NOTICE
: The products
in this
manual
are manual
coveredare
bycovered
one or by
more
Label
Please
referrefer
to the
Appendix
onon
141
Aliphatic and Aromatic Amines

Primary aliphatic and aromatic amines (Table 3.2) can be coupled reversibly to aldehydes and ketones to form hydrolytically unstable Schiff bases 11 (Figure 3.3.12). The reversibility of this modification makes reagents that contain amines less desirable unless the
Schiff base is reduced by sodium borohydride 52,53 or sodium cyanoborohydride.54 Chemical reduction also retains the amines original
charge. Sequencing of carbohydrate polymers using fluorescent derivatives has usually relied on derivatization of the reducing end of
the polymer with a fluorescent amine.55 Certain aromatic amines have
been extensively utilized for coupling to aldehydes, ketones, monosaccharides and the reducing end of carbohydrate polymers:
2-Aminoacridone (A6289) forms conjugates that can be separated
by HPLC 56,57 or, as their borate complexes, by polyacrylamide gel
electrophoresis, 55,58,59 capillary electrophoresis 6062 and micellar
electrokinetic capillary chromatography 63,64 (MECC). Starting
with as little as 25 g of a glycoprotein, researchers have efficiently released and purified the carbohydrates, and then derivatized them with 2-aminoacridone for subsequent structural
analysis.65 2-Aminoacridone derivatives of oligosaccharides have
C O
2
R
3
R NH
2
C NR
2
R
NaCNBH
3
CH NHR
2
R
Figure 3.3.12 Modifying aldehydes and ketones with amine derivatives.
Section 3.3
been directly analyzed by MALDI-TOF mass spectrometry.66

2-Aminoacridone is also used to prepare fluorogenic substrates
for proteases.67
7-Amino-4-methylcoumarin (A191), which is a common base of
protease substrates (Section 10.4), can be used for the reductive
derivatization of oligosaccharides.68,69
8-Aminopyrene-1,3,6-trisulfonic acid (APTS, A6257) has been
extensively used to derivatize carbohydrates prior to separation
by gel or capillary electrophoresis.70,71 Among the amines we offer,
APTS is the aromatic amine that has the most favorable combination of strong absorbance, high quantum yield and ionic charge.
ANTS (A350) has a high ionic charge, permitting electrophoretic
separation of its products with complex oligosaccharides.72
The aromatic diamine 1,2-diamino-4,5-dimethoxybenzene (DDB,
D1463), which forms heterocyclic compounds with certain aldehydes
and ketones, has been used to selectively detect aromatic aldehydes in
the presence of aliphatic aldehydes, including carbohydrates.73 DBB
has proven to be a useful reagent for HPLC analysis of the cytotoxic
metabolic by-product methylglyoxal in blood samples from diabetic
patients.74
Alternatively, aldehydes and ketones can be transformed into primary aliphatic amines by reductive amination with ammonia, ethylenediamine or other nonfluorescent diamines.75 This chemistry is
particularly useful because the products can then be coupled with
any of the amine-reactive reagents described in Chapter 1 such as the
succinimidyl esters of TAMRA dye 76 (C1171, C6121, C6122; Section
1.6). Derivatization by succinimidyl esters has been extensively utilized for tagging oligosaccharides that are to be separated by capillary
zone electrophoresis with laser-induced fluorescence detection.7679
REFERENCES
1. J Biomed Mater Res A (2007) 83:1176; 2. Anal Biochem (1987) 161:245;
3. Electrophoresis (2003) 24:588; 4. Nat Struct Mol Biol (2008) 15:494; 5. Proc Natl Acad
Sci U S A (2004) 101:7902; 6. Bioconjug Chem (1994) 5:436; 7. Bioconjug Chem (2003)
14:205; 8. Bioconjug Chem (1992) 3:262; 9. Bioconjug Chem (1994) 5:636; 10. J Immunol
(2009) 183:1551; 11. Methods Enzymol (1994) 247:30; 12. Anal Biochem (1988) 170:271;
13. Methods Enzymol (1987) 138:429; 14. Biochem Biophys Res Commun (1980)
92:1215; 15. J Supramol Struct (1977) 6:291; 16. Bioconjug Chem (2009) 20:1228;
17. Bioconjug Chem (2009) 20:1383; 18. Cytometry (2000) 41:316; 19. ACS Chem Biol
(2007) 2:247; 20. Mol Ther (2008) 16:1467; 21. Proc Natl Acad Sci U S A (2009) 106:3000;
22. Nature (1981) 292:17; 23. Angew Chem Int Ed Engl (2008) 47:7523; 24. Bioconjug
Chem (2008) 19:2543; 25. Nat Methods (2009) 6:207; 26. Electrophoresis (2007) 29:475;
27. BMC Urol (2005) 5:4; 28. J Am Chem Soc (2009) 131:10360; 29. Anal Bioanal Chem
(2007) 387:1883; 30. Angew Chem Int Ed Engl (2007) 46:561; 31. Anal Chem (2010)
82:2893; 32. J Chromatogr A (2002) 979:409; 33. J Cell Biol (1988) 106:1607; 34. Anal
Biochem (1969) 29:186; 35. Biochemistry (1985) 24:322; 36. Biochem Biophys Res
Commun (1983) 112:872; 37. Biochemistry (1988) 27:6039; 38. J Cell Biol (1985) 100:721;
39. Anal Biochem (1991) 198:119; 40. Physiol Res (1997) 46:407; 41. Fresenius J Anal
Chem (2000) 366:396; 42. Anal Chem (1999) 71:1893; 43. Anal Chem (1999) 71:3003;
44. Photochem Photobiol (2002) 76:123; 45. Anal Chem (2001) 73:2229; 46. Methods
(2000) 22:164; 47. Proc Natl Acad Sci U S A (2000) 97:686; 48. J Biol Chem (2000)
275:6741; 49. Anal Chem (2006) 78:6847; 50. Anal Biochem (2003) 312:113; 51. Anal
Bioanal Chem (2008) 391:2591; 52. Biochemistry (1987) 26:2162; 53. Biochim Biophys
Acta (1980) 597:285; 54. Biochim Biophys Acta (1981) 670:181; 55. Anal Biochem
(1994) 222:270; 56. Anal Chem (1998) 70:2530; 57. Anal Chem (1997) 69:4985; 58. Anal
Biochem (1994) 216:243; 59. Anal Biochem (1991) 196:238; 60. Anal Biochem (1996)
240:68; 61. Electrophoresis (1996) 17:406; 62. Anal Biochem (1995) 230:115; 63. Anal
Chem (1996) 68:4424; 64. J Chem Soc Chem Commun (1994) 14:1691; 65. Anal
Biochem (1998) 262:197; 66. Rapid Commun Mass Spectrom (1997) 11:1635; 67. Anal
Biochem (1988) 171:393; 68. Biophys J (1996) 71:2040; 69. Anal Biochem (1983) 128:41;
70. Nat Protoc (2006) 1:397; 71. Electrophoresis (2005) 26:2034; 72. Anal Biochem
(2000) 283:136; 73. J Chromatogr B Biomed Appl (1994) 659:85; 74. Diabetes Metab
(2006) 32:176; 75. Proc Natl Acad Sci U S A (1991) 88:2302; 76. J Chromatogr B Biomed
Appl (1994) 657:307; 77. Anal Biochem (1995) 227:368; 78. Carbohydr Res (1996)
296:203; 79. J Biomol Screen (1999) 4:239.
The
MolecularProbes
Probes Handbook:
Handbook: AAGuide
Probesand
andLabeling
Technologies
The
Molecular
Guide to
to Fluorescent
Fluorescent Probes
142
IMPORTANT
NOTICE:
The products
described
in this manual
coveredare
by covered
one or more
Limited
Use Label
License(s).
Please
refer to thePlease
Appendix
onto
IMPORTANT
NOTICE
: The products
described
in thisaremanual
by one
or more
Limited
Use Label
License(s).
refer
the Appendix on
Section 3.3
DATA TABLE 3.3 REAGENTS FOR MODIFYING ALDEHYDES AND KETONES

Cat. No.
MW
Storage
Soluble
Abs
EC
Em
Solvent
Notes
A191
175.19
L
DMF, DMSO
351
18,000
430
MeOH
353
7200
520
H2O
A350
427.33
L
H2O
424
19,000
505
pH 7
A6257
523.39
D,L
H2O
A6289
246.70
D,L
DMF, DMSO
425
5200
531
MeOH
1
493
71,000
517
pH 7
A10436
570.48
D,L
H2O
576
86,000
599
pH 7
2
A10437
730.74
D,L
H2O
588
97,000
613
pH 7
2
A10438
758.79
D,L
H2O
345
13,000
445
pH 7
A10439
349.29
L
H2O, DMSO
554
150,000
567
pH 7
A20501MP
~1150
D,L
H2O
649
250,000
666
pH 7
A20502
~1200
D,L
H2O
353
20,000
437
MeOH
3
A30627
584.52
F,D,L
H2O, DMSO
494
77,000
518
pH 7
3, 4, 5
A30629
895.07
F,D,L
H2O, DMSO
651
250,000
672
MeOH
3
A30632
~1220
F,D,L
H2O, DMSO
624
110,000
643
pH 7
A30634
~950
D,L
H2O, DMSO
B30300
339.24
F,D
DMSO
<300
none
C356
493.49
L
pH >7, DMF
492
78,000
516
pH 8
6
399
30,000
421
H2O
7, 8
C687
596.44
L
H2O
D100
265.33
L
EtOH
336
4400
534
MeOH
D355
275.31
D,L
MeCN, DMF
420
46,000
468
MeOH
D1463
241.12
D,L
EtOH
298
3100
359
MeOH
D2371
306.12
F,D,L
MeOH, MeCN
503
71,000
510
MeOH
9
D7918
158.20
L
DMSO, MeOH
340
5100
377
MeOH
10
F121
421.43
D,L
pH >7, DMF
492
85,000
516
pH 9
6
428
12,000
536
H2O
11, 12
L453
457.24
L
H2O
M20490
209.16
F,L
MeCN
487
24,000
none
MeOH
13
P101
302.38
D,L
MeCN, DMF
341
43,000
376
MeOH
14
T6256
620.74
F,L
DMF
582
109,000
602
MeOH
Notes
1. Spectra of this compound are in methanol containing a trace of KOH.
2. Maximum solubility in water is ~8% for A10437 and A10438.
3. Aqueous stock solutions should be used within 24 hours; long-term storage is NOT recommended.
4. The fluorescence lifetime () of the Alexa Fluor 488 dye in pH 7.4 buffer at 20C is 4.1 nanoseconds. Data provided by the SPEX Fluorescence Group, Horiba Jobin Yvon Inc.
5. Abs and Em of the Alexa Fluor 488 dye are red-shifted by as much as 16 nm and 25 nm respectively on microarrays relative to aqueous solution values. The magnitude of the spectral shift
depends on the array substrate material. (Biotechniques (2005) 38:127)
7. The Alexa Fluor 405 and Cascade Blue dyes have a second absorption peak at about 376 nm with EC ~80% of the 395400 nm peak.
8. Maximum solubility in water is ~1% for C687, ~1% for C3221 and ~8% for C3239.
9. The absorption and fluorescence spectra of BODIPY derivatives are relatively insensitive to the solvent.
10. Fluorescence of D7918 is weak. Reaction with -ketoaldehydes yields fluorescent benzoquinoxaline derivatives (Abs = 365 nm, Em = 540 nm in H2O at pH 8). (J Chromatogr B Biomed Sci Appl
(1999) 729:237)
11. The fluorescence quantum yield of lucifer yellow CH in H2O is 0.21. (J Am Chem Soc (1981) 103:7615)
12. Maximum solubility in water is ~8% for L453, ~6% for L682 and ~1% for L1177.
13. NBD methylhydrazine reacts with aldehydes and ketones in the presence of strong acid, yielding weakly fluorescent hydrazone products. (Anal Chem (1999) 71:1893) Abs = 493 nm,
Em = 552 nm in MeOH for reaction product with acetone.
14. Pyrene derivatives exhibit structured spectra. The absorption maximum is usually about 340 nm with a subsidiary peak at about 325 nm. There are also strong absorption peaks below
300 nm. The emission maximum is usually about 376 nm with a subsidiary peak at 396 nm. Excimer emission at about 470 nm may be observed at high concentrations.
The
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
TheMolecular
Molecular
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT
NOTICE:described
The products
described
thiscovered
manual are
by one
or moreUse
Limited
Label License(s).
to Appendix
the Appendix
IMPORTANT NOTICE
: The products
in this
manualinare
by covered
one or more
Limited
LabelUse
License(s).
PleasePlease
refer refer
to the
on on
143
Section 3.3
PRODUCT LIST 3.3 REAGENTS FOR MODIFYING ALDEHYDES AND KETONES

Cat. No.
Product
A30627
A30629
A30632
A10439
A10436
A20501MP
A10437
A10438
A30634
A20502
A6289
A191
A350
A6257
B30300
C356
C687
D1463
D7918
D355
D2371
D100
F121
L453
M20490
P101
T6256
Alexa Fluor 350 C5-aminooxyacetamide, trifluoroacetate salt (Alexa Fluor 350 hydroxylamine)
Alexa Fluor 488 C5-aminooxyacetamide, bis(triethylammonium) salt (Alexa Fluor 488 hydroxylamine)
Alexa Fluor 647 C5-aminooxyacetamide, bis(triethylammonium) salt (Alexa Fluor 647 hydroxylamine)
Alexa Fluor 350 hydrazide, sodium salt
Alexa Fluor 555 hydrazide, tris(triethylammonium) salt
Alexa Fluor 633 hydrazide, bis(triethylammonium) salt
Alexa Fluor 647 hydrazide, tris(triethylammonium) salt
2-aminoacridone, hydrochloride
7-amino-4-methylcoumarin *reference standard*
8-aminonaphthalene-1,3,6-trisulfonic acid, disodium salt (ANTS)
8-aminopyrene-1,3,6-trisulfonic acid, trisodium salt (APTS)
N-(t-BOC)-aminooxyacetic acid, tetrafluorophenyl ester
5-(((2-(carbohydrazino)methyl)thio)acetyl)aminofluorescein
Cascade Blue hydrazide, trisodium salt
1,2-diamino-4,5-dimethoxybenzene, dihydrochloride (DDB)
2,3-diaminonaphthalene
7-diethylaminocoumarin-3-carboxylic acid, hydrazide (DCCH)
4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-propionic acid, hydrazide (BODIPY FL hydrazide)
5-dimethylaminonaphthalene-1-sulfonyl hydrazine (dansyl hydrazine)
fluorescein-5-thiosemicarbazide
lucifer yellow CH, lithium salt
N-methyl-4-hydrazino-7-nitrobenzofurazan (NBD methylhydrazine)
1-pyrenebutanoic acid, hydrazide
Texas Red hydrazide *>90% single isomer*
Quantity
TheMolecular
MolecularProbes
Probes Handbook:
Handbook: AAGuide
and Labeling
Technologies
The
Guideto
toFluorescent
Fluorescent Probes
Probes and
144
IMPORTANT
NOTICE:
The products
described
in this manual
covered
bycovered
one or more
Limited
Use Label
License(s).
Please
refer to thePlease
Appendix
IMPORTANT
NOTICE
: The products
described
in thisare
manual
are
by one
or more
Limited
Use Label
License(s).
referonto
the Appendix on
1 mg
1 mg
1 mg
5 mg
1 mg
1 mg
1 mg
1 mg
1 mg
1 mg
25 mg
100 mg
1g
10 mg
25 mg
25 mg
10 mg
100 mg
100 mg
25 mg
5 mg
100 mg
100 mg
25 mg
25 mg
100 mg
5 mg
Section 3.4
Derivatization Reagents for Carboxylic

Acids and Carboxamides
3.4 Derivatization Reagents for Carboxylic Acids and Carboxamides

Carboxylic acids can be converted to esters, amides, acyl hydrazides or hydroxamic acids, all of which are discussed in this section. Alternatively, the half-protected tert-butyloxycarbonyl (t-BOC)
propylenediamine derivative (M6248) is useful for converting organic
solventsoluble carboxylic acids into aliphatic amines. Following coupling of the half-protected aliphatic diamine to an activated carboxylic
acid, the t-BOC group can be quantitatively removed with trifluoroacetic acid (Figure 3.4.1). The resultant aliphatic amine can then be modified with any of the amine-reactive reagents described in Chapter 1 or
coupled to solid-phase matrices for affinity chromatography.
Coupling Hydrazines, Hydroxylamines

and Amines to Carboxylic Acids
Modification in Aqueous Solutions
The carboxylic acids of water-soluble biopolymers such as proteins

can be coupled to hydrazines, hydroxylamines and amines (Table 3.2)
in aqueous solution using water-soluble carbodiimides such as 1-ethyl3-(3-dimethylaminopropyl)carbodiimide (EDAC, E2247). Including
N-hydroxysulfosuccinimide (H2249) in the reaction mixture has been
shown to improve the coupling efficiency of EDAC-mediated protein
carboxylic acid conjugations 1,2 (Figure 3.4.2). To reduce intra- and
inter-protein coupling to lysine residues,3 which is a common side
reaction, carbodiimide-mediated coupling should be performed in a
concentrated protein solution at a low pH, using a large excess of the
(CH3)3CO C NH(CH2)3NH2
RC OH
EDAC
nucleophile. EDAC-mediated coupling has been used to functionalize

Qdot 605 ITK carboxyl quantum dots (Q21301MP, Section 6.6) with
the GABA receptor agonist muscimol.4 EDAC has been shown to be
impermeable to membranes of live cells, which permits its use to distinguish between cytoplasmic and lumenal sites of reaction.5
Fluoresceinyl glycine amide (5-(aminoacetamido)fluorescein,
A1363) and various hydrazines and hydroxylamines may be the best
probes for this application because they are more likely to remain reactive at a lower pH than are aliphatic amines such as the cadaverines.6
Fluoresceinyl glycine amide has been coupled to the carboxylic acid of
a cyclosporin derivative by EDAC.7
ANTS (8-aminonaphthalene-1,3,6-trisulfonic acid, A350; Section
3.3) has a high ionic charge, which permits electrophoretic separation
of its products with complex oligosaccharides.8 Several of the fluorescent hydrazine and hydroxylamine derivatives described in Section 3.3
should have similar utility for carbodiimide-mediated derivatization
of carboxylic acids.
Modification in Organic Solvents
Peptide synthesis research has led to the development of numerous methods for coupling carboxylic acids to amines in organic solution. One such method involves the conversion of carboxylic acids to
succinimidyl esters or mixed anhydrides. Dicyclohexylcarbodiimide
and diisopropylcarbodiimide are widely used to promote amide formation in organic solution. Another recommended derivatization method for coupling organic solventsoluble carboxylic acids, including
CF3COOH
(CH3)3CO C NH(CH2)3NH CR
O
H2N(CH2)3NH CR
Figure 3.4.1 Conversion of a carboxylic acid group into an aliphatic amine. The activated carboxylic acid is derivatized with a half-protected aliphatic diamine (mono-N-(t-BOC)-propylenediamine, M6248), usually in an organic solvent, followed by removal of the t-BOCprotecting group with trifluoroacetic acid.
O
+
(CH ) NH(CH )
32
32
N C N CH CH
2 3
O
1
R COH
+
(CH ) NH(CH )
32
32
OC R
N
+
2
R NH
3
C N CH CH
2 3
O
1
2
R C NHR
O
HON
O
O
O
1
R C ON
+
2
R NH
3
O
1
2
R C NH R
O
Figure 3.4.2 Stabilization of an unstable O-acylisourea intermediate by N-hydroxysuccinimide in a carbodiimide-mediated (EDAC, E2247) modification of a carboxylic acid with a primary amine.
The
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
TheMolecular
Molecular
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT
NOTICE:described
The products
described
thiscovered
manual are
by one
or moreUse
Limited
Label License(s).
to Appendix
the Appendix
IMPORTANT NOTICE
: The products
in this
manualinare
by covered
one or more
Limited
LabelUse
License(s).
PleasePlease
referrefer
to the
on on
145

Section 3.4
Section 3.4 Derivatization Reagents for Carboxylic
peptides, to aliphatic amines without racemization is the combination

of 2,2-dipyridyldisulfide and triphenylphosphine.9,10 Unlike fluorescent aliphatic amines, fluorescent aromatic amines such as those derived from 7-amino-4-methylcoumarin (A191) and 2-aminoacridone
(A6289, Section 3.3) exhibit a shift in their absorption and emission (if
any) to much shorter wavelengths upon forming carboxamides. This
property makes these aromatic amines preferred reagents for preparing
peptidase substrates (Section 10.4). Aromatic amines can generally be
coupled to acid halides and anhydrides, with organic solvents usually
required for efficient reaction.
Hydrazine, Hydroxylamine and

Aliphatic Amine Derivatives
We provide a wide selection of carboxylic acidreactive reagents

(Table 3.2), including several different Dapoxyl, Alexa Fluor, BODIPY,
fluorescein, Oregon Green, rhodamine, Texas Red and QSY hydrazine derivatives, hydroxylamine derivatives and amine derivatives, all
of which are particularly useful for synthesizing drug analogs and as
probes for fluorescence polarization immunoassays 1113 (Fluorescence
Polarization (FP)Note 1.4). These probes all require a coupling agent
such as a carbodiimide to react with carboxylic acids; they do not spontaneously react with carboxylic acids in solution. They do, however, react spontaneously with the common amine-reactive functional groups
described in Section 1.1, including succinimidyl esters and isothiocyanates. Some of the more important probes and their applications include:
Alexa Fluor hydrazides (A10436, A10437, A10438, A10439, A30634,
A20501MP, A20502; Section 3.3), Alexa Fluor hydroxylamines
(A30627, A30629, A30632; Section 3.3) and Alexa Fluor cadaverines (A30674, A30675, A30676, A30677, A30678, A30679, A30680),
our brightest and most photostable carboxylic acidreactive probes
Figure 3.4.3 Absorption and fluorescence emission spectra of Dapoxyl (2-aminoethyl)

sulfonamide in methanol.
BODIPY aliphatic amines (D2390, D6251), for preparing pH-insensitive probes, such as BODIPY FL etoposide,14 from carboxylic
acid derivatives
Isomeric aminomethylfluoresceins (A1351, A1353), which are readily coupled to activated carboxylic acids 15
Dapoxyl (2-aminoethyl)sulfonamide (D10460) for preparing conjugates with strong UV absorption and a Stokes shift of ~200 nm
(Figure 3.4.3)
Dansyl ethylenediamine (D112), dansyl cadaverine (D113),
Dapoxyl (2-aminoethyl)sulfonamide (D10460) and Lissamine
rhodamine B ethylenediamine (L2424), for carboxylic acid derivatization 16 and glutamine transamidation reactions 17 (Figure
3.4.4)
Bimane amine (B30633), a small blue-fluorescent dye for carboxylic
acid derivatization
EDANS (A91), for preparing radioactive IAEDANS,13,18 energy
transferquenched substrates for endopeptidases 19 (Section
10.4) and an ATP substrate analog for DNA-dependent RNA
polymerase 20
QSY 7 amine (Q10464, Figure 3.4.5), which is an essentially nonfluorescent dye with strong visible absorption for preparing highly
efficient quenchers for bioassays based on fluorescence resonance
energy transfer (FRET) (Fluorescence Resonance Energy Transfer
(FRET)Note 1.2)
Hydrazine (Section 3.3) and amine derivatives of lucifer yellow
(A1339), Alexa Fluor 405 (A30675) and Cascade Blue (C621)
dyes, which are precursors of highly fluorescent, water-soluble
probes
Hydrazine and amine derivatives of biotin and desthiobiotin
(Section 4.2), which are versatile intermediates for synthesizing
biotin- and desthiobiotin-containing probes 21,22
Figure 3.4.5 QSY 7 amine, hydrochloride (Q10464).
N(CH3)2
N(CH3)2
O
+
H2N C CH2CH2
transglutaminase
+ NH3
PROTE I N
O
SO2NH(CH2)5NH2
SO2NH(CH2)5NH C CH2CH2
PROT E I N
Figure 3.4.4 Transglutaminase-mediated labeling of a protein using dansyl cadaverine (D113).
The Molecular Probes Handbook: A Guide to Fluorescent Probes and Labeling Technologies
146
peptides, to aliphatic amines without racemization is the combination

of 2,2-dipyridyldisulfide and triphenylphosphine.9,10 Unlike fluorescent aliphatic amines, fluorescent aromatic amines such as those derived from 7-amino-4-methylcoumarin (A191) and 2-aminoacridone
(A6289, Section 3.3) exhibit a shift in their absorption and emission (if
any) to much shorter wavelengths upon forming carboxamides. This
property makes these aromatic amines preferred reagents for preparing
peptidase substrates (Section 10.4). Aromatic amines can generally be
coupled to acid halides and anhydrides, with organic solvents usually
required for efficient reaction.
Hydrazine, Hydroxylamine and

Aliphatic Amine Derivatives
We provide a wide selection of carboxylic acidreactive reagents

(Table 3.2), including several different Dapoxyl, Alexa Fluor, BODIPY,
fluorescein, Oregon Green, rhodamine, Texas Red and QSY hydrazine derivatives, hydroxylamine derivatives and amine derivatives, all
of which are particularly useful for synthesizing drug analogs and as
probes for fluorescence polarization immunoassays 1113 (Fluorescence
Polarization (FP)Note 1.4). These probes all require a coupling agent
such as a carbodiimide to react with carboxylic acids; they do not spontaneously react with carboxylic acids in solution. They do, however, react spontaneously with the common amine-reactive functional groups
described in Section 1.1, including succinimidyl esters and isothiocyanates. Some of the more important probes and their applications include:
Alexa Fluor hydrazides (A10436, A10437, A10438, A10439, A30634,
A20501MP, A20502; Section 3.3), Alexa Fluor hydroxylamines
(A30627, A30629, A30632; Section 3.3) and Alexa Fluor cadaverines (A30674, A30675, A30676, A30677, A30678, A30679, A30680),
our brightest and most photostable carboxylic acidreactive probes
Figure 3.4.3 Absorption and fluorescence emission spectra of Dapoxyl (2-aminoethyl)

sulfonamide in methanol.
N(CH )
32
H N C CH CH
2
2
2
BODIPY aliphatic amines (D2390, D6251), for preparing pH-insensitive probes, such as BODIPY FL etoposide,14 from carboxylic
acid derivatives
Isomeric aminomethylfluoresceins (A1351, A1353), which are readily coupled to activated carboxylic acids 15
Dapoxyl (2-aminoethyl)sulfonamide (D10460) for preparing conjugates with strong UV absorption and a Stokes shift of ~200 nm
(Figure 3.4.3)
Dansyl ethylenediamine (D112), dansyl cadaverine (D113),
Dapoxyl (2-aminoethyl)sulfonamide (D10460) and Lissamine
rhodamine B ethylenediamine (L2424), for carboxylic acid derivatization 16 and glutamine transamidation reactions 17 (Figure
3.4.4)
Bimane amine (B30633), a small blue-fluorescent dye for carboxylic
acid derivatization
EDANS (A91), for preparing radioactive IAEDANS,13,18 energy
transferquenched substrates for endopeptidases 19 (Section
10.4) and an ATP substrate analog for DNA-dependent RNA
polymerase 20
QSY 7 amine (Q10464, Figure 3.4.5), which is an essentially nonfluorescent dye with strong visible absorption for preparing highly
efficient quenchers for bioassays based on fluorescence resonance
energy transfer (FRET) (Fluorescence Resonance Energy Transfer
(FRET)Note 1.2)
Hydrazine (Section 3.3) and amine derivatives of lucifer yellow
(A1339), Alexa Fluor 405 (A30675) and Cascade Blue (C621)
dyes, which are precursors of highly fluorescent, water-soluble
probes
Hydrazine and amine derivatives of biotin and desthiobiotin
(Section 4.2), which are versatile intermediates for synthesizing
biotin- and desthiobiotin-containing probes 21,22
Figure 3.4.5 QSY 7 amine, hydrochloride (Q10464).
N(CH )
32
O
+

transglutaminase
+ NH
PROTE I N
O
SO NH(CH ) NH C CH CH
2
25
2
2
SO NH(CH ) NH
2
25 2
Figure 3.4.4 Transglutaminase-mediated labeling of a protein using dansyl cadaverine (D113).
The
MolecularProbes
Probes Handbook:
Handbook: AAGuide
Probesand
andLabeling
Technologies
The
Molecular
Guide to
to Fluorescent
Fluorescent Probes
146
IMPORTANT
NOTICE:
The products
described
in this manual
coveredare
by covered
one or more
Limited
Use Label
License(s).
Please
refer to thePlease
Appendix
onto
IMPORTANT
NOTICE
: The products
described
in thisaremanual
by one
or more
Limited
Use Label
License(s).
refer
the Appendix on
PROT E I N
Section 3.4

Enzyme-Catalyzed Transamidation
A transglutaminase-catalyzed transamidation reaction of glutamine residues in some proteins and peptides enables their selective modification by amine-containing probes 23,24 (Figure
3.4.4). This unique method for selective protein modification requires formation of a complex
consisting of the glutamine residue, the aliphatic amine probe and the enzyme. It has been
found that a short aliphatic spacer in the amine probe enhances the reaction. The cadaverine
(NH(CH2)5NH) spacer is usually optimal. Although dansyl cadaverine (D113) has been probably the most widely used reagent,2527 Alexa Fluor cadaverines 24 (A30674, A30675, A30676,
A30677, A30678, A30679, A30680), Oregon Green 488 cadaverine (O10465), fluorescein cadaverine 2833 (A10466), tetramethylrhodamine cadaverine 34 (A1318), Texas Red cadaverine
(T2425) and BODIPY TR cadaverine (D6251) are among the most fluorescent transglutaminase
substrates available. The intrinsic transglutaminase activity in sea urchin eggs has been used to
covalently incorporate dansyl cadaverine during embryonic development. 35 Two biotin cadaverines (A1594, B1596; Section 4.2) are also available for transglutaminase-mediated reactions. 3638
Amine-terminated peptides and fluorescent and biotin hydrazides, including Cascade Blue hydrazide, have been successfully incorporated into protein fragments by transamidation during
enzyme-catalyzed proteolysis.39
Transamidation of cell-surface glutamine residues by the combination of a transglutaminase enzyme and a fluorescent or biotinylated aliphatic amine can form stable amides.27
Impermeability of the enzyme restricts this reaction to a limited number of proteins on the
cell surface. This technique was used to selectively label erythrocyte band 3 protein with dansyl cadaverine (D113) and proteins of the extracellular matrix with fluorescein cadaverine 31,32
(A10466). Following protease treatment, the dansylated peptides were isolated using an antidansyl affinity column.40
HO
C OH
O
CH2Br
Figure 3.4.6 5-(Bromomethyl)fluorescein (B1355).
CH2Br
H3C
N
H3C
CH3
N
F
CH3
Figure 3.4.7 BODIPY 493/503 methyl bromide

(8-bromomethyl-4,4-difluoro-1,3,5,7-tetramethyl-4-bora3a,4a-diaza-s-indacene, B2103).
Esterification of Carboxylic Acids with

Fluorescent Diazoalkanes
Biologically important molecules, especially the nonchromophoric fatty acids, bile acids
and prostaglandins, are typically esterified by carboxylic acidreactive reagents in organic solvents. Esterification of carboxylic acids in aqueous solution is usually not possible, and esters
tend to be unstable in water. Fluorescent derivatization reagents for biomedical chromatography
have been extensively discussed in reviews.41,42
HPLC derivatization reagents for carboxylic acids include two fluorescent analogs of the
common esterification reagent diazomethane. Diazoalkanes react without the addition of catalysts and may be useful for direct carboxylic acid modification of proteins and synthetic polymers. Fluorescent diazoalkanes also react with phosphates 43 and potentially with lipid-associated carboxylic acids in membrane-bound proteins or with free fatty acids.
The fluorescent diazomethyl derivative 9-anthryldiazomethane (ADAM, A1400) has been
commonly used to derivatize biomolecules. Unfortunately, ADAM is not very stable and may
decompose during storage. 1-Pyrenyldiazomethane 4447 (PDAM, P1405) is recommended as a
replacement for ADAM because it has much better chemical stability. Moreover, the detection
limit for PDAM conjugates is reported to be about 2030 femtomoles, which is five times better
than reported for detection of ADAM conjugates.45 In addition, fatty acids derivatized with these
reagents have been used to measure phospholipase A 2 activity 48 (Section 17.4). It has been reported that photolysis of pyrenemethyl esters liberates the free carboxylic acid,47 making PDAM
a potential protecting group for carboxylic acids.
Figure 3.4.8 2-(2,3-Naphthalimino)ethyl trifluoromethanesulfonate (N2461).
Fluorescent Alkyl Halides

The low nucleophilicity of carboxylic acids requires that they be converted to anions (typically cesium or quaternary ammonium are used as counterions) before they can be esterified with
alkyl halides in organic solvents. Conjugates of 6-bromoacetyl-2-dimethylaminonaphthalene
(badan, B6057) have a high Stokes shift, as well as spectral properties that are very sensitive
The
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
TheMolecular
Molecular
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT
NOTICE:described
The products
described
thiscovered
manual are
covered
by one
or moreUse
Limited
Label License(s).
the Appendix
IMPORTANT NOTICE
: The products
in this
manualinare
by one
or more
Limited
LabelUse
License(s).
PleasePlease
refer refer
to thetoAppendix
on on
147
to their environment. 5-(Bromomethyl)fluorescein (B1355, Figure

3.4.6) and BODIPY 493/503 methyl bromide (B2103, Figure 3.4.7)
have the strongest absorptivity and fluorescence of the currently available carboxylic acidderivatization reagents.49 An analytical method
for estimating the degree of EDAC crosslinking of collagen has been
developed based on derivatization of residual carboxyl groups by
5-bromomethylfluorescein.50
All of the alkyl halides in this section also react with thiol groups,
including those in proteins.51,52 Although more commonly used as thiol-reactive reagents, the monobromobimanes (M1378, M20381; Section
2.3) have been reported to react with carboxylic acids in organic solvents.53 The coumarin iodoacetamide DCIA (D404, Section 2.3) has
also been used to derivatize carboxylic acids; 54 other iodoacetamides
described in Chapter 2 will probably react similarly.
F
-
HO
SO
3
F
RCOH
RCO
SO
3
F
Figure 3.4.9 4-Sulfo-2,3,5,6-tetrafluorophenol (STP, S10490) can be used to prepare watersoluble activated esters from various carboxylic acids.
Section 3.4

Fluorescent Trifluoromethanesulfonate
2-(2,3-Naphthalimino)ethyl trifluoromethanesulfonate (N2461,
Figure 3.4.8) reacts rapidly with the anions of carboxylic acids in acetonitrile to give adducts that are reported to be detectable by absorption at
259 nm down to 100 femtomoles and by fluorescence at 394 nm down to
4 femtomoles.55 This naphthalimide sulfonate ester will likely react with
other nucleophiles too, including thiols, amines, phenols (e.g., tyrosine)
and probably histidine. 2-(2,3-Naphthalimino)ethyl trifluoromethanesulfonate has been used for the sensitive reverse-phase HPLC detection
of eicosanoids in brain tissue.56
4-Sulfo-2,3,5,6-Tetrafluorophenol (STP)
and N-Hydroxysulfosuccinimide (NHSS)
4-Sulfo-2,3,5,6-tetrafluorophenol
(STP,
S10490)
and
N-hydroxysulfosuccinimide (NHSS, H2249) can be used to prepare
water-soluble activated esters from various carboxylic acids (Figure
3.4.9). Coupling typically involves a carbodiimide such as EDAC
(E2247) and is performed in an organic solvent. We have found that
the resulting STP esters are much easier to purify and more stable than
activated esters prepared from N-hydroxysulfosuccinimide.57 NHSS
esters of biotin and other derivatives considerably increase the aqueous
solubility of the reagents.58 We offer a variety of amine-reactive STP
esters, which are discussed in Chapter 1.
REFERENCES
1. Bioconjug Chem (2008) 19:1880; 2. Anal Biochem (1986) 156:220; 3. Biophys
J (2000) 78:1449; 4. J Am Chem Soc (2006) 128:15701; 5. J Biol Chem (2000) 275:977;
6. Methods Enzymol (1987) 138:429; 7. Bioconjug Chem (1992) 3:32; 8. Anal Biochem
(2000) 283:136; 9. J Chromatogr (1993) 645:75; 10. Tetrahedron Lett (1970) 22:1901;
11. Anal Biochem (1987) 162:89; 12. Clin Chem (1985) 31:1193; 13. Biochemistry (1973)
12:4154; 14. Biochem Pharmacol (1997) 53:715; 15. Bioorg Med Chem Lett (2002)
12:1283; 16. Biochim Biophys Acta (1991) 1085:223; 17. Anal Biochem (1971) 44:221;
18. J Labelled Compounds Radiopharmaceut (1983) 20:1265; 19. J Biol Chem (2004)
279:20775; 20. Arch Biochem Biophys (1986) 246:564; 21. J Histochem Cytochem
(1990) 38:377; 22. Ann NY Acad Sci (1984) 463:214; 23. J Am Chem Soc (2006)
128:4542; 24. Protein Sci (2006) 15:640; 25. Anal Biochem (1992) 201:270; 26. FEBS
Lett (1991) 278:51; 27. Biochemistry (1978) 17:2163; 28. Toxicol in Vitro (1999)
13:773; 29. J Biol Chem (1999) 274:430; 30. Biochem J (1998) 331:105; 31. Exp Cell
Res (1998) 239:119; 32. Histochem J (1997) 29:593; 33. Biochemistry (1988) 27:3483;
34. Biochemistry (1988) 27:4512; 35. Biochemistry (1990) 29:5103; 36. J Biol Chem
(1998) 273:11991; 37. J Biol Chem (1994) 269:24596; 38. Anal Biochem (1992) 205:166;
39. J Biol Chem (1996) 271:28399; 40. J Biol Chem (1994) 269:22907; 41. J Chromatogr
B Biomed Appl (1994) 659:139; 42. J Chromatogr B Biomed Appl (1994) 659:85;
43. J Chromatogr B Analyt Technol Biomed Life Sci (2006) 831:63; 44. J Lipid Res
(1997) 38:1913; 45. Anal Chem (1988) 60:2067; 46. J Chromatogr (1988) 456:421;
47. Tetrahedron Lett (1987) 28:679; 48. J Biol Chem (1988) 263:5724; 49. Biomed
Chromatogr (1996) 10:193; 50. J Biomed Mater Res A (2007) 83:1176; 51. J Biol Chem
(1997) 272:17444; 52. J Biol Chem (1996) 271:19964; 53. J Org Chem (1981) 46:1666;
54. Anal Chem (1987) 59:1203; 55. J Chromatogr (1990) 508:133; 56. J Chromatogr B
Analyt Technol Biomed Life Sci (2004) 803:267; 57. Tetrahedron Lett (1999) 40:1471;
58. Biochemistry (1982) 21:3950.
The
MolecularProbes
Probes Handbook:
Handbook: A
Probesand
andLabeling
Technologies
The
Molecular
A Guide
Guide to
to Fluorescent
Fluorescent Probes
148
IMPORTANT
NOTICE:
The products
described
in this manual
coveredare
by one
or more
Limited
Use Label
License(s).
Please
refer to thePlease
Appendix
onto
IMPORTANT
NOTICE
: The products
described
in thisaremanual
covered
by one
or more
Limited
Use Label
License(s).
refer
the Appendix on
Section 3.4

DATA TABLE 3.4 DERIVATIZATION REAGENTS FOR CARBOXYLIC ACIDS AND CARBOXAMIDES
Cat. No.
MW
Storage
Soluble
Abs
EC
Em
Solvent
Notes
A91
288.30
L
pH >10, DMF
335
5900
493
pH 8
A191
175.19
L
DMF, DMSO
351
18,000
430
MeOH
1
A1318
514.62
F,D,L
DMF, EtOH
544
78,000
571
MeOH
425
12,000
532
H2O
A1339
491.57
L
H2O
426
11,000
531
H2O
A1340
533.65
L
H2O
A1351
397.81
L
pH >6, DMF
492
80,000
516
pH 9
2
A1353
397.81
L
pH >6, DMF
492
68,000
516
pH 9
2
A1363
404.38
L
pH >6, DMF
491
80,000
515
pH 9
2
A1400
218.26
FF,D,L
DMF, MeCN
364
6100
411
MeOH
A10466
653.38
D,L
pH >6, DMF
493
82,000
517
pH 9
2
353
20,000
437
MeOH
A30674
397.45
F,D,L
H2O
399
29,000
422
H2O
3
A30675
666.58
F,D,L
H2O
493
73,000
516
pH 7
4, 5
A30676
640.61
F,D,L
H2O
555
155,000
572
MeOH
A30677
~950
F,D,L
H2O
588
105,000
612
pH 7
A30678
806.94
F,D,L
H2O
651
245,000
672
MeOH
A30679
~1000
F,D,L
H2O
578
93,000
602
pH 7
A30680
812.95
F,D,L
H2O
B1355
425.23
F,D,L
pH >6, DMF
492
81,000
515
pH 9
B2103
341.00
F,D,L
DMSO, MeCN
533
62,000
561
CHCl3
B6057
292.17
F,L
DMF, MeCN
387
21,000
520
MeOH
B30633
207.23
F,D,L
DMSO
375
6000
458
MeOH
399
30,000
423
H2O
3
C621
624.49
L
H2O
D112
293.38
L
EtOH, DMF
335
4600
526
MeOH
D113
335.46
L
EtOH, DMF
335
4600
518
MeOH
D2390
370.64
F,D,L
DMSO, MeCN
503
76,000
510
MeOH
6
D6251
544.85
F,D,L
DMSO, MeCN
588
64,000
616
MeOH
6
D10460
386.47
L
DMF, DMSO
373
23,000
571
MeOH
7
<300
none
E2247
191.70
F,D
H2O
<300
none
H2249
217.13
D
H2O
L2424
600.75
L
DMF, DMSO
561
122,000
581
MeOH
M6248
174.24
D,A
DMF, MeCN
<300
none
260
59,000
395
MeOH
N2461
373.30
FF,DD,L
DMF, CHCl3
O10465
496.47
F,D,L
pH >6, DMF
494
75,000
521
pH 9
8
P1405
242.28
FF,L
DMF, MeCN
340
41,000
375
MeOH
Q10464
814.87
L
DMSO
560
92,000
none
MeOH
<300
none
S10490
268.11
D
H2O
T2425
690.87
L
DMF
591
85,000
612
pH 9
Notes
1. A191 in aqueous solution (pH 7.0): Abs = 342 nm (EC = 16,000 cm1M1), Em = 441 nm.
3. The Alexa Fluor 405 and Cascade Blue dyes have a second absorption peak at about 376 nm with EC ~80% of the 395400 nm peak.
4. The fluorescence lifetime () of the Alexa Fluor 488 dye in pH 7.4 buffer at 20C is 4.1 nanoseconds. Data provided by the SPEX Fluorescence Group, Horiba Jobin Yvon Inc.
5. Abs and Em of the Alexa Fluor 488 dye are red-shifted by as much as 16 nm and 25 nm respectively on microarrays relative to aqueous solution values. The magnitude of the spectral shift
depends on the array substrate material. (Biotechniques (2005) 38:127)
6. The absorption and fluorescence spectra of BODIPY derivatives are relatively insensitive to the solvent.
7. Fluorescence emission spectrum shifts to shorter wavelengths in nonpolar solvents.
8. Absorption and fluorescence of Oregon Green 488 derivatives are pH dependent only in moderately acidic solutions (pH <5).
The
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
TheMolecular
Molecular
Probes
Handbook:
A Guide
to Fluorescent
Probes
and
Labeling
Technologies
IMPORTANT
NOTICE:described
The products
described
thiscovered
manual are
by oneLimited
or moreUse
Limited
Use
Label License(s).
to the
Appendix
IMPORTANT NOTICE
: The products
in this
manualinare
by covered
one or more
Label
License(s).
PleasePlease
referrefer
to the
Appendix
on on
149
Section 3.4

PRODUCT LIST 3.4 DERIVATIZATION REAGENTS FOR CARBOXYLIC ACIDS AND CARBOXAMIDES
Cat. No.
Product
A30674
A30675
A30676
A30677
A30680
A30678
A30679
A1363
A1339
A91
A191
A1351
A1353
A1318
A1340
A10466
A1400
B30633
B2103
B6057
B1355
C621
D10460
D2390
D6251
D112
D113
E2247
H2249
L2424
M6248
N2461
O10465
P1405
Q10464
S10490
T2425
Alexa Fluor 350 cadaverine

Alexa Fluor 405 cadaverine, trisodium salt4
Alexa Fluor 488 cadaverine, sodium salt
Alexa Fluor 555 cadaverine, disodium salt
Alexa Fluor 568 cadaverine, diammonium salt
Alexa Fluor 594 cadaverine
Alexa Fluor 647 cadaverine, disodium salt
5-(aminoacetamido)fluorescein (fluoresceinyl glycine amide)
N-(2-aminoethyl)-4-amino-3,6-disulfo-1,8-naphthalimide, dipotassium salt (lucifer yellow ethylenediamine)
5-((2-aminoethyl)amino)naphthalene-1-sulfonic acid, sodium salt (EDANS)
7-amino-4-methylcoumarin *reference standard*
4-(aminomethyl)fluorescein, hydrochloride
5-(aminomethyl)fluorescein, hydrochloride
5-(and-6)-((N-(5-aminopentyl)amino)carbonyl)tetramethylrhodamine (tetramethylrhodamine cadaverine) *mixed isomers*
N-(5-aminopentyl)-4-amino-3,6-disulfo-1,8-naphthalimide, dipotassium salt (lucifer yellow cadaverine)
5-((5-aminopentyl)thioureidyl)fluorescein, dihydrobromide salt (fluorescein cadaverine)
9-anthryldiazomethane (ADAM)
bimane amine
BODIPY 493/503 methyl bromide (8-bromomethyl-4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene)
6-bromoacetyl-2-dimethylaminonaphthalene (badan)
5-(bromomethyl)fluorescein
Cascade Blue ethylenediamine, trisodium salt
Dapoxyl (2-aminoethyl)sulfonamide
4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-propionyl ethylenediamine, hydrochloride (BODIPY FL EDA)
5-(((4-(4,4-difluoro-5-(2-thienyl)-4-bora-3a,4a-diaza-s-indacene-3-yl)phenoxy)acetyl)amino)pentylamine, hydrochloride (BODIPY TR cadaverine)
5-dimethylaminonaphthalene-1-(N-(2-aminoethyl))sulfonamide (dansyl ethylenediamine)
5-dimethylaminonaphthalene-1-(N-(5-aminopentyl))sulfonamide (dansyl cadaverine)
1-ethyl-3-(3-dimethylaminopropyl)carbodiimide, hydrochloride (EDAC)
N-hydroxysulfosuccinimide, sodium salt (NHSS)
Lissamine rhodamine B ethylenediamine
mono-N-(t-BOC)-propylenediamine
2-(2,3-naphthalimino)ethyl trifluoromethanesulfonate
Oregon Green 488 cadaverine *5-isomer*
1-pyrenyldiazomethane (PDAM)
QSY 7 amine, hydrochloride
4-sulfo-2,3,5,6-tetrafluorophenol, sodium salt (STP)
Texas Red cadaverine (Texas Red C5)
Quantity
The
MolecularProbes
Probes Handbook:
Handbook: A
Probesand
andLabeling
Technologies
The
Molecular
A Guide
Guide to
to Fluorescent
Fluorescent Probes
150
IMPORTANT
NOTICE:
The products
described
in this manual
coveredare
by one
or more
Limited
Use Label
License(s).
Please
refer to thePlease
Appendix
onto
IMPORTANT
NOTICE
: The products
described
in thisaremanual
covered
by one
or more
Limited
Use Label
License(s).
refer
the Appendix on
1 mg
1 mg
1 mg
1 mg
1 mg
1 mg
1 mg
10 mg
25 mg
1g
100 mg
25 mg
10 mg
10 mg
25 mg
25 mg
25 mg
5 mg
5 mg
10 mg
10 mg
10 mg
10 mg
5 mg
5 mg
100 mg
100 mg
100 mg
100 mg
10 mg
1g
100 mg
5 mg
25 mg
5 mg
100 mg
5 mg

CH 3 Click Chemistry

Uploaded by

Copyright:

Available Formats

CH 3 Click Chemistry

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

CH 3 Click Chemistry

Uploaded by

Copyright:

Available Formats

The Molecular Probes Handbook

A GUIDE TO FLUORESCENT PROBES AND LABELING TECHNOLOGIES

Molecular Probes Handbook

BioProbes Journal of Cell Biology Applications

Access all Molecular Probes educational resources at lifetechnologies.com/mpeducat

Click Chemistry and

Principles of Bioorthogonal Labeling and Click Chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

Click-iT Tools for Cell Proliferation Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129

Click-iT TUNEL Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130

Data Table 3.1 Click Chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132

3.2 Reagents for Modifying Alcohols

Alcohols in Proteins: Serine, Threonine and Tyrosine Residues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134

Alcohols in Carbohydrates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135

Alcohol Modification in Organic Solvents. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136

Data Table 3.2 Reagents for Modifying Alcohols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

3.3 Reagents for Modifying Aldehydes and Ketones .

Introducing Aldehydes and Ketones into Biomolecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138

Chapter 3 Click Chemistry and Other Functional Group Modifications

Introducing a Hydroxylamine into a Biomolecule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139

Aliphatic and Aromatic Amines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142

3.4 Derivatization Reagents for Carboxylic Acids and Carboxamides

Coupling Hydrazines, Hydroxylamines and Amines to Carboxylic Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145

Esterification of Carboxylic Acids with Fluorescent Diazoalkanes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

Chapter 3 Click Chemistry and Other Functional Group Modifications

3.1 Click Chemistry

by employing bioorthogonal reactive chemistry, in which the reaction

Chapter 3 Click Chemistry and Other Functional Group Modifications

is a two-step process. First, one reaction partnereither an azide or

and Expression TechnologyNote 11.1), in situ labeling is obtained

Alexa Fluor 488

Both required for detection

Both required for detection

Table 3.1 Molecular Probes azide and alkyne derivatives.

Azide- or Alkyne-Modified Biomolecules for Metabolic or Enzymatic Labeling

Click-iT HPG (L-homopropargylglycine)

Click-iT farnesyl alcohol, azide

Click-iT geranylgeranyl alcohol, azide

Click-iT fucose alkyne (tetraacetylfucose alkyne)

Identification of fucoslyated proteins

Click-iT palmitic acid, azide

Identification of protein fatty acylation

Click-iT myristic acid, azide

Identification of isoprenylated proteins

Click-iT GalNAz (tetraacetylated N-azidoacetylgalactosamine)

Identification of O-linked glycoproteins, including O-GlcNAc

Click-iT ManNAz (tetraacetylated N-azidoacetylmannosamine)

Identification of sialic acidmodified glycoproteins

Click-iT ManNAz (tetraacetylated N-azidoacetylglucosamine)

Identification of O-GlcNAcmodified glycoproteins

Azide- or Alkyne-Modified Fluorophores and Haptens for Detection (Ex/Em)*

Fluorescent dye or hapten

Alexa Fluor 555 (555/565)

Alexa Fluor 594 (590/617)

Alexa Fluor 647 (650/668)

Oregon Green 488 (496/524)

Fluorescent dye or hapten

Tetramethylrhodamine (TAMRA) (555/580)

Fluorescent dye or hapten

Chapter 3 Click Chemistry and Other Functional Group Modifications