Chapter 1 Fluorophores and Their Amine-Reactive Derivatives

- Common Applications for Amine-Reactive Probes
- Labeling Biopolymers
- Preparing the Optimal Bioconjugate
- Derivatizing Low Molecular Weight Molecules
- Reactivity of Amino Groups
- Isothiocyanates
- Active Esters and Carboxylic Acids
- Succinimidyl Esters
- Carboxylic Esters and Their Conversion into Sulfosuccinimidyl Esters and STP Esters
- Tetrafluorophenyl (TFP) Esters
- Carbonyl Azides
- Sulfonyl Chlorides
- Other Amine-Reactive Reagents

- Kits for Labeling Proteins with a Fluorescent Dye or Biotin
- FluoReporter Protein Labeling Kits
- Easy-to-Use Protein Labeling Kits
- Alexa Fluor Microscale Protein Labeling Kits
- Monoclonal Antibody Labeling Kits
- FluoReporter Biotin-XX Protein Labeling Kit
- FluoReporter Mini-Biotin-XX Protein Labeling Kit
- Biotin-XX Microscale Protein Labeling Kits
- DSB-X Biotin Protein Labeling Kit
- FluoReporter Biotin/DNP Protein Labeling Kit
- Zenon Antibody Labeling Kits
- Nucleic Acid Labeling Kits
- ARES DNA Labeling Kits
- Alexa Fluor Oligonucleotide Amine Labeling Kits
- ULYSIS Nucleic Acid Labeling Kits
- Biotin Quantitation Assay Kits
- FluoReporter Biotin Quantitation Assay Kit for Biotinylated Proteins
- FluoReporter Biotin Quantitation Assay Kit for Biotinylated Nucleic Acids
- ElutaTube Microdialysis Vials
- Product List

- Features of the Alexa Fluor Dyes
- Alexa Fluor 488 Dye
- Alexa Fluor 500 and Alexa Fluor 514 Dyes
- Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 555, Alexa Fluor 568, Alexa Fluor 594 and Alexa Fluor 610 Dyes
- Alexa Fluor 633, Alexa Fluor 635, Alexa Fluor 647, Alexa Fluor 660, Alexa Fluor 680, Alexa Fluor 700 and Alexa Fluor 750 Dyes
- Alexa Fluor 350 Dye
- Alexa Fluor 405 Dye
- Alexa Fluor 430 Dye
- Alexa Fluor Labeling Reagents and Kits
- Alexa Fluor Bioconjugates and Tandem Conjugates
- Alexa Fluor Bioconjugates
- Alexa Fluor Tandem Conjugates of Phycobiliproteins
- DyeMer Bifluorophores
- Signal Amplification with Alexa Fluor Dyes
- Tyramide Signal Amplification
- Antibody-Based Signal Amplification Kits
- Alexa Fluor Conjugates of Anti-Fluorescein/Oregon Green Antibody
- Antibodies to the Alexa Fluor 488 and Alexa Fluor 405 Dyes
- Data Table
- Product List

- Overview of Our BODIPY Fluorophores
- BODIPY FL Dye: A Substitute for Fluorescein
- Longer-Wavelength BODIPY Dyes
- Amine-Reactive BODIPY Dyes
- BODIPY Dye Succinimidyl Esters
- Water-Soluble BODIPY FL Succinimidyl Esters and STP Esters
- BODIPY Carboxylic Acids
- BODIPY Dye Conjugates
- Peptides and Proteins
- BODIPY Dye Conjugates of Nucleotides and Oligonucleotides
- BODIPY Dye Conjugates of Lipids and Receptor Ligands
- BODIPY Dye Conjugates as Enzyme Substrates and for High-Throughput Screening Applications
- EnzChek Kits and DQ Reagents as Fluorogenic Enzyme Substrates
- EnzChek Polarization Assay Kit for Proteases
- Lipophilic BODIPY Substrates for Phospholipases and Other Enzymes
- BODIPY DyeBased Substrates for Chloramphenicol Acetyltransferase
- BODIPY DyeLabeled Nucleotides as Enzyme Substrates and for High-Throughput Screening Applications
- Conjugates of BODIPY Dyes for Fluorescence PolarizationBased Assays
- Additional Methods of Analysis Using BODIPY Dye Conjugates
- Data Table
- Product List

- Spectral Properties of Fluorescein
- Limitations of Fluoresceins
- NIST-Traceable Fluorescein Standard
- Reactive Derivatives of Fluorescein
- Single-Isomer Fluorescein Isothiocyanate (FITC) Preparations
- Mixed-Isomer and Single-Isomer Preparations of Carboxyfluorescein (FAM) Succinimidyl Ester
- Succinimidyl Esters of Fluorescein with Spacer Groups
- Fluorescein Dichlorotriazine (DTAF)
- Caged Fluorescein
- Oregon Green 488 and Oregon Green 514 Dyes
- Spectral Properties of the Oregon Green Dyes
- Advantages of the Oregon Green Dyes
- Reactive Oregon Green Dyes
- Oregon Green Protein and Nucleic Acid Labeling Kits
- Oregon Green 488 Tyramide Signal Amplification Kits
- Conjugates of Oregon Green Dyes
- Fluorescein Derivatives for Genetic Analysis
- Eosins and Erythrosins: Phosphorescent Probes and Photosensitizers
- Eosin and Erythrosin
- An Eosin Analog
- Rhodamine Green Dyes
- Reactive Rhodamine Green Dyes
- Rhodamine Green Conjugates
- Data Table
- Product List

- Tetramethylrhodamine
- Mixed-Isomer and Single-Isomer TRITC Preparations
- Succinimidyl Esters of Carboxytetramethylrhodamine (TAMRA)
- Lissamine Rhodamine B and Rhodamine Red-X Dyes
- Lissamine Rhodamine B Sulfonyl Chloride
- Rhodamine Red-X Succinimidyl Ester
- X-Rhodamine
- Texas Red and Texas Red-X Dyes
- Texas Red Sulfonyl Chloride
- Texas Red-X Succinimidyl Ester
- Texas Red-X STP Ester
- Texas Red C2-Dichlorotriazine
- Texas Red-X Conjugates and Texas Red-X Labeling Kits
- Naphthofluorescein
- Carboxyrhodamine 6G
- QSY Dyes: The Best Fluorescence Quenchers
- Nonfluorescent Malachite Green
- NANOGOLD Sulfosuccinimidyl Ester
- Data Table
- Product List

- Coumarin Derivatives
- Alexa Fluor 350 and AMCA-X Dyes
- Alexa Fluor 430 Dye
- Alexa Fluor and Zenon Labeling Kits
- Marina Blue and Pacific Blue Dyes
- Pacific Blue Tyramide Signal Amplification Kits
- Zenon Antibody Labeling Kits with the Marina Blue and Pacific Blue Dyes
- Alexa Fluor 350 and Pacific Blue Nucleic Acid Labeling Kits
- Other Hydroxycoumarin and Alkoxycoumarin Derivatives
- Pacific Orange Dye
- Cascade Blue and Other Pyrene Derivatives
- Cascade Blue Acetyl Azide
- Alexa Fluor 405 Dye
- Other Pyrenes
- Naphthalenes, Including Dansyl Chloride
- Bimane Derivative
- Pyridyloxazole Derivatives
- Cascade Yellow Dye
- Dapoxyl Dye
- UV LightExcitable Microspheres
- Data Table
- Product List

- Fluorescamine
- Dialdehydes: OPA and NDA
- Analyte Detection with OPA and NDA
- Sensitivity of NDA
- Applications for OPA and NDA
- ATTO-TAG Reagents
- Sensitivity of ATTO-TAG CBQCA and ATTO-TAG FQ
- ATTO-TAG Reagents and Kits
- 7-Nitrobenz-2-Oxa-1,3-Diazole (NBD) Derivatives
- Dansyl Chloride and Other Sulfonyl Chlorides
- Dansyl Chloride
- Dapoxyl Sulfonyl Chloride
- Pyrene Sulfonyl Chloride
- Chromophoric Sulfonyl Chloride
- FITC and Benzofuran Isothiocyanates
- Succinimidyl Esters and Carboxylic Acids
- The Smallest Reactive Fluorophore
- Chromophoric Succinimidyl Esters: Fluorescence Quenchers
- N-(t-BOC)-Aminooxyacetic Acid TFP Ester
- Biotinylation, Desthiobiotinylation, Crosslinking and Thiolation Reagents
- Data Table
- Product List
List of Tables
Table 1.1 Molecular Probes' amine-reactive dyes
Table 1.2 Active esters and kits for labeling proteins and nucleic acids
Table 1.3 Molecular Probes' kits for protein and nucleic acid labeling
Table 1.4 Alexa Fluor active esters and kits for labeling proteins and nucleic acids
Table 1.5 Fluorescence quantum yields (QY) and lifetimes (τ) for Alexa Fluor dyes
Table 1.6 R{0} values for some Alexa Fluor dyes
Table 1.7 Amine-reactive BODIPY dyes
Table 1.8 Amine-reactive xanthene derivatives in this section
Table 1.9 Amine-reactive, orange- and red-fluorescent fluorophores in this section
Table 1.10 Molecular Probes' nonfluorescent quenchers and photosensitizers
Table 1.11 R{o} values for QSY and dabcyl quenchers
Table 1.12 Amine-reactive, ultraviolet lightexcitable fluorophores for labeling proteins and nucleic acids
Table 1.13 Amine-reactive, environment-sensitive fluorophores
List of Figures
Figure 1.1 Reaction of a primary amine with an isothiocyanate
Figure 1.2 Reaction of a primary amine with a succinimidyl ester or a tetrafluorophenyl (TFP) ester
Figure 1.3 Reaction of a primary amine with an STP ester
Figure 1.4 Reaction of a primary amine with a sulfonyl chloride
Figure 1.5 Illustration of the three simple steps in the protocol for Molecular Probes' Protein Labeling Kits
Figure 1.6 Illustration of the three simple steps in the protocol for Molecular Probes' Monoclonal Antibody Labeling Kits
Figure 1.7 B6352; 6-((6-((biotinoyl)amino)hexanoyl)amino)hexanoic acid, sulfosuccinimidyl ester, sodium salt (biotin-XX, SSE)
Figure 1.8 Absorption and fluorescence emission spectra of fluorescein and Alexa Fluor 488 antibody conjugates
Figure 1.9 Photobleaching resistance of three green fluorophores, as determined by laser-scanning cytometry
Figure 1.10 Photobleaching comparison of fluorescein phalloidin and Alexa Fluor(R) 488 phalloidin
Figure 1.11 Bovine pulmonary artery endothelial cells (BPAEC). Alexa Fluor(R) 488 phalloidin, antiα-tubulin mouse monoclonal antibody, Alexa Fluor(R) 546 goat antimouse IgG antibody.
Figure 1.12 Comparison of pH-dependent fluorescence of green-fluorescent fluorophores
Figure 1.13 Comparison of the relative fluorescence of Alexa Fluor 488 and FITC conjugates
Figure 1.14 Brightness comparison of Molecular Probes' Alexa Fluor 488 dye and Cy2 dye antibody conjugates
Figure 1.15 A30005; Alexa Fluor 488 carboxylic acid, 2,3,5,6-tetrafluorophenyl ester (Alexa Fluor 488 5-TFP)
Figure 1.16 Stability of the tetrafluorophenyl (TFP) and succinimidyl (NHS) esters at basic pH
Figure 1.17 Absorption spectra of our intermediate-wavelength lightabsorbing Alexa Fluor dyes
Figure 1.18 Comparison of the absorption and fluorescence emission spectra of the Alexa Fluor 555 and Cy3 dyes
Figure 1.19 Neuronal cells in a 22-hour zebrafish embryo identified with antiHuC/HuD mouse monoclonal antibody.
Figure 1.20 Photobleaching profiles of the Alexa Fluor 555 and Cy3 dyes
Figure 1.21 Comparison of the relative fluorescence of Alexa Fluor 594 and Texas Red-X goat antimouse IgG antibody F(ab'){2} fragment conjugates
Figure 1.22 Flow cytometry comparison of the brightness of the Alexa Fluor 555 goat antimouse IgG antibody with commercially available Cy3 goat antimouse IgG antibody conjugates
Figure 1.23 Comparison of the fluorescence emission of Alexa Fluor 546 and Cy3 antibody conjugates
Figure 1.24 Absorption spectra of our long-wavelength lightabsorbing Alexa Fluor dyes
Figure 1.25 Comparison of the fluorescence spectra of the Alexa Fluor 647 and Cy5 dyes
Figure 1.26 Comparison of the fluorescence spectra of the unconjugated Alexa Fluor 680 and Cy5.5 dyes
Figure 1.27 Comparison of the fluorescence emission spectra of the Alexa Fluor 750 and Cy7 dyes
Figure 1.28 Photobleaching resistance of five red fluorophores, as determined by laser-scanning cytometry
Figure 1.29 Comparison of the relative fluorescence of goat antirabbit IgG antibody conjugates of the Alexa Fluor 555 and Cy3 dyes
Figure 1.30 Comparison of the brightness of Alexa Fluor 647 and Cy5 dye conjugates
Figure 1.31 Comparison of the brightness of Alexa Fluor 647 conjugates and Cy5 conjugates
Figure 1.32 Flow cytometry comparison of the brightness of the Alexa Fluor 647 goat antimouse IgG antibody conjugate with commercially available Cy5 goat antimouse IgG antibody conjugates
Figure 1.33 Comparison of the absorption spectra of Alexa Fluor 647 and Cy5 dye conjugates
Figure 1.34 Absorption spectra of our short-wavelength lightabsorbing Alexa Fluor dyes
Figure 1.35 Bovine pulmonary artery endothelial (BPAE) cell. Antibovine α-tubulin mouse monoclonal antibody and Alexa Fluor(R) 430 goat antimouse IgG antibody.
Figure 1.36 Bovine pulmonary artery endothelial (BPAE) cells labeled with mouse monoclonal antiα-tubulin antibody and detected using TSA Kit #7 with the HRP conjugate of goat antimouse IgG antibody and Alexa Fluor(R) 350 tyramide.
Figure 1.37 A zebrafish retina cryosection labeled with the mouse monoclonal antibody FRet 6 and detected using TSA Kit #9 with the HRP conjugate of goat antimouse IgG antibody and Alexa Fluor(R) 488 tyramide.
Figure 1.38 A zebrafish retina cryosection labeled with the mouse monoclonal antibody FRet 43 and detected using TSA Kit #9 with the HRP conjugate of goat antimouse IgG antibody and Alexa Fluor(R) 488 tyramide.
Figure 1.39 Bovine pulmonary artery endothelial cells (BPAEC) labeled with antiOxPhos Complex IV subunit I antibody and detected using TSA Kit #4 with the HRP conjugate of goat antimouse IgG antibody and Alexa Fluor(R) 568 tyramide.
Figure 1.40 Bovine pulmonary artery endothelial cells (BPAEC) labeled with antiOxPhos Complex IV subunit I (human) antibody and detected using TSA Kit #6 with the HRP conjugate of goat antimouse IgG antibody and Alexa Fluor(R) 647 tyramide.
Figure 1.41 Normalized fluorescence emission spectra of seven BODIPY fluorophores
Figure 1.42 Ring-numbering system of the BODIPY fluorophores
Figure 1.43 Emission spectra of fluorescein, TMR and TR conjugates
Figure 1.44 BODIPY FL/MeOH
Figure 1.45 NIH 3T3 cells. MitoTracker(R) CMXRos, BODIPY(R) FL phallacidin and POPO-1.
Figure 1.46 Comparison of photostability of green-fluorescent antibody conjugates
Figure 1.47 Demonstration of single-photon and two-photon excitation.
Figure 1.48 D6141; DISCONTINUED N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-propionyl)cysteic acid, succinimidyl ester, triethylammonium salt (DISCONTINUED BODIPY FL, CASE)
Figure 1.49 Microtubules of a sea urchin embryo visualized with a BODIPY(R) FL goat antirabbit IgG secondary antibody.
Figure 1.50 Mouse fibroblasts. BODIPY(R) TR-X phalloidin, DAPI, BODIPY(R) FL goat antirabbit IgG antibody.
Figure 1.51 Live bovine pulmonary artery endothelial cells (BPAEC) labeled with LysoTracker(R) Red and Hoechst 33342.
Figure 1.52 Fluorescein/pH 9.0
Figure 1.53 Photobleaching profiles of cells stained with Alexa Fluor 488 or fluorescein conjugates
Figure 1.54 Comparison of relative fluorescence of green-fluorescent antibody conjugates
Figure 1.55 F143; fluorescein-5-isothiocyanate (FITC 'Isomer I')
Figure 1.56 Proteobacterial symbionts. Fluorescein-5-isothiocyanate and Texas Red(R) sulfonyl chloride.
Figure 1.57 F6106; 6-(fluorescein-5-carboxamido)hexanoic acid, succinimidyl ester (5-SFX)
Figure 1.58 F6130; fluorescein-5-EX, succinimidyl ester
Figure 1.59 C20050; 5-carboxyfluorescein-bis-(5-carboxymethoxy-2-nitrobenzyl) ether, beta-alanine-carboxamide, succinimidyl ester (CMNB-caged carboxyfluorescein, SE)
Figure 1.60 Oregon Green 488 goat antimouse IgG antibody/pH 8.0
Figure 1.61 CRE BAG 2 fibroblasts. Oregon Green(R) 514 phalloidin and fluorescein phalloidin.
Figure 1.62 O6146; Oregon Green 488 carboxylic acid
Figure 1.63 O6138; Oregon Green 514 carboxylic acid
Figure 1.64 O6185; Oregon Green 488-X, succinimidyl ester
Figure 1.65 Normalized emission spectra of 5-FAM SE, 6-TET SE, 6-JOE SE, and 6-HEX SE
Figure 1.66 Structures of 6-JOE, SE, 6-HEX SE and 6-TET SE
Figure 1.67 C6166; DISCONTINUED 5-carboxy-2',4',5',7'-tetrabromosulfonefluorescein, succinimidyl ester, bis-(diisopropylethylammonium) salt
Figure 1.68 Conjugation of Rhodamine Green TFA SE to an amine
Figure 1.69 The julolidine ring structure of X-rhodamine, sulforhodamine 101 and Texas Red dyes
Figure 1.70 Normalized absorption spectra of the QSY 7, QSY 9, QSY 21 and QSY 35 dyes
Figure 1.71 Effect of protein conjugation on the absorption spectrum of tetramethylrhodamine
Figure 1.72 T6105; 6-(tetramethylrhodamine-5-(and-6)-carboxamido)hexanoic acid, succinimidyl ester (5(6)-TAMRA-X, SE)
Figure 1.73 L20; Lissamine rhodamine B sulfonyl chloride
Figure 1.74 Emission spectra of goat antimouse IgG antibody conjugates
Figure 1.75 R6160; Rhodamine Red-X, succinimidyl ester
Figure 1.76 Comparison of the relative fluorescence of Rhodamine Red-X and Lissamine rhodamine B conjugates
Figure 1.77 X491; X-rhodamine-5-(and-6)-isothiocyanate (5(6)-XRITC)
Figure 1.78 5-ROX/pH 7.0
Figure 1.79 C1309; 5-(and-6)-carboxy-X-rhodamine, succinimidyl ester (5(6)-ROX, SE)
Figure 1.80 Mouse fibroblasts. BODIPY(R) FL phallacidin, Texas Red(R) goat antimouse IgG (H+L) antibody and DAPI.
Figure 1.81 T353; Texas Red sulfonyl chloride
Figure 1.82 T20175; Texas Red-X, succinimidyl ester
Figure 1.83 Comparison of the relative fluorescence of Texas Red-X and Texas Red sulfonyl chloride conjugates
Figure 1.84 C653; 5-(and-6)-carboxynaphthofluorescein, succinimidyl ester
Figure 1.85 Carboxynaphthofluorescein/pH 10.0
Figure 1.86 Q10193; QSY 7 carboxylic acid, succinimidyl ester
Figure 1.87 Malachite green isothiocyanate/MeCN
Figure 1.88 M689; malachite green isothiocyanate
Figure 1.89 Reaction of NANOGOLD mono(sulfosuccinimidyl ester) with a primary amine
Figure 1.90 A10168; Alexa Fluor 350 carboxylic acid, succinimidyl ester
Figure 1.91 A6118; 6-((7-amino-4-methylcoumarin-3-acetyl)amino)hexanoic acid, succinimidyl ester (AMCA-X, SE)
Figure 1.92 Alexa Fluor 350 goat antimouse IgG antibody/pH 8.0
Figure 1.93 Microtubules of fixed bovine pulmonary artery endothelial cells (BPAEC). Antibovine α-tubulin antibody and Alexa Fluor(R) 350 goat antimouse IgG antibody.
Figure 1.94 A10169; Alexa Fluor 430 carboxylic acid, succinimidyl ester
Figure 1.95 Comparison of the pH-dependent fluorescence changes produced by attachment of fluorine atoms to a hydroxycoumarin
Figure 1.96 M10165; Marina Blue succinimidyl ester
Figure 1.97 P10163; Pacific Blue succinimidyl ester
Figure 1.98 A zebrafish retina cryosection visualized using TSA Kit #10 and the SYTOX(R) Orange nucleic acid stain.
Figure 1.99 C2284; Cascade Blue acetyl azide, trisodium salt
Figure 1.100 Emission spectra of Cascade Blue dye, aminomethylcoumarin and fluorescein
Figure 1.101 Cascade Blue BSA/pH 7.0
Figure 1.102 A30000; Alexa Fluor 405 carboxylic acid, succinimidyl ester
Figure 1.103 P6114; N-(1-pyrenebutanoyl)cysteic acid, succinimidyl ester, potassium salt
Figure 1.104 D6104; 6-((5-dimethylaminonaphthalene-1-sulfonyl)amino)hexanoic acid, succinimidyl ester (dansyl-X, SE)
Figure 1.105 B30250; bimane mercaptoacetic acid (carboxymethylthiobimane)
Figure 1.106 S6110; 1-(3-(succinimidyloxycarbonyl)benzyl)-4-(5-(4-methoxyphenyl)oxazol-2-yl)pyridinium bromide (PyMPO, SE)
Figure 1.107 C10164; Cascade Yellow succinimidyl ester
Figure 1.108 Emission spectra of Pacific Blue and Cascade Yellow antibody conjugates
Figure 1.109 D12800; Dapoxyl sulfonic acid, sodium salt
Figure 1.110 Dapoxyl (2-aminoethyl)sulfonamide/MeOH
Figure 1.111 Emission spectra of a Dapoxyl dye in five different solvents
Figure 1.112 Bovine pulmonary artery endothelial cells (BPAEC). LysoTracker(R) Blue-White DPX and MitoTracker(R) Red CMXRos.
Figure 1.113 Bovine pulmonary artery endothelial cells (BPAEC). ER-Tracker Blue-White DPX.
Figure 1.114 FluoSpheres(R) fluorescent microspheres.
Figure 1.115 Fluorogenic amine-derivitization reaction of fluorescamine
Figure 1.116 Fluorogenic amine-derivitization reaction of o-phthaldialdehyde (OPA)
Figure 1.117 Fluorogenic amine-derivitization reaction of naphthalene-2,3-dicarboxaldehyde (NDA)
Figure 1.118 Fluorogenic amine-derivitization reaction of CBQCA
Figure 1.119 C20260; 4-chloro-7-nitrobenz-2-oxa-1,3-diazole (NBD chloride; 4-chloro-7-nitrobenzofurazan)
Figure 1.120 D1537; DISCONTINUED 4-dimethylaminoazobenzene-4'-sulfonyl chloride (DISCONTINUED dabsyl chloride)
Figure 1.121 Normalized absorption spectra of the succinimidyl esters of dabcyl and QSY 35 dyes
Figure 1.122 D2245; 4-((4-(dimethylamino)phenyl)azo)benzoic acid, succinimidyl ester (dabcyl, SE)
Figure 1.123 Q20133; QSY 35 acetic acid, succinimidyl ester
List of Technical Notes and Product Highlights
Note 1.1 Product Highlight: The Alexa Fluor Dye Series Peak Performance across the Visible Spectrum
Note 1.2 Technical Focus: Fluorescence Resonance Energy Transfer (FRET)
Note 1.3 Product Highlight: Customer Testimonials for the Alexa Fluor Dyes
Note 1.4 Technical Focus: Fluorescence Correlation Spectroscopy (FCS)
Note 1.5 Technical Focus: Fluorescence Polarization (FP)