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Small Fluorescent Labeling Dyes
Small molecule fluorescent dyes are the workhorses of bioconjugation, enabling researchers to label proteins, antibodies, nucleic acids, and other biomolecules for detection across virtually any fluorescence-based platform. AAT Bioquest offers an extensive portfolio of reactive dyes spanning the UV to infrared spectrum, including proprietary platforms engineered for superior brightness, photostability, and water solubility. Whether you need innovative, best-in-class performance dyes or cost-effective replacements for classic dyes in established protocols, our selection provides flexible options for every labeling application.
Browse Small Fluorescent Labeling Dyes
Overview of Small Fluorescent Labeling Dyes
iFluor® Labeling Dyes
iFluor® dyes are AAT Bioquest's flagship fluorescent labeling platform, engineered to outperform classic dyes like Alexa Fluor® and DyLight™. With over 40 spectrally distinct options spanning UV to infrared, iFluor® dyes are ideal for labeling antibodies, proteins, and nucleic acids across microscopy, flow cytometry, and plate-based assays.
- Superior brightness and photostability compared to Alexa Fluor® and DyLight™ dyes
- Minimal pH sensitivity ensures consistent fluorescence across physiological conditions
- Excellent water solubility reduces aggregation and non-specific binding
- Available in NHS ester, maleimide, azide, alkyne, BCN, and other reactive forms
- Full spectral coverage from UV (~350 nm) to IR (~800 nm)
mFluor™ Multicolor Dyes
mFluor™ dyes are specifically optimized for flow cytometry applications, enabling high-resolution multicolor panels with a single laser line. Each dye is matched to common cytometer laser lines and designed for minimal spectral overlap, simplifying panel design and compensation.
- Optimized excitation profiles for 405 nm, 488 nm, 561 nm, and 640 nm lasers
- Narrow emission spectra reduce spillover in multicolor panels
- High brightness enables detection of low-abundance surface markers
- Available as reactive dyes or pre-conjugated to secondary antibodies
- Compatible with standard flow cytometry compensation workflows
XFD Labeling Dyes
XFD dyes are chemically similar, spectral equivalents to the popular Alexa Fluor® dye series, providing drop-in replacements for established protocols. Researchers can maintain experimental consistency while benefiting from significant cost savings.
- Direct spectral equivalents to Alexa Fluor® 488, 555, 647, and other common dyes
- Seamless integration into existing protocols without filter or instrument changes
- Comparable brightness and photostability to original dyes
- Available in multiple reactive forms for flexible conjugation chemistry
- Substantial cost savings for high-throughput labeling applications
AATOM™ Labeling Dyes
AATOM™ dyes are structural and spectral equivalents to ATTO dyes. These dyes excel in single-molecule detection, super-resolution microscopy, and other techniques requiring extended illumination.
- Outstanding photostability for prolonged imaging and time-lapse experiments
- High quantum yields deliver bright, stable signals
- Ideal for single-molecule localization microscopy (PALM, STORM, dSTORM)
- Excellent performance in confocal and TIRF microscopy
- Cost-effective alternative to ATTO dyes without compromising quality
Reactive Cyanines
Cyanine dyes (Cy3, Cy5, Cy7, and variants) are among the most widely used fluorophores in biological research. Their high extinction coefficients and established protocols make them popular choices for nucleic acid labeling, FRET applications, and multicolor imaging.
- High molar extinction coefficients for bright labeling
- Well-characterized spectral properties with extensive literature support
- Cy3/Cy5 pair widely used for FRET and dual-color imaging
- Cy7 and Cy7.5 extend detection into the near-infrared for in vivo imaging
- Available as sulfonated (water-soluble) and non-sulfonated variants
Reactive Fluoresceins
Fluorescein and its derivatives—including FITC—remain the most recognized green fluorescent dyes in life sciences. Their high quantum yield, low cost, and compatibility with standard FITC filter sets make them a reliable choice for routine labeling applications.
- Classic green fluorescence compatible with universal FITC filter sets
- High quantum yield (~0.9) delivers strong signal
- Extensive literature and established labeling protocols
- Available as FITC (isothiocyanate), NHS esters, maleimides, and other forms
- Cost-effective option for high-volume labeling
Reactive Rhodamines
Rhodamine-based dyes—including TRITC, Texas Red®, and rhodamine B derivatives—offer red-shifted emission relative to fluorescein, enabling two-color experiments and providing improved photostability for extended imaging.
- Red emission (550–620 nm) pairs well with fluorescein for dual-color detection
- Greater photostability than fluorescein derivatives
- Texas Red® equivalents provide far-red options for reduced autofluorescence
- Suitable for microscopy, flow cytometry, and FRET applications
- Multiple reactive groups available for diverse conjugation strategies
Reactive Coumarins
Coumarin dyes provide UV-excitable, blue-emitting fluorescence for applications requiring spectral separation from green and red channels. Common coumarins include AMCA, Pacific Blue™ equivalents, and aminomethylcoumarin derivatives.
- UV excitation (~350–400 nm) with blue emission (~450 nm)
- Excellent spectral separation from FITC, PE, and red fluorophores
- Useful as FRET donors with green-emitting acceptors
- Suitable for multicolor microscopy panels
- Available in NHS ester and other reactive formats
Other Reactive Dyes
Other Reactive Dyes encompass specialized fluorescent labeling reagents including includes oligonucleotide dyes for qPCR and sequencing, near-infrared probes for deep tissue imaging, pH-sensitive indicators for intracellular monitoring, and application-specific tools for amyloid detection, FRET assays, and thiol quantification.
- Oligonucleotide dyes (HEX, TET, VIC, NED, Helix Fluor™) optimized for qPCR, genotyping, and sequencing
- Bodi Fluor™ (BODIPY® equivalents) deliver pH-independent fluorescence and sharp emission peaks
- SNARF and Protonex™ pH indicators enable ratiometric intracellular pH measurements
- Environment-sensitive dyes (Dansyl, NBD) for binding site and conformational studies
- zFluor™ and xtraFluor™ series for super-resolution microscopy and instrument development
Document: 01.0185.251203r1
Last updated Fri Dec 12 2025