Fluorescent Dye Labeled Peptides

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Peptide fluorescent labeling

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Fluorescent peptides are short amino acid chains that emit light when exposed to certain wavelengths of light. These peptides are often used as probes in fluorescence microscopy, which allows for the visualization and tracking of biological molecules and processes. Additionally, fluorescent peptides can be used to monitor protein-protein interactions and enzymatic activities in real-time. The design and synthesis of fluorescent peptides involve various techniques, such as solid-phase peptide synthesis, click chemistry, and bioconjugation.

LifeTein offers an extensive range of fluorescent labeling options, including FITC, FAM, TAMRA, Cyanine Dye Cy3, Cy3.5, Cy5, Cy5.5, Cy7, Cy7.5, EDANS/Dabcyl, MCA, AZDye, BODIPY FL or Alexa Fluor (Alexa488, Alexa532, Alexa546, Alexa594, Alexa633, Alexa647), ATTO Dyes (Atto465, Atto488, Atto495, Atto550, Atto647), DyLight (DyLight 488, DyLight 550). Different fluorescent dyes cover a broad spectral range and offer various excitation and emission wavelengths to facilitate the detection of peptides using different fluorescence detection techniques, such as flow cytometry, live-cell imaging microscopy, and microarrays.

Probe Ex (nm) Em (nm) MW Notes
Methoxycoumarin (MCA) 360 410 317 Succinimidyl ester
Alexa 488 dye 490 525 699.7
FITC 495 519 389 pH sensitive
Cyanine Cy2 492 510
Cyanine Cy3 550 570
Alexa 555 dye 555 580 534.5
Rhodamine B 570 590
Abberior Star635 635 655 911 STED and Confocal Imaging
Cyanine Cy5 650 670
Silicon-Rhodamine (SiR) 652 674 472.61 Multicolour Live Cell Imaging

Fluorescent dyes are the primary means of labeling biomolecules. The most common such dyes are FITC derivatives, which have a wide range of applications in fluorescence microscopy, flow cytometry, and immunofluorescence-based assays.

Fluorescent cyclic Peptide

Fluorescence Resonance Energy Transfer (FRET) using peptides

Reference: FRET as a biomolecular research tool — understanding its potential while avoiding pitfalls

FRET Peptide synthesis: FRET Assay

Fluorescence resonance energy transfer (FRET) relies on the distance-dependent transfer of energy from a donor fluorophore to an acceptor fluorophore. FRET peptides, which are used to study the binding of peptides to proteins, conformational changes of peptides, protease activity, and measurement of molecular proximity, can be achieved using various FRET fluorophore/quencher pairs, including Abz/Dnp, EDANS/Dabcyl, Mca/Dnp, Trp/Dnp, FAM/Dabcyl, and TAMRA/BHQ3.

Standard dye combinations used for FRET:

Useful FRET calculator that provides a listing of key FRET pair information: www.fpbase.org/fret/

  1. FITC and Dabcyl:FAM/Lys(DABCYL)
  3. Methoxy-coumarin-acetic-acid(MCA) and 2,4-Dinitrophenyl(DNP): MCA/Lys(Dnp).
  4. Ortho-aminobenzoic acid (Abz) and 2,4-dinitrophenyl (DNP) or N-(2,4-dinitrophenyl)ethylenediamine (EDDnp): ABZ/Tyr (NO2), ABZ/EDDnp
  5. DABCYL and Glu(EDANS)
  6. Cy3, Cy3.5, Cy5, Cy5.5, Cy7, Cy7.5, Alexa fluor, ATTO dyes and other Near Infrared (NIR) Fluorescent Dyes are available


An Angiotensin-(1-7) Endopeptidase in the Kidney Cortex, Proximal Tubules and Human HK-2 Epithelial Cells that is Distinct from Insulin Degrading Enzyme, American Journal of Physiology - Renal Physiology, 7 January 2015Vol. no. , DOI: 10.1152/ajprenal.00609.2014

Fluorescent peptide Angiotensin 1-7 (Ang-(1-7)) with FRET pair Abz/[Tyr7(NO2)] was synthesized by LifeTein. This FRET peptide was used to study the Ang-(1-7) endopeptidase in the renal renin angiotensin system. It was found that the endopeptidase is expressed within the renal proximal tubule. It may regulate Ang-(1-7) tone.

... 100 µM Abz-Ang-(1-7)- [Tyr7(NO2)], an internally quenched fluorescent peptide (synthesized by LifeTein, South Plainfield, NJ, USA) for 20 hours or 0.5 nM 125I-(Ang-1-7) for 60 minutes at 37°C ...

Cell Penetration Monitoring

Fluorescent dyes are used to monitor the cell penetration of peptides and conjugated to various antibodies, proteins, and peptides for cellular labeling and detection. LifeTein offers to conjugate peptides to fluorescent cell-penetrating peptides (CPPs) of your choice, including R8, TAT, Maurocalcine, and penetratin, to detect their cell penetration using microscopy.


Atto dyes can be used to replace regular fluorescent dyes. Atto dyes have enhanced photostability and ozone resistance, long signal lifetimes, and reduced background for higher sensitivity. They are ideal for multiplex techniques using visible and near-IR emission wavelengths. For example, Atto 488 is a superior alternative to FITC and Alexa Fluor 488, producing conjugates with more photostability and brighter fluorescence. Atto 550 is an alternative to rhodamine dyes, Cy3, and Alexa Fluor 550, offering more intense brightness and increased photostability.

Fluorophores Recommended Atto Dye Alternative
Alexa Fluor 488 Atto 488
FITC Atto 488
FAM Atto 488
JOE Atto 520
TET Atto 520
Alexa Fluor 532 Atto 532
HEX™ Atto 532,Atto Rho6G
TAMRA Atto 550
Cy3 Atto 550
Cy3.5 Atto 565
ROX Atto 565,Atto Rho11
Alexa Fluor 594 Atto 590,Atto 594
Texas Red Atto 590
Alexa Fluor 633 Atto 633,Atto Rho14
Cy5 Atto 647,Atto 647N,Atto 655
Alexa Fluor 647 Atto 647,Atto 647N,Atto 655
Cy5.5 Atto 680,Atto 700

Frequently Asked Questions: Peptide Synthesis

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Case Study

The client requested a very hydrophobic peptide 68 amino acid in length (85% purity) with FITC modification at the N-terminus. The peptide was successfully synthesized in 4 weeks.

HPLC Results:

Peptide synthesis: FITC modification HPLC

MS Results:

Peptide synthesis: FITC modification MS


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