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Fluorescent Labeled Peptides

Fluorescent dye–labeled peptides with site-defined attachment (N-terminus, Lys, Cys) and expanded residue-specific options (D-Lys, DAP, Orn) plus fit-for-purpose QC.

Built for microscopy, FRET substrates, and quantitative assay workflows—QC included.

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Overview Design FRET pairs Dye categories Attachment sites Workflow QC FAQ Contact Reading

Overview

Custom fluorescent dye–labeled peptides

Fluorescent labels enable peptide tracking and quantitation in binding assays, FRET protease substrates, cell imaging, and high‑throughput screening. Labels can be introduced during SPPS or post‑synthetically depending on the dye, sequence, and site requirements.

Bio-Synthesis supports one of the most comprehensive fluorescent peptide labeling portfolios available, covering fluorophores, dark quenchers, chromogenic reporters, and site-defined attachment strategies.

This service complements our isotope-labeled peptides for quantitative LC–MS workflows, click chemistry peptides for modular fluorophore attachment, and cleavable linker peptides for activatable probes and substrates.

Bio-Synthesis fluorescent peptide labeling capabilities: We routinely support site-defined fluorescent labeling during solid-phase peptide synthesis (SPPS) or by post-synthetic conjugation, including N-terminal, C-terminal, and residue-specific modifications (Lys, D-Lys, Cys, DAP, Orn, His, Glu). In addition to the dyes listed below, Bio-Synthesis maintains access to an expanded internal inventory of fluorophores, quenchers, and chromogenic reporters. If a specific dye, linker, or attachment strategy is not shown, please contact us—custom sourcing and bespoke labeling strategies are routinely supported.

ISO 900:2015/ISO13485:2016 45+ Years of Expertise Site-defined labeling FRET donors/acceptors Quenchers + chromogenic substrates HPLC/LC-MS QC
FRET substrate design showing donor–quencher peptide before and after protease cleavage

FRET substrate design: donor and quencher remain non-fluorescent until protease cleavage separates the pair, producing a measurable signal.

Fluorescent dyes & reporters for labeled peptides (collapsible categories)

Expand a category to see representative dyes, common residue variants, typical use, and approximate excitation/emission. Wavelengths vary by vendor/derivative and measurement conditions—use these as planning guidance and provide your instrument/channel constraints with your quote request.

Not listed below? We support many additional dyes, quenchers, and custom linkers. Send your preferred dye/handle (or instrument channel) and we’ll recommend an attachment strategy and QC plan.
UV / Blue donors (Abz, NMA, coumarins) FRET donors • protease substrates
AbzNMAMCAcoumarin DAP labelingOrnithine dye
Dye / modification Residue / handle Typical function Ex (nm) Em (nm)
Abz (Anthranilyl) N-terminus / Lys FRET donor; protease substrates ~320 ~420
NMA Lys, DAP Enhanced FRET donor / reporter 340–360 440–450
DAP(NMA) DAP Site-defined donor placement 340–360 440–450
Lys(NMA) (Lys(2-(N-methylamino)benzoyl)) Lys Internal donor placement 340–360 440–450
MCA (Methoxycoumarin acetic acid) N-terminus / Lys Protease substrates; fluorescence reporter ~325 ~392
Lys(MCA) Lys Reporter placement via Lys ~325 ~392
Lys(MOC) (7-methoxycoumarin-3-yl formyl) Lys Coumarin reporter ~325 ~395
Lys(HOC) (7-hydroxycoumarin-3-yl formyl) Lys Coumarin reporter (environment-sensitive) ~360 ~450
Lys(HOMCA) Lys Coumarin-class reporter ~350 ~450
Ornithine(Coumarin343) Orn Compact fluorophore for internal labeling ~343 ~450

Note: Tryptophan (Trp) provides intrinsic fluorescence (Ex ~280 nm / Em ~350–360 nm) but is not a covalent dye label.

Green channel (fluorescein/FAM/FITC, DyLight 488, DY 495/505) imaging • binding assays
FITC5/6-FAMFluorescein DyLight 488DY 495DY 505
Dye / modification Residue / handle Typical function Ex Em
DyLight 488 N-terminus / Lys Bright labeling for imaging/flow ~493 ~518
DAP(DyLight 488) (DyLight 488 at diaminopropionic acid) DAP Site-defined label placement ~493 ~518
Lys(DyLight 488) Lys Internal/side-chain labeling ~493 ~518
Lys(5/6-Fluorescein) Lys General green labeling ~492 ~517
D-Lys(5/6-Fluorescein) D-Lys Stereo-defined variant ~492 ~517
Lys(5-Fluorescein) Lys Isomer-defined labeling ~492 ~517
Lys(6-Fluorescein) Lys Isomer-defined labeling ~492 ~517
Lys(Ahx-(5-Fluorescein)) Lys + spacer Reduces steric hindrance ~492 ~517
DY 495 N-terminus / Lys Green-channel labeling ~495 ~520
Lys(DY 495) Lys Side-chain installed DY 495 ~495 ~520
DY 505 N-terminus Green/green-yellow labeling ~505 ~530
Yellow / Orange channel (EDANS, DY 530/547/549) FRET donors • multiplexing
EDANSGlu(EDANS)DY 530DY 547DY 549
Dye / modification Residue / handle Typical function Ex Em
EDANS N-terminus / Lys / Glu FRET donor; protease substrates ~340 ~490
Glu(EDANS) Glu Internal donor placement ~340 ~490
DY 530 N-terminus / Lys Yellow/green multiplex channel ~530 ~555
Lys(DY 530) Lys Side-chain DY 530 labeling ~530 ~555
DY 547 N-terminus / Lys Orange channel labeling ~547 ~570
Lys(DY 547) Lys Side-chain DY 547 labeling ~547 ~570
DY 549 N-terminus Orange channel labeling ~549 ~570
Red channel (TAMRA, rhodamines, DY 590) FRET acceptors • imaging
TAMRARhodamine 110Rhodamine BRhodamine GreenDY 590
Dye / modification Residue / handle Typical function Ex Em
Lys(5/6-TAMRA) Lys Red fluorophore; FRET acceptor ~543 ~572
D-Lys(5/6-TAMRA) D-Lys Stereo-defined variant ~543 ~572
Lys(5-TAMRA) Lys Isomer-defined TAMRA ~543 ~572
Lys(6-TAMRA) Lys Isomer-defined TAMRA ~543 ~572
Rhodamine 110 N-terminus Enzyme substrates; imaging ~496 ~520
Rhodamine B N-terminus / Lys Imaging ~554 ~576
Lys(Rhodamine B) Lys Side-chain installed rhodamine B ~554 ~576
Rhodamine Green N-terminus / Lys Green-ish rhodamine; imaging ~503 ~527
Lys(DY 590) Lys Orange-red channel labeling ~590 ~620
Far‑red & NIR (DY 630/633/635/647/649/650/680/682/750/751/800, ATTO 655) low background • in vivo compatible channels
DY 630DY 633DY 635DY 647 DY 649DY 650DY 680/682 DY 750/751DY 800ATTO 655
Dye / modification Residue / handle Typical function Ex Em
DY 630 / Lys(DY 630) N-terminus / Lys Far‑red channel labeling ~630 ~650
DY 633 / Lys(DyLight 633) (Lys(DY633)) N-terminus / Lys Far‑red channel labeling ~633–638 ~658
DY 635 / Lys(DY 635) N-terminus / Lys Far‑red channel labeling ~635 ~658
DY 647 / Lys(DY 647) N-terminus / Lys Deep‑red channel labeling ~647 ~670
DY 647 (amino‑modified) amino-modified Deep‑red label with alternate coupling handle ~647 ~670
DY 649 N-terminus Deep‑red labeling ~649 ~673
Lys(DyLight 649) Lys Side-chain installed DY 649 ~649 ~673
DY 649P1 (amino‑modified) amino-modified Variant handle for coupling ~649 ~673
DY 650 / Lys(DY 650) N-terminus / Lys Deep‑red labeling ~650 ~673
DY 680 N-terminus NIR imaging channel ~680 ~700
DY 682 N-terminus NIR imaging channel ~682 ~705
DY 750 / DY 751 N-terminus NIR imaging channel ~750 ~775
DY 800 / Lys(DY 800) N-terminus / Lys Deep NIR channel labeling ~800 ~820
Lys(ATTO 655) Lys Super‑resolution / single‑molecule imaging ~663 ~680

Duplicates/aliases: Some catalogs list DY 750 twice; treat as the same dye family unless you provide a specific vendor derivative.

Quenchers & chromogenic reporters (non‑fluorescent) FRET quenchers • absorbance substrates
DabcylQSY21TQ2DYQ DNPEDDnppNA
Label / modification Residue / handle Function / notes
Lys(Dabcyl) Lys Dark quencher for FRET substrates (commonly paired with Abz/EDANS/FAM variants).
QSY21 N-terminus / Lys Dark quencher; broad absorption for FRET.
Tide Quencher 2 (TQ2) N-terminus Dark quencher for FRET assays.
DYQ 660 quencher dye DYQ-series quencher for deep-red channels.
Lys(DYQ 3) Lys DYQ-series quencher variant.
DyLight 504Q quencher dye DyLight-Q quencher family (project-dependent).
DyLight 543Q quencher dye DyLight-Q quencher family (project-dependent).
DyLight 554-R1 reporter dye DyLight family reporter variant (vendor-specific naming).
DyLight 683Q quencher dye NIR quencher for far-red/NIR readouts (project-dependent).
His(DNP) His DNP chromophore (absorbance / quenching); useful in mechanistic and FRET contexts.
Lys(2,4-DNP) Lys DNP chromophore variant.
Dinitrophenyl‑ethylenediamine (EDDnp) linker / handle Common quencher moiety in protease substrates.
para‑Nitroanilide (pNA) C-terminus Chromogenic enzyme substrate (absorbance readout; not fluorescent).
para‑Nitrophenyl ester activated handle Activated ester handle (chemistry intermediate; project-dependent).
Lys(Dde) Lys Orthogonal protecting group used to enable site-specific labeling (not a fluorophore).
Special / large fluorescent proteins & conjugates flow cytometry brightness
R‑Phycoerythrin
Label Type Typical use
R‑Phycoerythrin Phycobiliprotein Very bright label for flow cytometry and detection workflows (project-dependent; large conjugate behavior differs from small dyes).

Quality control & deliverables for fluorescently labeled peptides

Standard QC
  • Analytical HPLC/UPLC purity profile
  • Identity confirmation (LC-MS when feasible)
  • COA + method summary
FRET-specific checks
  • Verify donor/quencher installation
  • Residual starting material check
  • Optional fluorescence readout validation (project-dependent)
What to share for best results

Tell us your instrument settings (lasers/filters), assay format, and any constraints on termini or residues.

Attachment sites & design options

Attachment sites (site-defined)
  • N-terminus — simplest and most common; ideal when the N-terminus is not required for binding/activity.
  • C-terminus — useful when the N-terminus must remain free; supports oriented immobilization and defined presentation.
  • Lys / D-Lys — NHS-ester compatible; enables internal labeling; use site-defined designs to avoid mixed positional isomers.
  • Cys — maleimide/iodoacetyl chemistry; highly selective for single-site labeling.
  • DAP / Orn / His / Glu — residue-specific designs for advanced assays and controlled donor/quencher placement.
Linkers & spacing
  • Ahx (aminohexanoic acid) — classic spacer to reduce steric interference (e.g., Lys(Ahx‑fluorescein)).
  • Short PEG spacers — add hydrophilicity and often improve solubility for far‑red/NIR dyes.
  • Flexible vs. distance‑controlled — choose based on whether you need rotational freedom (imaging) or spacing control (FRET).
  • Amino‑modified dyes — helpful when you need custom linker orientation or post‑synthetic coupling.
Dye selection & assay fit
  • Spectral fit — match your lasers/filters; plan multiplexing to minimize bleed‑through.
  • Photostability — prioritize robust families for microscopy or long acquisitions.
  • pH sensitivity — fluorescein/FAM can vary with pH; consider alternatives for acidic conditions.
  • Background — far‑red/NIR often lowers autofluorescence in cellular samples.
  • Solubility — hydrophobic dyes may require a spacer or formulation support.
FRET / quencher designs
  • Pairing matters — select donors/acceptors with strong spectral overlap (e.g., EDANS–Dabcyl; Abz/NMA + DNP/EDDnp families).
  • Distance matters — spacing and peptide conformation strongly influence FRET efficiency.
  • Prefer dark quenchers (Dabcyl/QSY/TQ2/DYQ) for cleaner readouts with lower acceptor fluorescence.
Choose by common laser line
Laser Good starting families
405 nm Coumarin / Abz / AMCA‑type
488 nm Fluorescein (FITC/FAM), DyLight 488, Atto 488
532–561 nm DY 530/547/549, TAMRA/Rhodamine family
633–647 nm DY 630/633/635/647/649/650, ATTO 655
750–800 nm DY 750/751, DY 800
Quick tips
  • Protect labeled peptides from light; aliquot to avoid repeated freeze–thaw.
  • If you need a dye not shown, contact us—expanded inventories and custom sourcing are routinely supported.
  • For difficult solubility, request a hydrophilic spacer (PEG/Ahx) or a different dye family.

FRET substrate design (donor/quencher pairs)

Quick-start donor/quencher suggestions for quenched protease substrates and interaction probes. Pair selection depends on your instrument channels and the distance/geometry in your sequence.

Donor Quencher / acceptor Typical use Notes
EDANS Dabcyl Protease substrates (classic) Workhorse pair; strong quenching with good signal on cleavage.
Abz / NMA DNP, EDDnp Protease substrates Compact labels; useful when sterics are tight or you need minimal perturbation.
5/6‑FAM (Fluorescein) TAMRA (acceptor) or QSY21 (dark quencher) Protease / interaction probes TAMRA gives fluorescent acceptor readout; QSY21 reduces bleed-through (dark).
DyLight 488 / DY 495 DyLight 504Q (dark) Quenched substrates Bright donors; good for 488 nm channel; pick spacing to maximize quench.
TAMRA / Rhodamine family DyLight 543Q or TQ2 Protease substrates Useful when you want to avoid green channel autofluorescence.
DY 647 / DY 650 DYQ 660 (dark) Cellular assays, low background Far‑red channel often lowers background in cells/tissues.
DY 680 / DY 750 / DY 800 DyLight 683Q or DYQ series NIR probes Deep NIR for low autofluorescence; may need hydrophilic spacers for solubility.

Design tip: Put donor and quencher on opposite sides of the cleavage site, and consider a spacer (Ahx/PEG) if the dye is sterically hindered or the sequence is highly hydrophobic.

Workflow: from sequence to labeled peptide

1) Design review

Confirm dye choice, attachment site, and assay channel constraints.

  • Sequence + terminal state
  • Dye + isomer (when applicable)
  • FRET pair planning
2) Synthesis & labeling

Label is installed site-defined during synthesis or via selective chemistry.

  • N-term / Lys / Cys strategies
  • Residue-specific building blocks
  • Spacer and solubility planning
3) Purification & QC

Purification and analytics aligned to dye behavior and intended use.

  • HPLC/UPLC purification
  • LC-MS when feasible
  • COA and method notes

FAQ

Can you label peptides on a specific residue (not just the N-terminus)?

Yes. We support side-chain and residue-specific installations including Lys(dye), D-Lys(dye), DAP(dye), Ornithine dyes, and selected internal placements when designed into the sequence.

Do you support FRET substrates?

Yes. We prepare donor/quencher pairs (e.g., Abz/NMA/EDANS with Dabcyl/QSY/TQ2/DYQ/EDDnp) and can add chromogenic pNA substrates for absorbance-based enzyme assays.

How do I choose the right dye?

Choose based on your instrument channel (laser/filter), background considerations (far-red/NIR reduces autofluorescence), and whether you need a FRET pair or a single fluorophore. Tell us your channel constraints and we’ll recommend an option.

What information do you need for a quote?

Send the peptide sequence(s), desired dye(s) (and isomer/variant if applicable), attachment site (N-term/Lys/Cys/internal), quantity, purity target, and intended assay format.

More FAQ'sAll FAQ's

Troubleshooting (common issues)

Quick fixes for common fluorescent peptide probe issues. If you’re unsure, share your sequence, dye, buffer, and instrument channel(s).

Low fluorescence signal
  • Confirm excitation/emission settings match the dye and filter set.
  • Check pH sensitivity (fluorescein/FAM can drop at lower pH).
  • Minimize photobleaching: protect from light, use fresh aliquots, avoid repeated freeze–thaw.
  • Consider a spacer (Ahx/PEG) if steric quenching is likely.
Poor solubility after labeling
  • Hydrophobic dyes (often far‑red/NIR) can reduce solubility—request a hydrophilic spacer or switch dye family.
  • Reconstitute with a small % DMSO or acetonitrile, then dilute into buffer.
  • Consider a short polar tag (PEG/Arg/Lys) for challenging sequences.
High background or unexpected FRET behavior
  • Donor/quencher distance and geometry strongly influence FRET efficiency.
  • Switch to a dark quencher (Dabcyl/QSY/TQ2/DYQ) to reduce bleed‑through.
  • Use site-defined labeling to avoid mixed products that complicate interpretation.
My preferred dye isn’t listed
No problem. We support many additional fluorophores, quenchers, and custom linkers beyond this menu. Send your dye name/derivative (or your laser/filter channel) and we’ll recommend the best attachment strategy and QC plan.

Contact & quote request

For the fastest quote, send your peptide sequence(s), dye name(s) (include vendor derivative if known), attachment site constraints, quantity/purity targets, and instrument channel requirements (laser/filter). We’ll recommend a practical labeling plan plus purification/QC aligned to your application.

Fastest path
Request a Quote Review dye menu

What happens next: Our technical team reviews feasibility, confirms the best attachment site, and aligns a QC plan to your readout (imaging, binding, FRET, or chromogenic).

Fast quote checklist
  • Peptide sequence(s) + terminal state (free vs capped)
  • Dye name(s) + channel constraints (laser/filter)
  • Attachment site: N-term / Lys / Cys / internal (or “recommend”)
  • FRET pair needs (donor + quencher) if applicable
  • Quantity (mg) + purity target + intended use

If you have a legacy name (e.g., “DY 647 amino-modified” or “DY 649P1”), include it—our team will map it to a compatible coupling plan.

Talk to a chemist Request a quote

Recommended reading

References for fluorescent labeling strategies, FRET substrates, and bioconjugation concepts.

  • Bioconjugate Chemistry: Strategies and Applications
    Background on site-selective conjugation, dye coupling, and analytical considerations (review literature; journal/book-dependent).
  • FRET-based protease substrates in assay development
    Practical design considerations for donor/quencher spacing and substrate kinetics (review literature).
  • Fluorophore selection for imaging and multiplex assays
    Channel planning, autofluorescence, and photostability considerations (review literature).

Want specific papers added as live links? Share your preferred application (imaging, protease assays, flow cytometry) and I’ll insert peer-reviewed references with URLs.

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