⌘ Services
mob-logo
Contact Us 800.227.0627
Contact Quote Order Login / Register

Fluorescent Dye-Labeled Oligonucleotides

Custom fluorescent dye-labeled DNA and RNA oligos for qPCR, FISH, smFISH, smFRET, imaging, flow cytometry and multiplex assay workflows.

45+ Years of Expertise ISO 9001:2015 / ISO 13485:2016 Bench to Kilo Scale Confidential & IP-Protected U.S.A. Facilities - Texas
View Dye Catalog Request a Quote
Overview Dye Catalog Design Labeling Chemistry Applications Quality FAQ Contact
Overview

Fluorescent Oligo Labeling Built Around Signal, Spectra and Assay Fit

Bio-Synthesis supports custom fluorescent dye-labeled oligonucleotide synthesis for research, diagnostic development and advanced molecular biology workflows that require precise fluorescence detection.

Fluorescent dye selection should be matched to the instrument channel, target application, quencher compatibility, spectral overlap, probe position, linker spacing and downstream purification strategy.

Supported formats include 5′ dye-labeled oligos, 3′ dye-labeled oligos, internally labeled probes, dual-labeled hydrolysis probes, FRET probes, FISH/smFISH probes, near-infrared oligo probes and custom fluorescent oligo panels.

Visible Spectrum Guide for Fluorescent Oligo Design

405 nm
488 nm
520 nm
560 nm
610 nm
650 nm
750+ nm
Blue / Violet
405 nm: Alexa 405, DyLight 405, CF405
Green
488–520 nm: FAM, Alexa 488, ATTO 488, CF488A
Yellow–Orange
530–590 nm: HEX, JOE, TAMRA, Cy3, ATTO 550
Red / Far-Red / NIR
610–800+ nm: ROX, Cy5, Cy7, Alexa 647, CF680
Dye Catalog

Fluorescent Dye Catalog

Expanded catalog of 197 fluorescent dyes for common and specialty oligo labeling, with family, color, wavelength-range and global dye-name search. Spectral values are practical reference points; final dye choice and availability should be matched to your instrument, assay and labeling chemistry.

Quick navigation
Abberior Dyes Alexa Dyes ATTO Dyes BODIPY Dyes CF Dyes Chromeo & Coumarin Dyes Cyanine Dyes DyLight Dyes CAL Fluor Dyes Quasar & Pulsar Dyes Common qPCR & Fragment-Analysis Reporter Dyes IRDye / Near-IR Dyes Dyomic Dyes Epoch & Eterneon Dyes Fluorescein, Janelia & LightCycler Dyes Molecular Probe & Other Dyes

Search Dye by Color

Use the color band to quickly view fluorescent dye options by emission color before opening the full catalog family tables below.

Blue dye options

Abberior STAR 440SX 440/460 nm Alexa Fluor 350 346/442 nm Alexa Fluor 405 401/421 nm CF350 347/448 nm CF405S 404/431 nm CF405M 408/452 nm 7-Hydroxycoumarin 325/450 nm Coumarin 102 375/450 nm AMC 350/440 nm DyLight 350 353/432 nm DyLight 405 400/420 nm DY-405 405/421 nm Epoch Blue 405/450 nm Bimane 370/482 nm Pyrene dye 345/375 nm Pacific Blue 410/455 nm Cascade Blue 400/420 nm Marina Blue 362/459 nm

Cyan dye options

ATTO 390 390/479 nm ATTO 425 425/484 nm Chromeo 488 488/517 nm Coumarin 6 375/495 nm DY-350XL UV-MegStokes 350/460 nm DY-430 430/470 nm

Green dye options

Abberior Cage 500 500/514 nm Abberior STAR 488 488/510 nm Alexa Fluor 430 433/541 nm Alexa Fluor 488 495/519 nm ATTO 465 465/503 nm ATTO 488 488/520 nm ATTO 514 514/532 nm BODIPY 493/503 493/503 nm BODIPY FL 503/512 nm BODIPY FL-X 504/510 nm CF488A 490/515 nm CF503R 503/532 nm Chromeo 505 505/526 nm Coumarin 153 420/530 nm DyLight 488 493/518 nm DY-490 490/515 nm Epoch Green 488/520 nm Eterneon Green 488/510 nm 6-FAM 495/520 nm 6-FAM dT 495/520 nm 6-FAM NHS Ester 495/520 nm 6-FITC 495/519 nm JOE 520/548 nm Janelia Fluor 525 525/545 nm Oregon Green 488 496/524 nm Acridine Orange 500/526 nm Dansyl 340/520 nm Thiazole Orange 510/530 nm NBD 465/535 nm Oregon Green 514 511/530 nm Rhodamine Green 502/527 nm NBD-X 465/535 nm Oregon Green 488-X 494/517 nm Rhodol Green 496/523 nm Rhodamine Green-X 503/528 nm

Yellow-Green dye options

Abberior Cage 532 532/547 nm Alexa Fluor 514 518/540 nm ATTO 532 532/553 nm ATTO 542 542/564 nm ATTO 550 550/575 nm BODIPY 530/550 530/550 nm BODIPY 564/570 C3 564/570 nm BODIPY TMR 542/574 nm BODIPY R6G-X 529/547 nm CF405L 395/545 nm CAL Fluor Gold 540 522/544 nm CAL Fluor Orange 560 538/559 nm VIC 538/554 nm DY-530 530/555 nm DY-547 547/572 nm DY-550 550/570 nm HEX 535/556 nm TET 521/536 nm DyLight 485-LS 485/559 nm Yakima Yellow 530/549 nm BODIPY R6G 528/547 nm Pacific Orange 400/551 nm Cascade Yellow 405/550 nm Lucifer Yellow 428/536 nm

Yellow dye options

Abberior Cage 552 552/567 nm Alexa Fluor 532 530/554 nm BODIPY 558/569 559/568 nm CF532 527/558 nm Cy3 550/570 nm Cy3B 559/570 nm Quasar 570 548/566 nm NED 546/575 nm Epoch Yellow 530/550 nm BODIPY TMR-X 544/570 nm TYE 563 549/563 nm

Orange dye options

Abberior FLIP 565 565/580 nm Abberior STAR 580 580/600 nm Alexa Fluor 546 556/573 nm Alexa Fluor 555 555/565 nm ATTO 565 565/590 nm BODIPY 576/589 576/589 nm BODIPY 581/591 581/591 nm CF543 541/560 nm Chromeo 546 545/561 nm Cy3.5 581/596 nm DyLight 550 562/576 nm CAL Fluor Red 590 569/591 nm PET 558/595 nm TAMRA 560/583 nm DY-555 555/580 nm Epoch Orange 540/570 nm Janelia Fluor 549 549/571 nm B-Phycoerythrin B-PE 496/578 nm DyLight 510-LS 509/590 nm Rhodamine Red-X 570/590 nm

Orange-Red dye options

Alexa Fluor 568 578/603 nm ATTO Rho101 592/609 nm CF555 555/565 nm DyLight 594 593/618 nm CAL Fluor Red 610 590/610 nm ROX 587/607 nm Texas Red 595/615 nm TEX 615 596/613 nm Texas Red-X 583/603 nm

Red dye options

Alexa Fluor 594 590/617 nm Alexa Fluor 635 633/648 nm ATTO 590 590/617 nm ATTO 594 594/627 nm ATTO 620 620/642 nm BODIPY TR 589/617 nm CF568 562/584 nm CF594 593/614 nm Chromeo 494 ~494/~628 nm CAL Fluor Red 635 618/637 nm Pulsar 650 ~460/650 nm Epoch Red 590/615 nm Eterneon Red 590/615 nm LightCycler Red 610 610/630 nm Amplex Red 563/587 nm BODIPY TR-X 588/616 nm BODIPY 630/650-X 625/640 nm

Far-Red dye options

Abberior STAR 635 635/657 nm Abberior STAR 635P 635/660 nm Alexa Fluor 633 632/647 nm Alexa Fluor 647 650/665 nm Alexa Fluor 660 663/691 nm ATTO 610 610/635 nm ATTO 633 633/657 nm ATTO 647N 646/664 nm ATTO 643 643/665 nm ATTO 655 663/684 nm BODIPY 630/650 630/650 nm BODIPY 650/665 650/665 nm BODIPY 650/665-X 651/660 nm CF633 630/650 nm CF640R 642/662 nm CF647 647/665 nm Chromeo 642 642/660 nm Cy5 649/670 nm Cy5.5 675/694 nm DyLight 633 638/658 nm DyLight 650 652/672 nm Quasar 670 647/670 nm LIZ 638/655 nm IRDye 680LT 676/693 nm IRDye 680RD 672/694 nm Epoch Far Red 635/660 nm Janelia Fluor 635 635/656 nm Janelia Fluor 646 646/664 nm LightCycler Red 640 625/645 nm Allophycocyanin (APC) 650/660 nm DyLight 515-LS 519/648 nm DyLight 521-LS 526/666 nm Nile Red 552/636 nm TYE 665 645/665 nm

NIR dye options

Alexa Fluor 700 702/723 nm Alexa Fluor 750 749/775 nm Alexa Fluor 680 681/704 nm Alexa Fluor 790 782/805 nm ATTO 680 680/700 nm CF680 681/701 nm CF770 770/797 nm CF790 783/806 nm CF850 850/870 nm Cy7 743/767 nm DyLight 680 692/712 nm DyLight 755 754/776 nm DyLight 800 777/794 nm Quasar 705 690/705 nm IRDye 800CW 774/789 nm IRDye 700 684/702 nm Epoch Infrared 750/770 nm Eterneon IR 800 775/800 nm LightCycler Red 705 690/705 nm ATTO 700 700/719 nm TYE 705 686/704 nm Dy 750 747/776 nm

IR/NIR dye options

ATTO 740 740/775 nm

Search Dye by Spectrum Range

Choose a wavelength band to find dyes by emission range. This is useful when selecting fluorophores for lasers, filters, qPCR channels, microscopy or multiplex panels.

UV / Blue dye options (350–450 nm)

Alexa Fluor 350 Ex 346 / Em 442 Alexa Fluor 405 Ex 401 / Em 421 CF350 Ex 347 / Em 448 CF405S Ex 404 / Em 431 7-Hydroxycoumarin Ex 325/450 / Em 450 Coumarin 102 Ex 375/450 / Em 450 AMC Ex 350 / Em 440 DyLight 350 Ex 353 / Em 432 DyLight 405 Ex 400 / Em 420 DY-405 Ex 405 / Em 421 Epoch Blue Ex 405 / Em 450 Pyrene dye Ex 345 / Em 375 Cascade Blue Ex 400 / Em 420

Blue-Green dye options (451–520 nm)

Abberior Cage 500 Ex 500 / Em 514 Abberior STAR 440SX Ex 440 / Em 460 Abberior STAR 488 Ex 488 / Em 510 Alexa Fluor 488 Ex 495 / Em 519 ATTO 390 Ex 390 / Em 479 ATTO 425 Ex 425 / Em 484 ATTO 465 Ex 465 / Em 503 ATTO 488 Ex 488 / Em 520 BODIPY 493/503 Ex 493 / Em 503 BODIPY FL Ex 503 / Em 512 BODIPY FL-X Ex 504 / Em 510 CF405M Ex 408 / Em 452 CF488A Ex 490 / Em 515 Chromeo 488 Ex 488 / Em 517 Coumarin 6 Ex 375/495 / Em 495 DyLight 488 Ex 493 / Em 518 DY-350XL UV-MegStokes Ex 350 / Em 460 DY-430 Ex 430 / Em 470 DY-490 Ex 490 / Em 515 Epoch Green Ex 488 / Em 520 Eterneon Green Ex 488 / Em 510 6-FAM Ex 495 / Em 520 6-FAM dT Ex 495 / Em 520 6-FAM NHS Ester Ex 495 / Em 520 6-FITC Ex 495 / Em 519 Bimane Ex 370 / Em 482 Dansyl Ex 340 / Em 520 Pacific Blue Ex 410 / Em 455 Marina Blue Ex 362 / Em 459 Oregon Green 488-X Ex 494 / Em 517

Green-Yellow dye options (521–560 nm)

Abberior Cage 532 Ex 532 / Em 547 Alexa Fluor 430 Ex 433 / Em 541 Alexa Fluor 514 Ex 518 / Em 540 Alexa Fluor 532 Ex 530 / Em 554 ATTO 514 Ex 514 / Em 532 ATTO 532 Ex 532 / Em 553 BODIPY 530/550 Ex 530 / Em 550 BODIPY R6G-X Ex 529 / Em 547 CF405L Ex 395 / Em 545 CF503R Ex 503 / Em 532 CF532 Ex 527 / Em 558 CF543 Ex 541 / Em 560 Chromeo 505 Ex 505 / Em 526 Coumarin 153 Ex 420/530 / Em 530 CAL Fluor Gold 540 Ex 522 / Em 544 CAL Fluor Orange 560 Ex 538 / Em 559 VIC Ex 538 / Em 554 DY-530 Ex 530 / Em 555 Epoch Yellow Ex 530 / Em 550 HEX Ex 535 / Em 556 JOE Ex 520 / Em 548 TET Ex 521 / Em 536 Janelia Fluor 525 Ex 525 / Em 545 Oregon Green 488 Ex 496 / Em 524 Acridine Orange Ex 500 / Em 526 Thiazole Orange Ex 510 / Em 530 NBD Ex 465 / Em 535 DyLight 485-LS Ex 485 / Em 559 Yakima Yellow Ex 530 / Em 549 Oregon Green 514 Ex 511 / Em 530 Rhodamine Green Ex 502 / Em 527 BODIPY R6G Ex 528 / Em 547 Pacific Orange Ex 400 / Em 551 Cascade Yellow Ex 405 / Em 550 Lucifer Yellow Ex 428 / Em 536 NBD-X Ex 465 / Em 535 Rhodol Green Ex 496 / Em 523 Rhodamine Green-X Ex 503 / Em 528

Yellow-Orange dye options (561–600 nm)

Abberior Cage 552 Ex 552 / Em 567 Abberior FLIP 565 Ex 565 / Em 580 Abberior STAR 580 Ex 580 / Em 600 Alexa Fluor 546 Ex 556 / Em 573 Alexa Fluor 555 Ex 555 / Em 565 ATTO 542 Ex 542 / Em 564 ATTO 550 Ex 550 / Em 575 ATTO 565 Ex 565 / Em 590 BODIPY 564/570 C3 Ex 564 / Em 570 BODIPY 576/589 Ex 576 / Em 589 BODIPY 581/591 Ex 581 / Em 591 BODIPY TMR Ex 542 / Em 574 BODIPY 558/569 Ex 559 / Em 568 CF555 Ex 555 / Em 565 CF568 Ex 562 / Em 584 Chromeo 546 Ex 545 / Em 561 Cy3 Ex 550 / Em 570 Cy3B Ex 559 / Em 570 Cy3.5 Ex 581 / Em 596 DyLight 550 Ex 562 / Em 576 CAL Fluor Red 590 Ex 569 / Em 591 Quasar 570 Ex 548 / Em 566 NED Ex 546 / Em 575 PET Ex 558 / Em 595 TAMRA Ex 560 / Em 583 DY-547 Ex 547 / Em 572 DY-550 Ex 550 / Em 570 DY-555 Ex 555 / Em 580 Epoch Orange Ex 540 / Em 570 Janelia Fluor 549 Ex 549 / Em 571 B-Phycoerythrin B-PE Ex 496 / Em 578 Amplex Red Ex 563 / Em 587 DyLight 510-LS Ex 509 / Em 590 Rhodamine Red-X Ex 570 / Em 590 BODIPY TMR-X Ex 544 / Em 570 TYE 563 Ex 549 / Em 563

Red dye options (601–650 nm)

Alexa Fluor 568 Ex 578 / Em 603 Alexa Fluor 594 Ex 590 / Em 617 Alexa Fluor 633 Ex 632 / Em 647 Alexa Fluor 635 Ex 633 / Em 648 ATTO 590 Ex 590 / Em 617 ATTO 594 Ex 594 / Em 627 ATTO 610 Ex 610 / Em 635 ATTO Rho101 Ex 592 / Em 609 ATTO 620 Ex 620 / Em 642 BODIPY 630/650 Ex 630 / Em 650 BODIPY TR Ex 589 / Em 617 CF594 Ex 593 / Em 614 CF633 Ex 630 / Em 650 Chromeo 494 Ex ~494 / Em ~628 DyLight 594 Ex 593 / Em 618 CAL Fluor Red 610 Ex 590 / Em 610 CAL Fluor Red 635 Ex 618 / Em 637 Pulsar 650 Ex ~460 / Em 650 ROX Ex 587 / Em 607 Texas Red Ex 595 / Em 615 Epoch Red Ex 590 / Em 615 Eterneon Red Ex 590 / Em 615 LightCycler Red 610 Ex 610 / Em 630 LightCycler Red 640 Ex 625 / Em 645 DyLight 515-LS Ex 519 / Em 648 BODIPY TR-X Ex 588 / Em 616 BODIPY 630/650-X Ex 625 / Em 640 Nile Red Ex 552 / Em 636 TEX 615 Ex 596 / Em 613 Texas Red-X Ex 583 / Em 603

Far-Red dye options (651–700 nm)

Abberior STAR 635 Ex 635 / Em 657 Abberior STAR 635P Ex 635 / Em 660 Alexa Fluor 647 Ex 650 / Em 665 Alexa Fluor 660 Ex 663 / Em 691 ATTO 633 Ex 633 / Em 657 ATTO 647N Ex 646 / Em 664 ATTO 680 Ex 680 / Em 700 ATTO 643 Ex 643 / Em 665 ATTO 655 Ex 663 / Em 684 BODIPY 650/665 Ex 650 / Em 665 BODIPY 650/665-X Ex 651 / Em 660 CF640R Ex 642 / Em 662 CF647 Ex 647 / Em 665 Chromeo 642 Ex 642 / Em 660 Cy5 Ex 649 / Em 670 Cy5.5 Ex 675 / Em 694 DyLight 633 Ex 638 / Em 658 DyLight 650 Ex 652 / Em 672 Quasar 670 Ex 647 / Em 670 LIZ Ex 638 / Em 655 IRDye 680LT Ex 676 / Em 693 IRDye 680RD Ex 672 / Em 694 Epoch Far Red Ex 635 / Em 660 Janelia Fluor 635 Ex 635 / Em 656 Janelia Fluor 646 Ex 646 / Em 664 Allophycocyanin (APC) Ex 650 / Em 660 DyLight 521-LS Ex 526 / Em 666 TYE 665 Ex 645 / Em 665

Near-IR dye options (701+ nm)

Alexa Fluor 700 Ex 702 / Em 723 Alexa Fluor 750 Ex 749 / Em 775 Alexa Fluor 680 Ex 681 / Em 704 Alexa Fluor 790 Ex 782 / Em 805 ATTO 740 Ex 740 / Em 775 CF680 Ex 681 / Em 701 CF770 Ex 770 / Em 797 CF790 Ex 783 / Em 806 CF850 Ex 850 / Em 870 Cy7 Ex 743 / Em 767 DyLight 680 Ex 692 / Em 712 DyLight 755 Ex 754 / Em 776 DyLight 800 Ex 777 / Em 794 Quasar 705 Ex 690 / Em 705 IRDye 800CW Ex 774 / Em 789 IRDye 700 Ex 684 / Em 702 Epoch Infrared Ex 750 / Em 770 Eterneon IR 800 Ex 775 / Em 800 LightCycler Red 705 Ex 690 / Em 705 ATTO 700 Ex 700 / Em 719 TYE 705 Ex 686 / Em 704 Dy 750 Ex 747 / Em 776

Availability note: Dye names and spectral values are practical reference points. Proprietary or specialty fluorophores may require custom sourcing, licensing, minimum scale, or project-specific confirmation. Contact Bio-Synthesis to confirm current availability, attachment format, labeling position and purification options.

Search the Complete Dye Catalog

Type a dye name (for example, DyLight, DyLight 510, ATTO 655 or Texas Red). Matching collapsible family tables open automatically.

Search across all dye-family tables. All collapsible family sections remain visible.
Product Excitation (nm) Emission (nm) Color Highlights
Abberior Cage 500 500 514 Green Caged dye activated by 405 nm light; used in super-resolution microscopy
Abberior Cage 532 532 547 Yellow-Green Photocaged dye activated under green laser; useful for optical control
Abberior Cage 552 552 567 Yellow Visible-light activated caged dye
Abberior FLIP 565 565 580 Orange Fluorogenic dye activated by chemical environment
Abberior STAR 440SX 440 460 Blue Photostable blue dye for STED and multicolor imaging
Abberior STAR 488 488 510 Green Photostable Alexa Fluor 488 analog for confocal/STED
Abberior STAR 580 580 600 Orange Long-lasting orange dye for multicolor STED microscopy
Abberior STAR 635 635 657 Far-Red Cy5-like dye for STED with high photostability
Abberior STAR 635P 635 660 Far-Red Polar STAR 635 variant for live-cell STED
Product Excitation (nm) Emission (nm) Color Highlights
Alexa Fluor 350 346 442 Blue UV-excitable blue dye; useful for nucleic acid staining
Alexa Fluor 405 401 421 Blue Bright violet-blue dye with minimal overlap with green fluorophores
Alexa Fluor 430 433 541 Green Alternative to AMCA for multicolor detection
Alexa Fluor 488 495 519 Green Standard FITC replacement for flow cytometry and imaging
Alexa Fluor 514 518 540 Yellow-Green Used in qPCR and confocal microscopy
Alexa Fluor 532 530 554 Yellow Bright yellow fluorophore; useful for FRET
Alexa Fluor 546 556 573 Orange TRITC alternative with good spectral separation
Alexa Fluor 555 555 565 Orange High quantum yield dye often paired with Alexa 647
Alexa Fluor 568 578 603 Orange-Red Photostable orange-red dye
Alexa Fluor 594 590 617 Red Common red dye for immunofluorescence
Alexa Fluor 633 632 647 Far-Red Cy5 analog for far-red applications
Alexa Fluor 647 650 665 Far-Red Widely used Cy5 replacement
Alexa Fluor 700 702 723 NIR Near-IR dye with low autofluorescence background
Alexa Fluor 750 749 775 NIR NIR dye optimized for in vivo imaging
Product Excitation (nm) Emission (nm) Color Highlights
ATTO 390 390 479 Cyan UV-excitable dye with low autofluorescence background
ATTO 425 425 484 Cyan Blue-violet dye for DNA labeling and microscopy
ATTO 465 465 503 Green Green dye for flow cytometry and cellular imaging
ATTO 488 488 520 Green Alexa 488 alternative for FACS and imaging
ATTO 514 514 532 Green Bright green dye for confocal microscopy
ATTO 532 532 553 Yellow-Green Alternative to Alexa 532
ATTO 542 542 564 Yellow-Green Photostable green-yellow dye
ATTO 550 550 575 Yellow-Green Useful with yellow laser lines
ATTO 565 565 590 Orange Bright orange dye with low background
ATTO 590 590 617 Red Red-orange dye for long-term imaging
ATTO 594 594 627 Red Photostable red dye for super-resolution
ATTO 610 610 635 Far-Red Deep red dye with minimal green-channel overlap
ATTO 633 633 657 Far-Red Cy5 alternative
ATTO 647N 646 664 Far-Red Photostable ATTO 647 variant
ATTO 680 680 700 Near-IR NIR dye for deep-tissue imaging
ATTO 740 740 775 IR/NIR Extended NIR dye for long-term tracking
Product Excitation (nm) Emission (nm) Color Highlights
BODIPY 493/503 493 503 Green Bright green dye for lipid labeling and live-cell imaging
BODIPY 530/550 530 550 Yellow-Green Compatible with FITC filters
BODIPY 564/570 C3 564 570 Yellow-Green Cell-permeant dye for nucleic acid and protein labeling
BODIPY 576/589 576 589 Orange Useful in FRET applications
BODIPY 581/591 581 591 Orange Lipid peroxidation sensor with ratiometric redox detection
BODIPY 630/650 630 650 Far-Red Near-IR imaging with low background
BODIPY 650/665 650 665 Far-Red Suitable for deep tissue imaging and Cy5 filters
BODIPY FL 503 512 Green FITC alternative with high photostability
BODIPY TMR 542 574 Yellow-Green Tetramethylrhodamine-like dye
BODIPY TR 589 617 Red Texas Red alternative
Product Excitation (nm) Emission (nm) Color Highlights
CF350 347 448 Blue UV-excitable blue dye
CF405S 404 431 Blue Bright 405 nm dye for SIM and violet lasers
CF405M 408 452 Blue Pacific Blue alternative
CF405L 395 545 Yellow-Green 405 nm excitable dye with orange emission
CF488A 490 515 Green Bright photostable Alexa 488 alternative
CF503R 503 532 Green Spectrally unique dye for spectral flow
CF532 527 558 Yellow Water-soluble Alexa 532 alternative
CF543 541 560 Orange Optimized for 543 nm lasers
CF555 555 565 Orange-Red Brighter than Cy3 and validated in STORM
CF568 562 584 Red Photostable Alexa 568 alternative
CF594 593 614 Red Highly photostable red dye
CF633 630 650 Far-Red Similar to Alexa 647
CF640R 642 662 Far-Red Far-red dye for imaging
CF647 647 665 Far-Red Widely used far-red dye
CF680 681 701 NIR NIR dye for in vivo imaging
CF770 770 797 NIR NIR dye with minimal tissue autofluorescence
CF790 783 806 NIR Optimized for in vivo NIR imaging
CF850 850 870 NIR Deep NIR dye
Product Excitation (nm) Emission (nm) Color Highlights
Chromeo 505 505 526 Green FITC/Alexa 488 replacement; photostable and pH-insensitive
Chromeo 546 545 561 Orange Bright orange dye for microscopy
Chromeo 642 642 660 Dark Red Cy5/Alexa 647 replacement
Chromeo 488 488 517 Cyan-Green Alternative to Alexa 488/FITC
Chromeo 494 ~494 ~628 Red Large Stokes shift dye for multiplex assays
7-Hydroxycoumarin 325/450 450 Blue Good quantum yield laser dye
Coumarin 102 375/450 450 Blue Bright green-shifted emission
Coumarin 6 375/495 495 Cyan-Green Solvatochromic dye for polarity sensors
Coumarin 153 420/530 530 Green Used for oligo or protein labeling
AMC 350 440 Blue Protease and peptidase substrate
Product Excitation (nm) Emission (nm) Color Highlights
Cy3 550 570 Yellow Widely used orange dye for oligo and antibody labeling
Cy3B 559 570 Yellow Brighter and more photostable Cy3 analog
Cy3.5 581 596 Orange Intermediate between Cy3 and Cy5
Cy5 649 670 Far-Red Standard far-red dye for DNA probes
Cy5.5 675 694 Far-Red Longer-wavelength Cy5 variant
Cy7 743 767 NIR Near-IR dye for deep tissue and in vivo imaging
Product Excitation (nm) Emission (nm) Color Highlights
DyLight 350 353 432 Blue UV-excitable blue dye; Alexa Fluor 350/AMCA-range alternative
DyLight 405 400 420 Blue Violet-excitable blue dye for multiplex fluorescence workflows
DyLight 488 493 518 Green Green fluorophore comparable to Alexa Fluor 488/FITC
DyLight 550 562 576 Orange Orange fluorophore in the Cy3/TRITC range
DyLight 594 593 618 Orange-Red Red fluorophore in the Texas Red/Alexa Fluor 594 range
DyLight 633 638 658 Far-Red Far-red fluorophore near the 633 nm excitation line
DyLight 650 652 672 Far-Red High-sensitivity far-red dye in the Cy5/Alexa Fluor 647 range
DyLight 680 692 712 NIR Near-IR dye for 700-channel fluorescence detection
DyLight 755 754 776 NIR Near-IR dye in the Alexa Fluor 750 range
DyLight 800 777 794 NIR Deep near-IR dye for 800-channel detection
Product Excitation (nm) Emission (nm) Color Highlights
CAL Fluor Gold 540 522 544 Yellow-Green qPCR reporter; VIC/TET/JOE-range dye; commonly paired with BHQ-1
CAL Fluor Orange 560 538 559 Yellow-Green qPCR reporter; VIC/HEX/JOE-range dye; commonly paired with BHQ-1
CAL Fluor Red 590 569 591 Orange TAMRA-range qPCR reporter; commonly paired with BHQ-2
CAL Fluor Red 610 590 610 Orange-Red Texas Red/ROX-range qPCR reporter; commonly paired with BHQ-2
CAL Fluor Red 635 618 637 Red LC Red 640-range reporter for red/far-red qPCR channels
Product Excitation (nm) Emission (nm) Color Highlights
Quasar 570 548 566 Yellow Cy3-range reporter for qPCR and molecular probe applications
Quasar 670 647 670 Far-Red Cy5-range far-red reporter; commonly paired with BHQ-2 or BHQ-3
Quasar 705 690 705 NIR Cy5.5-range long-wavelength reporter for multiplex detection
Pulsar 650 ~460 650 Red Large-Stokes-shift long-wavelength reporter used in probe-based assays; confirm project-specific availability
Product Excitation (nm) Emission (nm) Color Highlights
VIC 538 554 Yellow-Green Common real-time PCR reporter for green/yellow multiplex channels
NED 546 575 Yellow Orange-channel reporter used in multiplex PCR and fragment analysis
PET 558 595 Orange Orange-red reporter used in fragment analysis and multiplex detection
TAMRA 560 583 Orange Rhodamine reporter historically used in qPCR and probe labeling
ROX 587 607 Orange-Red Red reporter/reference dye used in qPCR and oligonucleotide probes
Texas Red 595 615 Orange-Red Red fluorophore for imaging and probe labeling
LIZ 638 655 Far-Red Far-red sizing-standard/fragment-analysis dye; specialized instrument use
Product Excitation (nm) Emission (nm) Color Highlights
IRDye 680LT 676 693 Far-Red 700-channel near-IR dye; high-intensity option for supported conjugation workflows
IRDye 680RD 672 694 Far-Red 700-channel near-IR dye used in imaging and molecular detection workflows
IRDye 800CW 774 789 NIR 800-channel near-IR dye available in amine/click-compatible reactive formats
IRDye 700 684 702 NIR 700-channel near-IR fluorophore for labeled oligonucleotide detection
Product Excitation (nm) Emission (nm) Color Highlights
DY-350XL UV-MegStokes 350 460 Cyan UV MegaStokes dye with large Stokes shift
DY-405 405 421 Blue Violet-excitable dye for microscopy and flow
DY-430 430 470 Cyan Blue fluorescent Alexa 430 alternative
DY-490 490 515 Green FITC/Alexa 488 alternative
DY-530 530 555 Yellow-Green Excitable at 532 nm; useful for FRET
DY-547 547 572 Yellow-Green Orange-red dye for multicolor flow
DY-550 550 570 Yellow-Green Bright orange-channel dye
DY-555 555 580 Orange Photostable orange-red fluorophore
Product Excitation (nm) Emission (nm) Color Highlights
Epoch Blue 405 450 Blue Bright blue dye for flow cytometry
Epoch Green 488 520 Green FITC replacement for qPCR and immunofluorescence
Epoch Yellow 530 550 Yellow Yellow dye for multiplex detection
Epoch Orange 540 570 Orange TRITC-channel dye
Epoch Red 590 615 Red Alexa 594 alternative
Epoch Far Red 635 660 Far-Red Cy5 replacement
Epoch Infrared 750 770 NIR Low-background in vivo imaging dye
Eterneon Green 488 510 Green Photostable FITC alternative
Eterneon Red 590 615 Red Red dye for antibody and nucleic acid labeling
Eterneon IR 800 775 800 NIR NIR dye for animal imaging and diagnostics
Product Excitation (nm) Emission (nm) Color Highlights
6-FAM 495 520 Green Standard green dye for qPCR, oligo labeling and sequencing
6-FAM dT 495 520 Green FAM linked to deoxythymidine for modified oligos
6-FAM NHS Ester 495 520 Green Amine-reactive FAM
6-FITC 495 519 Green Isothiocyanate fluorescein for conjugation
HEX 535 556 Yellow-Green Multiplex qPCR and capillary electrophoresis
JOE 520 548 Green qPCR and Sanger sequencing
TET 521 536 Yellow-Green DNA sequencing, qPCR and primer labeling
Janelia Fluor 525 525 545 Green Bright dye for live-cell imaging
Janelia Fluor 549 549 571 Orange Photostable dye for STED/super-resolution
Janelia Fluor 635 635 656 Far-Red Cy5 replacement
Janelia Fluor 646 646 664 Far-Red Red-shifted dye for confocal microscopy
LightCycler Red 610 610 630 Red qPCR detection with minimal green overlap
LightCycler Red 640 625 645 Far-Red Multiplex qPCR and hybridization probes
LightCycler Red 705 690 705 NIR Long-wavelength real-time PCR detection
Product Excitation (nm) Emission (nm) Color Highlights
Oregon Green 488 496 524 Green Photostable fluorescein analog
Acridine Orange 500 526 Green DNA/RNA intercalating dye
Bimane 370 482 Blue Small label for thiol-specific labeling
Dansyl 340 520 Green Polarity-sensitive dye
Thiazole Orange 510 530 Green Intercalating nucleic acid dye
Allophycocyanin (APC) 650 660 Far-Red Flow cytometry phycobiliprotein
B-Phycoerythrin B-PE 496 578 Orange Bright phycobiliprotein for FACS
Amplex Red 563 587 Red HRP/H2O2 detection substrate
NBD 465 535 Green Lipid and protein labeling dye
Pyrene dye 345 375 Blue Fluorescent probe for environment sensing
DyLight 485-LS 485 559 Yellow-Green Large-Stokes-shift DyLight specialty fluorophore
DyLight 510-LS 509 590 Orange Large-Stokes-shift DyLight specialty fluorophore
DyLight 515-LS 519 648 Far-Red Large-Stokes-shift DyLight specialty fluorophore
DyLight 521-LS 526 666 Far-Red Large-Stokes-shift DyLight specialty fluorophore
Yakima Yellow 530 549 Yellow-Green Yellow reporter dye used in fluorescent probe and qPCR workflows
ATTO 700 700 719 NIR Near-IR ATTO fluorophore for long-wavelength detection
Oregon Green 514 511 530 Green Photostable Oregon Green-family fluorophore
Rhodamine Green 502 527 Green Bright green rhodamine-family fluorophore
Rhodamine Red-X 570 590 Orange Orange-red rhodamine label with spacer chemistry
BODIPY R6G 528 547 Yellow-Green Bright BODIPY fluorophore in the yellow-green region
BODIPY TMR-X 544 570 Yellow Tetramethylrhodamine-like BODIPY derivative with spacer
BODIPY TR-X 588 616 Red Red BODIPY derivative with spacer chemistry
BODIPY 630/650-X 625 640 Red Far-red BODIPY-X fluorophore for oligonucleotide and biomolecule labeling
Pacific Blue 410 455 Blue Violet-excited blue fluorophore
Pacific Orange 400 551 Yellow-Green Violet-excited large-Stokes-shift fluorophore
Cascade Blue 400 420 Blue Blue fluorophore with good water solubility
Cascade Yellow 405 550 Yellow-Green Violet-excited large-Stokes-shift yellow fluorophore
Lucifer Yellow 428 536 Yellow-Green Water-soluble fluorescent label with large Stokes shift
Nile Red 552 636 Far-Red Environment-sensitive red fluorescent probe
NBD-X 465 535 Green Reactive NBD-family fluorescent label with spacer chemistry
TYE 563 549 563 Yellow Cy3-range fluorescent oligo label
TYE 665 645 665 Far-Red Cy5-range fluorescent oligo label
TYE 705 686 704 NIR Cy5.5-range long-wavelength fluorescent oligo label
TEX 615 596 613 Orange-Red Texas Red-range reporter for fluorescent oligo and probe applications
Dy 750 747 776 NIR Near-IR dye for long-wavelength oligonucleotide labeling
Marina Blue 362 459 Blue Blue fluorescent label available for custom oligonucleotide modification
Oregon Green 488-X 494 517 Green Spacer-equipped Oregon Green derivative for oligonucleotide labeling
Rhodol Green 496 523 Green Green rhodol-family fluorescent oligonucleotide label
Rhodamine Green-X 503 528 Green Spacer-equipped Rhodamine Green derivative for oligonucleotide labeling
Texas Red-X 583 603 Orange-Red Spacer-equipped Texas Red derivative for fluorescent oligonucleotide labeling
Probe Design Strategy

Design Considerations for Fluorescent-Labeled Oligos

Start with the experimental constraint that matters most. The guide below keeps the full design logic visible without turning every consideration into another card.

Instrument fit

Match the reporter to the instrument before optimizing anything else

Choose excitation and emission windows that align with the available laser, lamp, filter set, or qPCR detection channel. In multiplex panels, spectral separation and detector bleed-through should be evaluated together.

Laser / filter fit Emission spacing Multiplex planning

Design checkpoints

01
Excitation

Confirm the instrument can efficiently excite the selected dye.

02
Emission

Match the detector window and avoid unnecessary channel overlap.

03
Panel fit

Consider all reporters and quenchers together for multiplex work.

Labeling Chemistry Options

Choose the Labeling Route Around the Oligo Architecture

Rather than presenting six equal cards, this section separates direct synthesis-integrated approaches from post-synthetic conjugation routes and then shows the specialty formats that bridge both.

Synthesis-integrated

Build the fluorescent architecture during oligo synthesis

Best when dye phosphoramidites or controlled internal reporter placement can be incorporated directly with predictable spacing and positional control.

01

Select 5′, 3′, or internal dye position

02

Choose dye phosphoramidite or protected labeling handle

03

Complete synthesis, cleavage, purification, and QC

Post-synthetic

Attach the dye through an orthogonal reactive handle

Useful for specialty, sensitive, bulky, or custom fluorophores where reaction conditions and free-dye removal benefit from a dedicated conjugation step.

01

Prepare amino, thiol, azide, alkyne, or carbonyl handle

02

Use NHS, maleimide, click, aminooxy, or hydrazide chemistry

03

Purify labeled product away from unreacted dye and side products

Specialty formats supported:

NHS-ester amine coupling Maleimide–thiol coupling CuAAC / SPAAC click TCO–tetrazine Oxime / hydrazone Dual-dye & FRET
Applications & Downstream Workflows

Explore Fluorescent Oligos by Experimental Goal

Select the workflow that best matches the experiment. This keeps the section visually active while avoiding another six-card grid.

Amplification & detection

qPCR & dPCR Probes

Hydrolysis probes, molecular beacons, and other dual-labeled probe formats require coordinated reporter selection, quencher pairing, probe architecture, and instrument-channel compatibility.

Design focus

Reporter / quencher spectral fit

Typical labels

FAM, HEX, ROX, Cy5-class reporters

QC emphasis

Purity, mass, and probe-specific performance

Explore related service →
Quality & Deliverables

Purification, Analytical Confirmation and Delivery

One integrated release view replaces another row of cards and gives this section a stronger visual finish.

QC

Application-aligned fluorescent oligo release

Purification, analytical confirmation, formulation, and documentation are selected together based on dye chemistry, oligo architecture, scale, and downstream use.

Purification Strategy RP-HPLC or PAGE as appropriate, with desalting for selected workflows and purity targets aligned to the application.
Analytical QC Analytical HPLC/UPLC with ESI-MS or MALDI when applicable, plus optional spectral or functional checks.
Delivery & Documentation Tubes, plates, normalized molarity, custom buffers, light-protected handling, CoA, and project documentation.
RP-HPLC PAGE HPLC / UPLC ESI-MS / MALDI CoA Light-protected delivery

Frequently Asked Questions

FAQ

Which dye should I choose for qPCR hydrolysis probes?
Common single-plex choices are 6-FAM with a compatible dark quencher. For multiplexing, use spectrally separated reporters such as HEX/VIC, ROX/TAMRA, Cy5 or Quasar-style far-red dyes with matched quenchers.
How do I pick a reporter dye for my instrument?
Match the dye excitation/emission values to the cycler, microscope, imager or flow cytometer filter set. Avoid reporters with overlapping emission peaks when designing multiplex panels.
Can Bio-Synthesis label oligos at 5′, 3′ and internal positions?
 
Yes. Bio-Synthesis supports 5′, 3′ and internal fluorescent labeling, including single-labeled, dual-labeled and application-specific probe formats.
 
Which quencher should I pair with my reporter?
 
As a general starting point, BHQ-1 or QSY-7 are used for green-yellow reporters, BHQ-2 or QSY-21 for orange-red reporters and BHQ-3 for far-red dyes.
 
What purification and QC are recommended?
Fluorescent-labeled oligos are commonly RP-HPLC or PAGE purified with analytical HPLC/UPLC and ESI-MS or MALDI confirmation when applicable.
Can Bio-Synthesis help with multiplex dye panel design?
Yes. Dye selection can be matched to filter sets, excitation/emission windows, quencher compatibility, channel spacing and assay background requirements.
More FAQsAll FAQs
Contact & Quote Request

Need help selecting a fluorescent dye or probe format?

Share your sequence, dye preference, labeling position, assay type, instrument/filter channel, quencher needs, scale, purification target and QC requirements. Bio-Synthesis can help match dye chemistry and probe design to your workflow.
Request a Quote Speak to a Scientist

Need help before quoting?

Email: info@biosyn.com
Phone: 800-227-0627 (US/CAN)
Phone: +001-972-420-8505 (INT)

Related Services

Explore connected fluorescent probe and labeling services.

Dual-Labeled Probes Quencher Oligos Click-Ready Oligos Biotinylated Oligos

Fast Quote Checklist

Include sequence, dye, position, assay type, instrument channel, scale and QC needs.

Sequence Dye Position Assay QC

Why Choose Bio-Synthesis

Trusted by biotech leaders worldwide for over 45 years of delivering high-quality, fast, and scalable synthetic biology solutions.

Greetings, Researchers,

Please be advised that any information, guidelines, write-ups, and oral/video/graphic content on our website are intended solely as general guidelines.

It is the researcher's sole responsibility to conduct thorough research on the design of products intended for their experiments before submitting
their designs to Biosynthesis for production feasibility review.

Thank you for your understanding.

Quick Links