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Fluorescent Dye-Labeled Oligonucleotides

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

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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

Fluorescent Dye Catalog

Visible, organized dye-family catalog for common fluorescent oligo labeling options. Values are practical reference points; final dye choice should be matched to your instrument filter set and assay conditions.

Search Dye by Color

Use the color band to quickly view fluorescent dye options by emission color.

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 325/450/450 nm Coumarin 102 375/450/450 nm AMC 350/440 nm DyLight 405 400/421 nm DY-405 405/421 nm Epoch Blue 405/450 nm Bimane 370/482 nm Pyrene dye 345/375 nm

Cyan dye options

ATTO 390 390/479 nm ATTO 425 425/484 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 CF488A 490/515 nm CF503R 503/532 nm Chromeo 505 505/526 nm Coumarin 153 420/530/530 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

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 CF405L 395/545 nm DY-530 530/555 nm DY-547 547/572 nm DY-550 550/570 nm HEX 535/556 nm TET 521/536 nm

Yellow dye options

Abberior Cage 552 552/567 nm Alexa Fluor 532 530/554 nm CF532 527/558 nm Epoch Yellow 530/550 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 550/570 nm Cy3B 559/570 nm DyLight 550 562/576 nm DY-555 555/580 nm Epoch Orange 540/570 nm Janelia Fluor 549 549/571 nm B-Phycoerythrin B-PE 496/578 nm

Orange-Red dye options

Alexa Fluor 568 578/603 nm CF555 555/565 nm Cy3.5 581/596 nm

Red dye options

Alexa Fluor 594 590/617 nm ATTO 590 590/617 nm ATTO 594 594/627 nm BODIPY TR 589/617 nm CF568 562/584 nm CF594 593/614 nm Chromeo 494 ~494/~628 nm DyLight 594 593/618 nm Epoch Red 590/615 nm Eterneon Red 590/615 nm LightCycler Red 610 610/630 nm Amplex Red 563/587 nm

Far-Red dye options

Abberior STAR 635 Abberior STAR 635P Alexa Fluor 633 Alexa Fluor 647 ATTO 610 ATTO 633 ATTO 647N CF633 CF640R CF647 Cy5 Cy5.5 DyLight 650 Epoch Far Red Janelia Fluor 635 Janelia Fluor 646 LightCycler Red 640 APC

NIR dye options

Alexa Fluor 700 Alexa Fluor 750 CF680 CF770 CF790 CF850 Cy7 DyLight 680 DyLight 800 Epoch Infrared Eterneon IR 800 LightCycler Red 705

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 405 Ex 400 / Em 421 DY-405 Ex 405 / Em 421 Epoch Blue Ex 405 / Em 450 Pyrene dye Ex 345 / Em 375

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 CF405M Ex 408 / Em 452 CF488A Ex 490 / Em 515 Chromeo 488 Ex 488 / Em 517 Coumarin 6 Ex 375/495 / Em 495 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

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 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 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

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 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 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

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 ATTO 590 Ex 590 / Em 617 ATTO 594 Ex 594 / Em 627 ATTO 610 Ex 610 / Em 635 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 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

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 ATTO 633 Ex 633 / Em 657 ATTO 647N Ex 646 / Em 664 ATTO 680 Ex 680 / Em 700 BODIPY 650/665 Ex 650 / Em 665 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 650 Ex 652 / Em 672 DyLight 680 Ex 679 / Em 700 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

Near-IR dye options (701+ nm)

Alexa Fluor 700 Ex 702 / Em 723 Alexa Fluor 750 Ex 749 / Em 775 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 800 Ex 777 / Em 794 Epoch Infrared Ex 750 / Em 770 Eterneon IR 800 Ex 775 / Em 800 LightCycler Red 705 Ex 690 / Em 705
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 Orange Widely used orange dye for oligo and antibody labeling
Cy3B 559 570 Orange Brighter and more photostable Cy3 analog
Cy3.5 581 596 Orange-Red 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
DyLight 405 400 421 Blue Bright blue dye for multiplex imaging
DyLight 550 562 576 Orange TRITC alternative
DyLight 594 593 618 Red Texas Red replacement
DyLight 650 652 672 Far-Red High-sensitivity far-red dye
DyLight 680 679 700 NIR NIR dye for in vivo imaging
DyLight 800 777 794 NIR Deep-tissue NIR dye
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

Design Considerations for Fluorescent-Labeled Oligos

Fluorescent probes perform best when the dye is selected together with probe architecture, assay type, channel spacing and QC plan.

CH

Channel Matching

Match excitation/emission to your instrument filters and avoid overlapping reporters in multiplex panels.

POS

Label Position

Choose 5′, 3′ or internal placement based on whether the dye acts as a reporter, FRET donor/acceptor, immobilized signal or imaging probe.

SPC

Spacer & Linker Length

Use spacers when dye proximity affects hybridization, quenching, surface presentation or steric access.

Q

Quencher Pairing

Select compatible dark quenchers such as BHQ or QSY options based on reporter emission window.

Tm

Tm & Probe Behavior

Consider dye effects on duplex stability, probe length, GC content and background fluorescence.

QC

Analytical Readout

Specify purity, mass confirmation and optional functional testing when signal performance is critical.

Labeling Chemistry Options

Bio-Synthesis supports multiple fluorescent labeling chemistries for terminal, internal and post-synthetic dye attachment workflows.

NHS

NHS-Ester Amine Coupling

For 5′, 3′ or internal amino-modified oligos such as Amino-C6; forms stable amide linkages.

SH

Maleimide–Thiol Coupling

For thiol-modified oligos after reduction and desalting; useful for rapid, stable thioether dye attachment.

CLK

Click Chemistry

CuAAC, SPAAC and TCO–tetrazine strategies for modular dye placement and copper-free labeling workflows.

ALD

Aldehyde-Reactive Coupling

Aminooxy or hydrazide coupling for oxime or hydrazone-style dye attachment to carbonyl-bearing partners.

PHO

Dye Phosphoramidites

Direct solid-phase insertion for controlled position, spacing and reproducible fluorescent probe architecture.

FRET

Dual-Dye & FRET Formats

Reporter/quencher, donor/acceptor and dual-labeled probe formats for qPCR, molecular beacon and FRET assays.

Applications for Fluorescent-Labeled Oligonucleotides

Fluorescent oligos are used across amplification, imaging, spatial biology, molecular detection and single-molecule workflows.

Hydrolysis probes, molecular beacons and multiplex reporter/quencher probe formats.

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Donor/acceptor dye placement for distance-sensitive nucleic acid interaction studies.

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Donor/acceptor dye placement for distance-sensitive nucleic acid interaction studies.

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Far-red and NIR dye-labeled oligos for low-background imaging and deeper wavelength detection.

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Fluorescent oligo panels for chromosome painting, spatial biology and imaging workflows.

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Channel-matched fluorescent oligos for probe-based plate, bead and multiplex detection systems.

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Purification, QC and Delivery Formats

PUR

Purification

  • RP-HPLC or PAGE as appropriate
  • Desalting for selected workflows
  • Purity target aligned to application
MS

Analytical QC

  • Analytical HPLC/UPLC profile
  • ESI-MS or MALDI when applicable
  • Optional spectra or functional checks
DEL

Delivery

  • Tubes, plates or normalized molarity
  • Custom buffers and light-protected handling
  • CoA and project documentation

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.

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.

Related Services

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Fast Quote Checklist

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

Sequence Dye Position Assay QC

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