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Quencher Modification Listing

Quencher Modification Listing

Quencher Family Effective Quenching Range (nm) 5' Internal 3' NHS Ester Available Typical Synthesis Chemistry
BHQ-0 BHQ 430–480 ✓ – ✓ No 5' phosphoramidite, 3' CPG
BHQ-1 BHQ 480–580 ✓ ✓ ✓ Limited 5' phosphoramidite, internal dT phosphoramidite, 3' CPG
BHQ-2 BHQ 560–670 ✓ ✓ ✓ Limited 5' phosphoramidite, internal dT phosphoramidite, 3' CPG
BHQ-3 BHQ 620–730 ✓ ✓ ✓ Limited 5' phosphoramidite, internal dT phosphoramidite, 3' CPG
Dabcyl Dabcyl 400–500 ✓ ✓ ✓ ✓ Phosphoramidite, dT phosphoramidite, CPG, NHS
Dabsyl Dabsyl 420–520 ✓ Rare ✓ ✓ Phosphoramidite, NHS
Eclipse® Epoch/Eclipse 400–650 ✓ Limited ✓ No Phosphoramidite, CPG
Deep Dark Quencher I (DDQ I) Eurogentec ~480–580 – – ✓ No 3' CPG
Deep Dark Quencher II (DDQ II) Eurogentec ~560–700 – – ✓ No 3' CPG
Iowa Black® FQ IDT 420–620 ✓ – ✓ No 5' phosphoramidite, 3' CPG
Iowa Black® RQ IDT 500–700 ✓ – ✓ No 5' phosphoramidite, 3' CPG
Iowa Black® RQ-Sp IDT ~600–750 ✓ – ✓ No 5' phosphoramidite, 3' CPG
QSY® 7 Thermo Fisher ~470 ✓ Rare ✓ ✓ Phosphoramidite or NHS
QSY® 9 Thermo Fisher 650–700 ✓ Rare ✓ ✓ Phosphoramidite or NHS
QSY® 21 Thermo Fisher ~650 ✓ Rare ✓ ✓ Phosphoramidite or NHS
QSY® 35 Thermo Fisher 650–800 ✓ Rare ✓ ✓ Phosphoramidite or NHS
ATTO 540Q ATTO 525–600 ✓ Limited ✓ ✓ Phosphoramidite or NHS
ATTO 580Q ATTO 550–610 ✓ Limited ✓ ✓ Phosphoramidite or NHS
ATTO 612Q ATTO 620–680 ✓ Limited ✓ ✓ Phosphoramidite or NHS
BBQ-650® Berry & Associates 550–750 ✓ Limited ✓ ✓ Phosphoramidite or NHS
DYQ-1 Dyomics 430–520 ✓ – ✓ ✓ Phosphoramidite or NHS
DYQ-2 Dyomics 500–580 ✓ – ✓ ✓ Phosphoramidite or NHS
DYQ-4 Dyomics 510–600 ✓ – ✓ ✓ Phosphoramidite or NHS
DYQ-425 Dyomics 520–620 ✓ – ✓ ✓ Phosphoramidite or NHS
DYQ-505 Dyomics 530–640 ✓ – ✓ ✓ Phosphoramidite or NHS
DYQ-660 Dyomics 620–680 ✓ – ✓ ✓ Phosphoramidite or NHS
DYQ-661 Dyomics 640–700 ✓ – ✓ ✓ Phosphoramidite or NHS
DYQ-700 Dyomics 680–750 ✓ – ✓ ✓ Phosphoramidite or NHS
QXL® 520 QXL 480–550 – – ✓ No 3' CPG
IQ-530 Microsynth ~530 – ✓ – No Internal phosphoramidite
MGB-Q530 Microsynth ~530 – – ✓ No 3' MGB-CPG
MGB-NFQ Applied Biosystems ~500–650 – – ✓ No Proprietary 3' MGB-CPG
TAMRA (fluorescent quencher) Rhodamine 540–580 ✓ ✓ ✓ ✓ Phosphoramidite, dT phosphoramidite, CPG, NHS
ROX (FRET acceptor) Rhodamine 580–610 ✓ Limited ✓ ✓ Phosphoramidite or NHS
Cy5 (FRET acceptor) Cyanine 650–670 ✓ Limited ✓ ✓ Phosphoramidite or NHS

Note: Availability of specific quencher formats may vary by supplier, scale, and oligonucleotide design. Terminal quenchers are commonly introduced using 5' phosphoramidites or 3' CPG supports. Internal quenchers are typically introduced using internal dT phosphoramidites or other internal quencher phosphoramidite formats. NHS ester quenchers are generally used for post-synthetic labeling of amino-modified oligonucleotides.
 

Summary by Modification Format

Modification Format Common Quenchers
5′ Phosphoramidite BHQ-0, BHQ-1, BHQ-2, BHQ-3, Dabcyl, Iowa Black® FQ, Iowa Black® RQ, Iowa Black® RQ-Sp, QSY® 7, QSY® 9, QSY® 21, QSY® 35, ATTO 540Q, ATTO 580Q, ATTO 612Q, BBQ-650®, DYQ-1, DYQ-2, DYQ-4, DYQ-425, DYQ-505, DYQ-660, DYQ-661, DYQ-700, TAMRA, ROX and Cy5.
Internal Phosphoramidite BHQ-1-dT, BHQ-2-dT, Dabcyl-dT, IQ-530, TAMRA-dT, proprietary internal quenchers such as ZEN™ and TAO™.
3′ CPG Support BHQ-0, BHQ-1, BHQ-2, BHQ-3, Dabcyl, Eclipse®, Iowa Black® FQ/RQ/RQ-Sp, Deep Dark Quencher I (DDQ I), Deep Dark Quencher II (DDQ II), QXL® 520, MGB-NFQ and MGB-Q530.
NHS Ester Dabcyl, Dabsyl, QSY® dyes, ATTO Q quenchers, DYQ quenchers, BBQ-650®, TAMRA, ROX and Cy5. NHS ester derivatives are typically coupled to amino-modified oligonucleotides following synthesis.

Product Information

 

Product Name:
Quencher Modification Listing

Purification:
Dual HPLC/SEC

Delivery Format:
Lyophilized

Shipping Conditions:
Room Temperature

Storage Conditions:

-20°C To -70°C
Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Properly reconstituted material stored at -20°C should be stable for at least 6 months. Dried DNA (when kept at 20°C) in a nuclease-free environment should be stable for years.

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