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Custom Oligonucleotide Quencher Labeling Services
Custom Oligonucleotide Quencher Labeling Services

Custom Quencher Oligonucleotide Labeling

A quencher is a molecule that is able to absorb the energy emitted by a fluorophore. Through FRET (Fluorescence Resonance Energy Transfer), it emits the energy at different wavelength, reducing the fluorescence of the fluorophore. This quencher any also act through collisional quenching where the fluorophore and quencher are in close contact.

Dual labeled oligonucleotides are commonly used to monitor the kinetics of PCR amplification and other biological processes in real time. In one version of this method, the oligonucleotides are designed to hybridize to the 3' side ("downstream") of an amplification primer so that the 5'-3' exonuclease activity of a polymerase digests the 5' end of the probe, cleaving off one of the dyes. The fluorescence intensity of the sample increases and can be monitored as the probe is digested during the course of amplification.

In recent years TAMRA, as well as other fluorescent acceptor molecules in dual labeled probes, have been replaced with one or another of the growing family of dark quencher molecules such as our IQ™, Instant Quencher™ family of dyes. Quenchers are a class of chromophores that, instead of emitting absorbed fluorescence resonance energy as light, have the useful property of transforming the light energy to heat. Such kind of probe design can greatly simplify many fluorescence assays since there will be no background fluorescence.

Bio-Synthesis can incorporate oligonucleotide with several quenchers. We offer the fourth generation of Instant Quenchers™, IQ4™, as an alternative to BHQ1,2,3. It has unique fluorescence quenching properties with an operational range between 500 nm and 700 nm and can therefore be utilized in multiplexed assays pairing IQ-4 quencher dye with different fluorophores.

See details and price listing on Quencher Modified Oligonucleotides.

Contact your Account Representative for pricing on quencher dye labeled oligonucleotides. For additional information, please Contact us. Price/labeling, purification and synthesis is an additional charge

Dyes Scales Label position
5' Int 3'
DABCYL 250 nmol $170 $480 $150
1.0 µmol $320 $850 $190
TAMRA 250 nmol $220 - $175
1.0 µmol $295 - $250
Eclipse Dark Quencher 250 nmol $220 - $175
1.0 µmol $220 - $190
IQ4 250 nmol $150 300 $150
1.0 µmol $220 300 $190
Black Hole Quencher 1 250 nmol $290 - $380
1.0 µmol $255 $360 $295
Black Hole Quencher 2 250 nmol $225 $330 $265
1.0 µmol $255 $360 $295
Black Hole Quencher 3 250 nmol $285 - $145
1.0 µmol $315 - $350

Purification
Desalt or cartridge (RP1) purification is acceptable for most common phosphoramidite modifiers. However, additional purification is strongly recommended for modifiers that require NHS-ester chemistry to conjugate a dye through an amine linker such as Molecular Probes dyes.

Minimum Guarantee Purified Yield
Due to the chemistry of many modifications, yield will be approximately 40 - 60 % less than a standard oligo. Please see our yield chart for details.

Quality Controls
Every oligo synthesized is strictly controlled for quality by using either MALDI-TOF mass spectrometry or polyacrylamide gel electrophoresis (PAGE) analysis.  Final yields are determined using UV absorbance at OD260  In addition, we perform QC methods tailored to specific modifications, such as OD ratio measurement where appropriate. 

For additional information, please Contact us.

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