Miner groove binder - urgent, help, what is it? (Sep/22/2010 )

Hi everyone,

I am used to order probes for the TaqMan assay that look like 5'-dye-xxxxx-3', but today I need to order a probe I found in a paper that goes like this:
VIC-XXX(sequence)XX-MGB-NFQ
They say MGB is for minor groove binder and no idea what NFQ is.
What is a minor groove binder? what it is doing and what is NFQ?
Do you think ABI will understand if I just submit the sequence like that?
Heeeeeelp. I need to order these today, but I want to make sure that we'll be able to follow a regular TaqMan protocol to run this.

Thanks a lot

Maddie

Minor groove binder
NFQ = nonfluorescent quencher or dark quencher

Dark quenchers are nowadays standard, ABI offers "TaqMan® MGB Probes" with NFQ, check Product Description.

Trof on Wed Sep 22 14:15:33 2010 said:

All Taqman probes I know have two "dyes", it's the principle - reporter dye (FAM or VIC or so) transfers its energy to the other dye, quencher, while the probe is intact. But when it binds to the target sequence and is cleaved by the 3' exonuclease activity of the polymerase, it's now free from the quencher and you see the fluorescence in the reporters channel. First the quenchers used to be TAMRA, a fluorescent dye that emits in different part of the spectra, now better non fluorescent quenchers are used that absorbs the energy from reporter dye and emits in the infrared spectra I think, so there is no spectral crosstalk between the dyes.

So it works the same as any other Taqman and uses same mixes, it just needs Taq polymerase to have 3'exo activity.

(trivia: That's the reason why its called Taq-man, like the game PacMan, that eats everything in the way as it goes )

Trof on Wed Sep 22 15:00:21 2010 said:

All Taqman probes I know have two "dyes", it's the principle - reporter dye (FAM or VIC or so) transfers its energy to the other dye, quencher, while the probe is intact. But when it binds to the target sequence and is cleaved by the 3' exonuclease activity of the polymerase, it's now free from the quencher and you see the fluorescence in the reporters channel. First the quenchers used to be TAMRA, a fluorescent dye that emits in different part of the spectra, now better non fluorescent quenchers are used that absorbs the energy from reporter dye and emits in the infrared spectra I think, so there is no spectral crosstalk between the dyes.

So it works the same as any other Taqman and uses same mixes, it just needs Taq polymerase to have 3'exo activity.

(trivia: That's the reason why its called Taq-man, like the game PacMan, that eats everything in the way as it goes )