Taqman Probe sequence problem - (May/06/2013 )

Hello, I want to report the problem I meet with Taqman probe here.

I have two Taqman Probe synthesized by ABI. One probe is with right sequence as I required. The other one is with wrong sequence with one base lost during the synthesis. But the result is that the wrong probe gave very good signal but the right one gave very bad signal. Actually, I have used the wrong probe done a lot of experiment. I just got a new one with right sequence but found the experiment result is not good. It is a coincidence that I check the report document given by ABI and found that the sequence of two probe is different.

My question is : the right probe should be 17bases. The wrong probe is 16, with a T lost at close to 5' end, which is like 5FAMCCATC-----3MGB, but should be 5FAMCCATTC----3MGB. If T is lost at 4th/5th position of probe, can the fluorescence signal be detected? If under this situation, fluorescence signal can not be detected, then I can say only the report was wrong, and the sequence was actually right. But for the exact right new probe, it is so weird that I can not get good result.

Have you checked that the product is the correct one by sequencing?

I have no time and money to check the sequence of one ordered probe:)

No - not the probe, the sequence you are producing with it...

Primers are the same, so I think the sequence produced is the same.