In Molecular beacon based qPCR assays, when the probe-target hybridization takes place, do quenching occur between the fluorophore of one molecular beacon molecule (in open state) and quencher of other molecular beacon molecule (in open state) since at the time of annealing, there will be multiple probe molecules bound to their complementary targets and there can be interaction between the fluorophore of probe and quencher of adjacent probe (both probes are in open state)?
If this thing happens (i.e quenching), then isn't it limiting the efficiency or advantage of Molecular Beacon probes?
Normally the inter-molecular interaction between a fluorophore and a quencher from two different beacons is practically non existing, since even if the molecules come close to each other (and it is very difficult due to the low concentration) the possible interaction is highly transient since there is no possible chemical binding to keep them close to each other (each beacon is actually bound to its target) and therefore it has virtually no effect on the fluorescence efficiency of the fluorophore.
Here is a reference: http://www.molecular-beacons.org/MB_intro_full.html
Thank you for the valuable reply. Now it is very much clear to me.
I went through the reference too...However it is not containing information about my query.
Can I find the exact answer to this in some other article, just if it is available....
I am searching for this for a very long time.
Sorry Neetika, but I don't think you would find this in an article, but you should not need it, it is a chemico-physical consideration: the probe being a single-stranded DNA molecule can only bind to a complementary DNA sequence, it's target, and in general it is designed not to interact with itself (so, no palindromic sequences or stretches of complementary sequences), except for the stem sequence that is needed for the quenching when not bound to the target. Therefore, stable interaction between different probe molecules bound to their target has no chemico-physical possibility to occur. That's why molecular beacons are very clean and efficient, although among the most expensive probe type.
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