probe size: please help
mes at zoo.toronto.edu
Thu May 12 00:50:38 EST 1994
Aplogies for what may appear to be a naive query. I am a molecular
neophyte and hope to soon remedy that.
Here's my situation: I am armed with sequences for ribosomal genes for
two related parasites. I desire a probe that will light-up parasite1 if
it is there but not parasite2 and not the host. Notably, the ssu rDNA
gene, as a whole is highly conserved across taxa. On the other hand I
can find regions of hypervariability (across species but not within a
Here's my question: for a descent probe, how long should it be? Will
20 bp do it? How much sequence similarity with the non-target parasite2
and host can I have without non-specific binding problems? And is
A-T : G-C composition going to be a problem for specificity? Ideally
I want to keep the prob(es) short as I may use them for priming
PCR reactions at a later date.
Any help/pointers/redirections are most welcome!
Thanks in advance.
Mark E. Siddall "In saying what is obvious, never choose cunning.
mes at vims.edu Yelling works better." - C. Ozick
Virginia Inst. Marine Sci.
Gloucester Point, VA, 23062
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