probe size: please help

[Mark Siddall]

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
species).
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


-- 
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