S1 analysis with oligonucleotides

Bonnie Baxter bkbaxter at students.wisc.edu
Fri Jan 10 07:06:14 EST 1997

I am attempting to use S1 analysis to quantitate RNA levels of
individual members of a highly homologous family.  I've designed oligos
complementary to the 5' UTR and the beginning of the coding region of
each gene--each oligo has a tail that is not complementary to the
message, which should be cut off by S1.

I expected to get one product band from each primer, but I am getting
multiple bands.  For example, a message that should be giving a 52 nt
product is giving 52, 53, and 54.  I could understand getting products
smaller than expected, but I'm surprised to be seeing things that are
larger than expected.

The complementarity in each case ends before the 5' end, so the cap
structure should not be the problem.

Is this a normal phenomenon?  Anyone else seen it?  Any suggestions?

My e-mail is bkbaxter at students.wisc.edu

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