is it possible to just cut the 1-2 base mismatched hairpin?

Basavaraju Shankarappa bsh at MED.PITT.EDU
Wed Jun 2 14:06:47 EST 1993

Dear friends:

I am trying to explore some netwisdom and pointers in an experiment 
that will involve something analogous to RNA finger printing.

I would like to identify the presence of mutant sequences in a population
that predominantly contains wild type sequences.  So, I will make an
oligo specific to the wild type and hybridize with this population.
Now I am wondering whether it is possible to use DNA polyI's proof
reading capability to chew the 1-2 base mismatch.  If I do not add the 
dNTPs, can I assume that nicks do not get repaired?  Also, is it 
possible to modify the 3' and 5' ends of the oligo probe such that 
they are not susceptible to any sort of exonuclease activity?
Is it possible to use S1 nuclease or any other enzyme to just cleave
at the mismatch and do nothing else.  

I will sure appreciate all the pointers in this regard. 

Raj Shankarappa
Univ of Pittsburgh
bsh at

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