Tm of antisense-target duplex

Nirav Shah shah2 at husc9.harvard.edu
Thu Jul 1 00:32:35 EST 1993


Hello All!

        I am targeting stem and loop structures within a single strand of
cDNA with antisense oligomers, and need some way of computing melting
temperatures (Tm) for the antisense-target duplex, including mismatches
for the self-annealed target strand as well as the perfect homology of the
antisense-target duplex.  MacVector only computes Tm for completely
complementary sequences, and will not give me what I'm looking for.  I
have access to Macintosh, IBM and UNIX platforms.
        I have some programming experience (C) or can set up
spreadsheets to do the calculations if necessary.  Any suggestions on how
to account for the mismatches would be greatly appreciated.  If there is
interest and sufficient response, I will summarize and post any findings.
Please respond either by posting to bionet.software or by e-mailing me
directly at "shah2 at husc.harvard.edu".  Thanks in advance,

                                                Nirav Shah
                                                Roswell Park Cancer Institute




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