Antisense design

Michael Schmitz schmitz at lcbvax.cchem.berkeley.edu
Sat Mar 21 02:52:31 EST 1998

Starr Hazard wrote:
> A user approached me the other day with the problem
> of desiging an antisense oligo to discriminate
> between two related sequences.
> I aligned the two sequences and I see regions
> of mismatch, but I do not immediately see how to
> quantify/rank the mismatch regions in say kcal/mol.

>Would any of you care to share your thoughts on 
>antisense oligo design within existing GCG/EGCG

Have a look at


It calculates melting profiles of double stranded DNA, RNA or hybrids, 
you can specify the position of mismatches and directly observe mismatch
effects on the melting temperature. 
The publication in Steger, G. (1994) Nucleic Acids Res. 22, 2760-2768. 
describes application to oligos (PCR primer design, but should be close 
enough to what you want to do) among others. 

I think it was included in one of the recent EGCG releases; in case I'm
there: source at


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