My objective is to design control experiments to antisense
oligonucleotides action. As part of control assays, I intend to use
oligonucleotides differing from the original antisense moiety by a
limited number of mismatches. These mutations are introduced to
destabilize duplex formation between the target RNA and the
oligonucleotide, and avoid specific antisense effects. Problems arise
when considering how to choose mismatch positions and number, being
clear that the closer to the original the better. A calculation of
duplex stability seem necessary for each one of the possible
alterations to the original sequence. The problem is comparable with
the search for the "worst" hybridization probe.
I tried using OLIGO 4.0, but the program is unable to accept
mismatched probes. So, if you have or heard about software able to
solve the problem, please contact.
Thank you in advance.