I am designing LNA probes to discriminate SNPs. I need to know an approximate delta G value at which the probe will/will not bind to compare match with mismatch and probability of discrimination. If generally dG more negative than -9 kcal/mol is likely to be formed, would a -8.7 kcal/mol mismatch vs -14 kcal/mol result in discrimination? I can't find any literature on this.
Mrs/Miss Downs,
This depends on the method, which has been employed in determining DG.
Thank you Bojidarka B. Ivanova - I am using the calculator on IDT website - http://biophysics.idtdna.com/ - but I am also open to suggestion.
Mrs/Miss Downs,
I have not focused attention to IDT website, but you could pay attention to Gaussian's (www.gaussian.com) capability of simulation within a large scale of methodologies.
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