CHARMM Development Project Forums User Discussion & Questions General Chemistry Discussions question about point substitution A to U

Hi everyone,

I'm working with DNA-RNA complex and trying to convert an adenine group into a uracil in RNA strand. In addition to, I want to retain hydrogen bonding (Watson-crick) between aforementioned uracil and thymine (in DNA strand) after conversion. Could anyone lead me towards how to perform this task?

Thank you very much for any suggestion.

Best regards,
Parya.

I thought Watson-Crick meant G:C or A:T (A:U) pairs; the U:T pair resulting from A-->U conversion does not seem to correspond to that.

You could try applying a restraint (e.g. NOE) with some minimization and possibly brief dynamics with more distant regions held rigid to get the desired geometry.

Thank you for your precious guidance.

Please help me how to perform an NOE distance restraint to U:T pair. thank you in advance.

With respect,
Parya.

Start with the NOE section of cons.doc