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#36719 - 12/30/17 01:52 PM question about point substitution A to U
parya Offline
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Registered: 01/22/17
Posts: 11
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.


Edited by parya (12/30/17 01:58 PM)

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#36720 - 12/30/17 02:51 PM Re: question about point substitution A to U [Re: parya]
rmv Online   content

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Registered: 09/17/03
Posts: 8314
Loc: 39 03 48 N, 77 06 54 W
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.
_________________________
Rick Venable
computational chemist


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#36721 - 12/31/17 03:52 AM Re: question about point substitution A to U [Re: parya]
parya Offline
Forum Member

Registered: 01/22/17
Posts: 11
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.

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#36722 - 12/31/17 01:57 PM Re: question about point substitution A to U [Re: parya]
rmv Online   content

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Registered: 09/17/03
Posts: 8314
Loc: 39 03 48 N, 77 06 54 W
Start with the NOE section of cons.doc
_________________________
Rick Venable
computational chemist


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