Re: [AMBER] Regarding filling missing residues in a DNA strand

From: Sruthi Sudhakar <>
Date: Wed, 25 Aug 2021 18:28:53 +0530

The main problem is that the DNA is unwound in the central position but
bound at the terminal positions. So some of the techniques are not easy. If
someone could comment on some techniques, it would be really helpful
Sruthi Sudhakar

On Wed, Aug 18, 2021 at 5:58 PM David A Case <>

> On Tue, Aug 17, 2021, Sruthi Sudhakar wrote:
> >
> >We are working on a DNA protein system and the crystal structure under
> >consideration has around 5 missing residues in the DNA strand. The DNA
> >duplex is in an unwound form, but we know what bases should be added in
> >those places. Is there a methodology in NAB or directly in leap by which
> we
> >could fill those residues ?
> This is a hard problem, and neither NAB nor leap are likely to be of much
> help. If the missing nucleotides are not at a chain terminus, filling in
> missing ones is equivalent to a "loop building" exercise, which is
> common for proteins and RNA, but less so for DNA. I didn't find anything
> easily with a Google search, but maybe someone on the list will have
> some thoughts on this. You could look at RNAmake, which attacks this sort
> of problem for RNA: Joe Yesselman or others might have some thoughts about
> using it for DNA.
> If you just need to add "unwound" DNA at the end off a chain, look for
> articles (e.g. from the Lois Pollack group) about modeling single-stranded
> DNA.
> ...good luck...dac
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Received on Wed Aug 25 2021 - 06:00:02 PDT
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