Re: [AMBER] generating g-quadruplex DNA structures from a sequence

From: David Case <>
Date: Wed, 22 Jan 2020 13:05:18 +0000

On Wed, Jan 22, 2020, Vaibhav Dixit wrote:

>In a project, I am required to generate g-quadruplex structures for
>sequences for which crystal structure data in not available.
>Using amber tutorial B1 like procedure it is very easy to generate a
>variety of normal DNA helix structures.
>But I can't find a similar procedure for generating g-quadruplex structure
>only from a sequence.
>Thus I'm wondering if an expert on the list can suggest how can I approach
>this requirement using AmberTools.
>Will it make sense if I use an existing quadruplex PDB entry of identical
>length and simply delete coordinates for the bases (keep sugar-coordinates)
>and change residue names to required base e.g. DG to DA?

I'd keep the N1/N9 atoms of the bases, and give it a try.

Presumably(?), the guanine tetrads will be unchanged. However, there
are lots of topological ways that the "connecting" bases can be
arranged. Unless you know that your unknown structure has the same
general arrangement as your input structure, you could generate a
structure that is entirely wrong.


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Received on Wed Jan 22 2020 - 05:30:07 PST
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