Re: [AMBER] slightly off topic: suggestions for DNA single strand simulations

From: Thomas Cheatham <>
Date: Tue, 13 Apr 2010 21:13:55 -0600 (Mountain Daylight Time)

> While I have found plenty of biblio for DS DNA, apart from a review by
> Nilsson 2001 on tetramers, I have not been able to find references
> furnishing details and issues for simulations (with or without NMR data)
> of SS DNA sequences.

There are very few examples in the literature; if I remember correctly
Nilsson's group has a few published studies and there may be some protein
+ single strand simulations by others. However isolated single strands
with AMBER have not been published much, if at all.

I have performed a series of single stranded simulations, yet never
published; if you start with a helical stacked structure, i.e. by deleting
a strand from a duplex (particularly with purines), the structure will
remained stacked for at least ~10-25 ns. If you start with random single
stranded structure, the structures will start to stack.

I have yet to fully converge single stranded simulations. Do not
underestimate the conformational entropy available and set of accessible
conformational states. If I were to reinvestigate now, I would apply
temperature based replica-exchange simulation. Note further that
experiment is complicated here; adenine bases free in solution will stack.
polyG will form higher order structures (quadruplex). I do not know what
polyT or polyC is supposed to do.


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Received on Tue Apr 13 2010 - 20:30:04 PDT
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