Re: [AMBER-Developers] Langridge B-DNA vs Arnott B-DNA

From: David Case <>
Date: Wed, 18 Dec 2019 17:21:58 +0000

On Wed, Dec 18, 2019, Pengfei Li wrote:
>Do you know any research (experimental or computational) that has been
>done about the sequence dependence of DNA duplex structures? Thanks!

Tons and tons of work. The "ABC" consortium spent years doing
simulations aimed at this, and their papers cite relevant experimental
data as well. Most recent paper in this series is this:

%A M. Pasi
%A J.H. Maddocks
%A D. Beveridge
%A T.C. Bishop
%A D.A. Case
%A T. Cheatham III
%A B. Jayaram
%A F. Lankas
%A C. Laughton
%A J. Mitchel
%A R. Osman
%A M. Orozco
%A D. Petkeviciute
%A N. Spackova
%A J. Sponer
%A K. Zakrzewska
%A R. Lavery
%T `micro`ABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA
%J Nucl. Acids Res.
%V 42
%P 12272-12283
%D 2014

Note that sequence dependence of structures is probably different
(smaller) in solution that in crystal structures. There is scant
evidence in solution (a few good quality NMR structures), but some
quasi-recent computational work is here:

%A I. Ivani
%A P.D. Dans
%A A. Noy
%A A. P�rez
%A I. Faustino
%A A. Hopsital
%A J. Walther
%A P. Andri�
%A R. Go�i
%A A. Balaceanu
%A G. Portella
%A F. Battistini
%A J.L. Gelp�
%A C. Gonz�lez
%A M. Vendruscolo
%A C.A. Laughton
%A S. Harris
%A D.A. Case
%A M. Orozco
%T Parmbsc1: A refined force field for DNA simulations
%J Nature Meth.
%V 13
%P 55-58
%D 2016

Apologies for mainly citing my own work (it's what is at hand), and Tom
can probably provide a better overview. (But if you are thinking about
working on this yourself, my personal recommendation would be to avoid's been more or less beaten to death, at least in my view.)



David A. Case |
Dept. of Chemistry & Chemical Biology |
Rutgers University | office: +1-848-445-5885
174 Frelinghuysen Road, Rm. 208b | cell: +1-609-751-8668
Piscataway, NJ 08854 USA | web:
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Received on Wed Dec 18 2019 - 10:00:01 PST
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