>>more or less beaten to death
Bold claims Dave! Maybe true for equilibrium B-duplex in water and mild
salt, certainly not for A,C,Z and others. I think the first high quality
(more than a 4-5 bp, and not complexed) structure for Z was only deposited
in 2014 (4ocb.pdb), and only achieved by SAD rather than by crystallography.
Josh
On Wed, 18 Dec 2019 at 18:34, David Case <david.case.rutgers.edu> wrote:
> 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
> it....it's been more or less beaten to death, at least in my view.)
>
> ....dac
>
> --
>
> ====================================================================
> David A. Case | david.case.rutgers.edu
> 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: casegroup.rutgers.edu
> ====================================================================
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Received on Thu Dec 19 2019 - 01:00:02 PST
