Subject: Re: CCL:question about DNA

From: andre mauricio de oliveira <[email-masked]>
Date: Fri, 11 Apr 2003 09:33:26 -0300 (BSC)

Dear Dr Cozmuta,

1. Usually minor/major grooves width can be measured as the distance
between P-P atoms in nearest residues in both chains. Some free programs
(like 3DNA and Curves) make it automatically when PDB file is furnished.
C4` - C4` are also taken as the reference distance for grooves width, but
results are similar to those w/ P-P.

2. Program Curves and 3DNA also calculate other parameters, some of them
more suitable for evaluating distortion than helicity itself. See:  (1)
Calladine, C. R. & Drew, H. R. (1984) "A base-centered explanation of the
B-to-A transition in DNA," J. Mol. Biol. 178, 773-782. (2)Fratini, A. V.,
Kopka, M. L., Drew, H. R. & Dickerson, R. E. (1982)  "Reversible bending
and helix geometry in a B-DNA dodecamer:  CGCTAATTCGCG," J. Biol. Chem.
24, 14686-14707. (3) Dickerson, R. E., Goodsell, D. S., Neidle, S. A.
....The tyrany of the lattice.... Proc. Natl. Acad. Sci. USA (1994) 91,
3579-83.

Best regards.

On Wed, 9 Apr 2003, Ioana Cozmuta wrote:

> Hi CCL users,
>
>
> I've run Molecular Dynamics for a single stranded nucleic acid homopolymer
> in water with the initial configuration being helical and the final sort
> of bulky.
> I was thinking that a way to characterize the "distortion" is to
> follow during the dynamics the values of the minor/major grooves and also
> the helicity.
> I have two questions:
> 1. Between which atoms exactly one should measure the minor/major grooves
> 2. What is the best way to calculate the helicity of a strand?
>
> Any advice on this matter would be appreciated.
>
> Thanks in advance,
> Ioana
>
>
> -= This is automatically added to each message by mailing script =-
> [email-masked] -- To Everybody  | [email-masked] -- To Admins
> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: [email-masked]
>
>
>
>
>
>

Andre Mauricio de Oliveira

VOICE +55-031-374-1325
      +55-031-499-5765
FAX   +55-031-499-5700

Laboratorio de QSAR e Modelagem Molecular
Nucleo de Estudos em Quimica Medicinal (NEQUIM)
NEQUIM's Homepage: http://www.qui.ufmg.br/~nequim
Departamento de Quimica ICEx
Federal University of Minas Gerais
Av Antonio Carlos 6627 Pampulha ZIP CODE 31270-901
Belo Horizonte MG Brazil