[gmx-users] Groove width

mesguerran mesguerran at unal.edu.co
Sun Jun 3 18:08:42 CEST 2018


> On Jun 2, 2018, at 9:22 PM, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Den 2018-06-02 kl. 11:06, skrev spss4 at iacs.res.in:
>> Hi all
>> I am doing simulation of DNA molecule. I want to calculate groove width of
>> DNA in GROMACS. How to do this? Someone please help.
>> Thanks
>> Sunipa
> Just out of curiosity, what does that tell you? I understand it may be interesting for structure prediction or qualitative structure comparisons, but what chemistry is encoded in the groove width?

Traditionally the groove width will initially be seen as a consequence of the sugar puckers.
Sugar puckers can be engineered chemically with modifications, so-called Locked Nucleic Acids (LNA's), are popular (among others) to “lock” a deoxyribose pucker into the C3’-endo conformation common in the A-RNA conformation, but not the “natural” C2’-endo B-conformation of DNA. 

There’s also a wealth of studies on intercalators (https://en.wikipedia.org/wiki/Intercalation_(biochemistry) <https://en.wikipedia.org/wiki/Intercalation_(biochemistry)>), which can stack between base-pair steps, provided there’s enough space. 

Additionally there is crosslinking (https://en.wikipedia.org/wiki/Crosslinking_of_DNA <https://en.wikipedia.org/wiki/Crosslinking_of_DNA>), and ,in this case, one can imagine some “chemistry” happening, if by chemistry one assumes the naive bond breaking/formation interpretation.

I would suggest using X3DNA for your analysis and reading the definition of what is geometrically measured in the appendix of:

M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.



 Mauricio Esguerra Neira, Ph.D.              
 Department of Cell and Molecular Biology
 Uppsala University
 Phone Number: (+46)073-678-5334             
 mauricio.esguerra at icm.uu.se              

> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
> http://www.icm.uu.se
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