Ions are imperfect due to lack of polarization
and exaggeration of short-range repulsion.
This leads to notorious imbalances of solute-cation interactions.
The ions look too large and the binding is underestimated.
Then, especially if you use some parametrization
which substantially exaggerates the short-range repulsion,
K+ can be artificially expelled from the G-DNA stem.
(what parameters of ions do you use?)
It is not possible to simultaneously balance solute - ion
interactions and solvation effects.
E. Fadrna, et al.
Single stranded loops of quadruplex DNA as key benchmark for testing
nucleic acids force fields.
Journal of Chemical Theory and Computation, 5, 2009, 2514-2530
See specifically Figure 2.
I would suggest to use Na+ instead.
There are some other suggestions described there.
cf also.
J. Sponer, N. Spackova: Molecular dynamics simulations and their application to four-stranded DNA. Methods 43, 2007, 278-290
best wishes
-------------------------------------------------------
Jiri Sponer
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
e-mail: sponer.ncbr.chemi.muni.cz
fax: 420 5412 12179
phone: 420 5415 17133
http://www.ibp.cz/labs/LSDNA/
-----------------------------------------------------------
> Hi,
>
> In the crystal structure, I have two K+ ions in the centre of DNA
> (quadruplex). After production run, one of the ions move out from the tetrad
> to the bulk solution and no K+ ion from the bulk solution replaces it.
>
> I guess that the K+ should be present in the tetrad as it was found in the
> crystal structure. Is the result feasible?
>
> Asfa.
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Received on Fri May 28 2010 - 00:00:04 PDT
