Yes, I agree. We have used them in our first
G-DNA papers Spackova et al JACS 1999 and 2001, as
explicitely stated. These are good for G-stem, especially Na+.
Refs. 5a and 3a in our studies, respectively.
Later I have got confused by the ion literature a little,
there are too many parametrizations.
Jiri
> > You should include ions,
> > one per each cavity.
> > Use Na+ instead, K+ are oversized.
>
> This paper has lots on this issue, including reparameterizing
> ions for quadruplex vs. water:
>
> Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy
> Perturbation Studies. W.S. Ross and C.C. Hardin
> Journal of the American Chemical Society 116, 6070 (1994).
>
> Bill
>
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Received on Thu Jun 10 2010 - 12:00:03 PDT
