I think Rosa di Felice was doing something in that
direction.
Stability and migration of metal ions in G4-wires by molecular dynamics simulations
Author(s): Cavallari M, Calzolari A, Garbesi A, et al.
Source: JOURNAL OF PHYSICAL CHEMISTRY B Volume: 110 Issue: 51 Pages: 26337-26348 Published: DEC 28 2006
But I not remember details. We were less active in the "G-NA"
field due to the force field problems with loops.
Jiri
> I wonder if anyone has ever tested for longer quadruplex strands,
> e.g. in junk DNA? They might form interesting macro structures, e.g.
> stacking with porphyrin (if not in nature, maybe by man). We figured
> that if the ion-oxygen stacking provided conductivity like known
> organic conductors (hand-wave here), then there might be nanowires
> in the nucleus, or pipes for flows of ions which by their sequence
> could also carry information.
>
> Bill
>
>
> > 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 Fri Jun 11 2010 - 04:00:03 PDT
