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 Thu Jun 10 2010 - 20:00:03 PDT
