AMBER Archive (2006)

Subject: Re: AMBER: double stranded polyribocytidylic acid

From: Jiri Sponer (
Date: Tue Feb 14 2006 - 06:56:07 CST

Dear Kateryna,
I would tell it is quite possible, check the experimental
papers on i-DNA, whether there are any hints.

The charge-charge repulsion between multiple consecutive
protonated cytosines is a big problem. I-DNa is capable
to overcome this repulsion due to its overall topology,
but the same interaction in C+.GC triplexes is very unstable.
Each NA form has a different degree of solvent screening, I
would tell for duplex it is not going to be easy to stabilize
consecutive protonated pairs.
The gas phase stacking would be +30 kcal/mol.
i-DNA is unique in doing so, to my knowledge the only nucleic
acid form which has repulsive intrinsic stacking.

If your model shows such instability when attempting MD,
then the start is most likely not
correct. I does not ultimately rule out that there exist
a duplex, but likely would have to be markedly different from
that proposed.

All the best Jiri

> Dear Dr. Sponer,
> Thank you very much for you prompt response.
> So can I conclude that poly(rC) doesn't exist in the double stranded
> form?
> > There is i-RNA too,
> > The RNA i-motif
> > Snoussi K et al
> I haven't heard of this work earlier. And therefore thought that
> only DNA can form i-motif (this was the opinion of my more experienced
> colleagues).
> I've tryed to model tetrameric i-motif RNA structure (modifying
> 190d.pdb). And in this case the initial stucture remained intact
> during the minimization. As for the 100ps md simulation in the implicit
> solvent, the planarity of bases was coserved, though one of the narrow
> grooves became significantly wider compared to the initial structure.
> ********************************************
> Kateryna Miroshnychenko
> post-graduate student
> Department of Biological Physics,
> Institute of Radiophysics and Electronics,
> National Academy of Sciences of Ukraine,
> 12, Proskura st., Kharkiv, 61085, Ukraine
> ********************************************
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