[gmx-users] Intercalation DNA-Ethidium bromide

Paulo Netz paulo.netz at gmail.com
Sun Sep 30 03:39:15 CEST 2012

Dear Hovakim

Actually it is possible that the ethidium bromide is
indeed intercalating in the DNA, because this is
expected to happen (experimentally)  but if you really
see the intercalation, it could be just luck. The time
scale needed, in order that such even happens in
classical molecular dynamics simulations, is
usually very large. Nevertheless, the presence of
intercalation could be easily checked by visual
inspection of the structures and by looking at the
values of some key base-pair step parameters,
such as rise and twist.  In my opinion, it is better
to generate an artificial gap in the DNA structure,
in order to sample the intercalation binding mode
as a reasonable starting point for MD simulations.

Best regards

Paulo Netz

On Thu, Sep 27, 2012 at 3:15 AM, Hovakim Grabski
<hovakim_grabski at yahoo.com>wrote:

> Dear Gromacs users,
> I've been running several simulations involving 26 base pairs B-DNA  and
> ethidium bromide.
> I used Autodock vina for finding inital binding sites and found one in the
> small groove.
> After that I ran a simulation of 14 ns.
> When I check the rmsd of Ethidium Bromide,there's a sudden change.
> Is there any chance I could see intercalation?
> P.S.  Or I should create an artifical gap between dna bases and then set
> up a simulation?
> Thanks in advance,
> Best regards,
> Hovakim Grabski
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