RE: terminal base pair opening

From: Guanglei Cui <>
Date: Mon 2 Apr 2001 09:27:19 -0400

    The terminal base pair opening isn't very frequent in explicit solvent
dynamics. However, I've see far more often opening of this type is implicit
solvent dynamics (Generalized Born). In explicit solvent dynamics, the
opening I've seen only involved the first terminal base pair. In GB, the
opening goes much deeper. The second one can be affected. In short time, the
opened base pairs can reform. So can the opened ones in explicit solvent
dynamics. I guess if the structure you are interested is not likely being
affected by the opening, it may be fairly safe not to use distance
restraints. This's just based on my experience.

Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790

-----Original Message-----
From: Peter Varnai []
Sent: Monday, April 02, 2001 8:20 AM
Subject: terminal base pair opening

Dear Amber users,

I wonder what people think of the terminal base
pair opening of short (e.g. 12mer) DNA sequences
in MD simulations at 300 K. Should it be prevented
by e.g. small distance constraints between H-bonded
atoms to mimic a normal stacking in a longer DNA
strech, or it would introduce a bigger artifact in
the model. Would this effect be significant 3-4 steps

Thanks for your comments.

Peter Varnai
Received on Mon Apr 02 2001 - 06:27:19 PDT
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