AMBER Archive (2009)

Subject: RE: [AMBER] How to denature DNA

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Tue Sep 08 2009 - 11:29:57 CDT

Dear Dr. Adrian !

Thank you for your reply !

I think i could not have communicated completely.

One can denature DNA as you said , AFM(atomic force microscopy ) and all will do .

what i meant to ask is suppose, I have a duplex and on applying considerable force
opposite to each other along the dna by pulling one atom at each strand so that the base pair got
broken and the strands goes away from each other.

Is it possible to do with amber !

regards
balaji.

> Date: Tue, 8 Sep 2009 10:04:30 -0400
> From: roitberg_at_qtp.ufl.edu
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] How to denature DNA
>
> Dear balaji,
>
> You are confusing a number of issues here.
> DNA can denature by a number of methods, 99% of which does not involve
> pulling anything.
> The usual methods involve raising the temperature, adding chemical
> denaturants, etc.
>
> Pulling DNA strands is a state of the art experimental technique, that
> probably has little to do with denaturation.
>
> Adrian
>
>
> balaji nagarajan wrote:
> > Dear Amber !
> >
> > I would like to denature the DNA,
> > is it possible to pull the DNA on both the strands
> > so that one can study how it denature.
> >
> > regards
> > balaji
> >
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>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project
> Department of Chemistry
>
> Senior Editor. Journal of Physical Chemistry
> American Chemical Society
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
>
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