AMBER Archive (2009)

Subject: RE: [AMBER] How to denature DNA

From: balaji nagarajan (balaji_sethu_at_hotmail.com)
Date: Tue Sep 08 2009 - 11:58:36 CDT

Dear Dr. Adrian !

 Thank you for the reply ,

I can not understand the flat restraint ..
if you can , could you explain me a little

regards
balaji

> Date: Tue, 8 Sep 2009 12:46:51 -0400
> From: roitberg_at_qtp.ufl.edu
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] How to denature DNA
>
> Balaji.
> all right, yes it is doable, however, unless you are a real expert in
> Amber, you really know DNA, and you are to study deeply what it means to
> apply "considerable force", I do not recommend you try.
>
> What you need to do is apply a flatwell potential restraint to the ends
> of DNA. You can have a moving center if you want to apply a constant
> velocity pull, or user the ends of the flatwell restraint to fake
> constant force pullings (Thanks to Dan Roe for this last insight!).
>
> Now, you must keep in mind that you will be pulling roughly 10^10 times
> faster than experimentalists would pull, so the interpretation of your
> data is not going to be trivial. There is something called the Bell
> model that might help you.
>
> Adrian
>
>
> balaji nagarajan wrote:
> > 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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> >
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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
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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