AMBER Archive (2009)

Subject: Re: [AMBER] How to denature DNA

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Tue Sep 08 2009 - 11:46:51 CDT

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

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