AMBER Archive (2009)

Subject: Re: [AMBER] How to denature DNA

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Tue Sep 08 2009 - 12:12:00 CDT

Balaji,
That was, in some sense, the gist of my previous email.

If you cannot understand a flat well potential, then trying to pull DNA
might be a very hard project for you.

Have you ever used a flat well potential under nmr restraints in amber ?
  If not, please read the manual, or google flatwell restraints in amber.

Adrian

balaji nagarajan wrote:
>
> 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
>>>>>
>>>>> _________________________________________________________________
>>>>> One stop at MSN India to catch up with what’s hot in the world around you today
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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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>> --
>> 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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-- 
                            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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