DNA and low pH

From: Gaurav Sharma (sharma_at_coe.neu.edu)
Date: Wed Jan 31 2007 - 15:06:46 CST

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Hi All,

I want to study DNA-protein interaction at low pH.

For protein I can use the protonated forms of His, Glu and Asp but I am
not sure what changes to make in the dna structure to simulate low pH.
Is the negative charge on the dna partially neutralized at low pH (~4)?
If yes, how can I simulate it using NAMD?

Any help is appreciated.

Thanks,
Gaurav

-- 
Gaurav Sharma
Computational BioNano Robotics Lab
Northeastern University
Boston, MA - 02115
Tel: 617-373-2970

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