Molecular Dynamics Simulation is done by CHARMM and Constant Force is applied on one atom each of the two terminal bases.
Hi Angana,
Single molecule experiments on G-quadruplex DNA, performed on optical tweezers platforms suggest forces in the 30-40 pN range, for telomeric G-quadruplex DNA disruption.
See this paper: Nat Chem. 2011 Aug 28;3(10):782-7. doi: 10.1038/nchem.1126.
Marco
Thank u so much for ur suggestion Marco. But what Im concerned about is during MD Simulation, Im using implicit water, i.e, dielectric=4, so in that case would this force be applicable. Thank u again
I unfortunately have no experience on MD simulation, I have suggested that paper in which you could have taken inspiration in terms of real forces measured in single molecule experiments, I am sorry not being able to help you further
Marco
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