Friday 26
Multiscale DNA modelling - from QM to coarse grained simulations

› 10:45 - 11:30 (45min)
DNA and its environment: a close look at ion binding
Richard Lavery  1@  , Marco Pasi, Pablo Dans, Modesto Orozco, Krystyna Zakrzewska, John Maddocks@
1 : Bases Moléculaires et Structurales des Systèmes Infectieux  (BMSSI)  -  Website
CNRS : UMR5086
IBCP, 7 passage du Vercors, 69367 Lyon -  France

Molecular dynamics simulations of DNA now easily reach the microsecond timescale and reflect the fact that DNA undergoes very significant thermal fluctuations at room temperature. These fluctuations make it difficult to follow what is happening in solution close to the solute molecule. To overcome this problem, we have recently developed an analysis technique using the instantaneous helical axis of the nucleic acid to convert ion or water positions into curvilinear helicoidal coordinates.This approach enables us to calculate ion populations and local ion molarities in well defined regions around DNA. The results of this analysis show that monovalent ions bind very selectively to DNA, in some cases with surprisingly high occupancies and with sequence selectivity which extends beyond base pairs or base pair steps. We have used this technique to show that ions are capable of triggering conformational changes in DNA and it seems likely that they can play a significant role in recognition processes.


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