Abstract
Molecular modelling with the JUMNA program has been used to study the conformational and energetic aspects of base pair opening within a B-DNA double helix. Using new geometrical restraints, it has been possible to map base opening into the minor and major grooves of the double helix, without fixing an axis of rotation or the plane in which the base moves. The results show notably that minor groove opening is favoured by locally unwound DNA. Although the modelling is carried out with a simple distance-dependent dielectric function, the DelPhi program is also used to check that more realistic Poisson-Boltzmann electrostatics yields similar results.
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