Accueil > Publications > Recherche par années > Années 1990 > 1991

Briki, F ; Lavery, R ; Genest, D ; Ramstein, J

Modeling the b-DNA base pair opening reaction

Journal de Chimie Physique et de Physico-Chimie Biologique 88 (11-12) 2567-2572

par Administrateur - publié le

Abstract :

Molecular modelling has been used to study the opening of the central base pair of a B-DNA oligonucleotide (dA)5.(dT)5. In our model, opening occurs by rotating the bases around an axis passing through the centre of the sugar connected to the opening base and oriented perpendicularly to the plane of the base. The results of this study show that the opening energies obtained for a single base pair are compatible with the activation energies deduced from hydrogen exchange experiments. Studies of possible opening pathways show that many possibilities exist although there is an overall preference for opening towards the major groove. In addition, we have demonstrated that a coupling exists between opening and DNA bending : bending the double helix facilitates base pair opening and, conversely, opening a base pair bends DNA and increases its local flexibility. Finally, based on the opening energetics obtained, we have carried out a Brownian dynamics study of the opening kinetics which again leads to results in good correlation with experimental findings and indicates that the base pair opening reaction is of a stochastic nature.