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Biophys J, November 1999, p. 2366-2376, Vol. 77, No. 5

From Atomic to Mesoscopic Descriptions of the Internal Dynamics of DNA

N. Bruant,* D. Flatters,# R. Lavery,# and D. Genest*

 *Centre de Biophysique Moléculaire, CNRS UPR 4301 and the University of Orléans, 45071 Orléans, and  #Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 75005 Paris, France

An analysis of four 1-ns molecular dynamics trajectories for two different 15-bp oligonucleotides is presented. Our aim is to show which groups of atoms can be treated as rigid bodies within a bead representation of DNA, independently of the base sequence and for any conformations belonging to the A/B family. Five models with moderate intragroup deformations are proposed in which the groups are formed of atoms belonging to a single nucleotide or to a complementary nucleotide pair. The influence of group deformation in two of these models is studied using canonical correlation analysis, and it is shown that the internal DNA dynamics is indeed dominated by the rigid motion of the defined atom groups. Finally, using one of the models within a bead representation of duplex DNA makes it possible to obtain stretching, torsional, and bending rigidities in reasonable agreement with experiment but points to strongly correlated stretching motions.

Biophys J, November 1999, p. 2366-2376, Vol. 77, No. 5
© 1999 by the Biophysical Society   0006-3495/99/11/2366/11  $2.00


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Copyright © 1999 by the Biophysical Society.