Acta Pharm. 49 (1999) 237-255

First order elasticity in the superstructural transformations of DNAs

CLAUDIO ANSELMI¹,  GIANFRANCO BOCCHINFUSO¹,  PASQUALE de SANTIS^1*,   MARIO FUA²,   MARIA SAVINO², and ANITA SCIPIONI¹

¹Dipartimento di Chimica, Universita di Roma »La Sapienza«, Rome, Italy
²Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy

A theoretical model to predict intrinsic and induced superstructures of DNAs is presented. The intrinsic sequence-dependent superstructure was obtained by integrating local deviations from the canonical B-DNA of different dinucleotide steps. The induced superstructures were obtained by adopting the principle of minimum deformation energy evaluated in the Fourier space in the framework of first-order elasticity. The same bending and twisting elastic force constants were adopted independently of the sequence. The model works very satisfactorily in predicting gel electrophoresis retardation, thermodynamic constants of the sequence-dependent circularisation reaction, first writhing transitions as well as the nucleosome positioning of several DNA sequences.

Keywords: DNA curvature, electrophoretic retardation, circularisation, writhe transition, nucleosome positioning