SEARCH FOR RIGID SUB DOMAINS IN DNA FROM MOLECULAR-DYNAMICS SIMULATIONS

A strategy is presented for searching which atoms can be regrouped wit hin rigid sub-units during the time course of Molecular Dynamics simul ations of biopolymers. The root mean square fluctuations of the intera tomic distances are used as a criterion. The number of rigid sub-units which are found depends on the tolerance r(c) for the definition of a rigid body, i.e. until which value the fluctuations can be neglected. The method is applied to two self-complementary oligonucleotides belo nging to the B-form family which give identical results. With r(c)=0.0 27 nm each nucleotide may be described as 3 rigid sub-units: the sugar ring, the base and the backbone (PO4 + C5' atoms). With r(c)=0.01 nm, the same sub-units are obtained except that C5' can no more be regrou ped with the PO4 atoms. It is shown that the variation of the coulombi c potential owing to the deformation of the sub-units during the time course of the simulation is on the same order of magnitude as the inac curacy due to the choice of the force field parameters.