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Biophysical Journal 85:2872-2883 (2003)
© 2003 The Biophysical Society

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

Filip Lankas * {dagger}, Jirí Sponer {dagger} {ddagger}, Jörg Langowski * and Thomas E. Cheatham, III §

* German Cancer Research Centre, 69120 Heidelberg, Germany; {dagger} J. Heyrovsky Institute of Physical Chemistry and Centre for Complex Molecular Systems and Biomolecules, 182 23 Prague, Czech Republic; {ddagger} Institute of Biophysics, Academy of Sciences of the Czech Republic, 612 65 Brno, Czech Republic; and § Departments of Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112 USA

Correspondence: Address reprint requests to Filip Lankas, E-mail: fillip.lankas{at}jh-inst.cas.cz.

The sequence-dependent DNA deformability at the basepair step level was investigated using large-scale atomic resolution molecular dynamics simulation of two 18-bp DNA oligomers: d(GCCTATAAACGCCTATAA) and d(CTAGGTGGATGACTCATT). From an analysis of the structural fluctuations, the harmonic potential energy functions for all 10 unique steps with respect to the six step parameters have been evaluated. In the case of roll, three distinct groups of steps have been identified: the flexible pyrimidine-purine (YR) steps, intermediate purine-purine (RR), and stiff purine-pyrimidine (RY). The YR steps appear to be the most flexible in tilt and partially in twist. Increasing stiffness from YR through RR to RY was observed for rise, whereas shift and slide lack simple trends. A proposed measure of the relative importance of couplings identifies the slide-rise, twist-roll, and twist-slide couplings to play a major role. The force constants obtained are of similar magnitudes to those based on a crystallographic ensemble. However, the current data have a less complicated and less pronounced sequence dependence. A correlation analysis reveals concerted motions of neighboring steps and thus exposes limitations in the dinucleotide model. The comparison of DNA deformability from this and other studies with recent quantum-chemical stacking energy calculations suggests poor correlation between the stacking and flexibility.




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