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Dohnalova, Hana; Drsata, Tomas; Sponer, Jiri; Zacharias, Martin; Lipfert, Jan and Lankas, Filip (2020): Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation. In: Journal of Chemical Theory and Computation, Vol. 16, No. 4: pp. 2857-2863

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Abstract

Changes in the structure of double-stranded (ds) DNA with temperature affect processes in thermophilic organisms and are important for nanotechnological applications. Here we investigate temperature-dependent conformational changes of dsDNA at the scale of several helical turns and at the base pair step level, inferred from extensive all-atom molecular dynamics simulations of DNA at temperatures from 7 to 47 degrees C. Our results suggest that, contrary to twist, the overall bending of dsDNA without A-tracts depends only very weakly on temperature, due to the mutual compensation of directional local bends. Investigating DNA length as a function of temperature, we find that the sum of distances between base pair centers (the wire length) exhibits a large expansion coefficient of similar to 2 X 10(-4 )degrees C-1, similar to values reported for thermoplastic materials. However, the wire length increase with temperature is absorbed by expanding helix radius, so the length measured along the helical axis (the spring length) seems to suggest a very small negative thermal expansion coefficient. These compensatory mechanisms contribute to thermal stability of DNA structure on the biologically relevant scale of tens of base pairs and longer.

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