SIMULATING A-TRACT DNA: THE INFLUENCE OF SUBSTATES AND THE MEASURE OF BENDING

F. Lankaš¹, J. Špačková², J. Šponer²

¹ Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, CZ-166 10 Prague

² Institute of Biophysics, Královopolská 135, CZ-612 65 Brno

A-tracts, or stretches of duplex DNA comprising at least four consecutive adenines or thymines without a TA step, exhibit special features in the context of the B-DNA conformational family. A-tracts embedded in a DNA sequence composed of G or C result in a structure bent by roughly 20 deg into the minor groove of the A-tract; moreover, both experiments and simulations suggest that they are exceptionally stiff and adopt a particular structure. Since their discovery more than 25 years ago [1], a large number of crystallographic [2], NMR [3], and other [4] experimental studies have been devoted to A-tracts, trying to decipher their structural features and in particular the origin of bending. Existing computational studies using atomistic molecular dynamics (MD) either include now obsolete force fields and trajectories too short by contemporary standards [5], or use restraints on the A-tract geometry [6]. With the emergence of the Amber parmbsc0 force field which fixes a fundamental deficiency of the previous parm94/99 versions (namely the irreversible flips in alpha/gamma backbone torsions resulting in the unwinding of the double helical structure in long simulations), the question arises as to how this new force field is able to reproduce A-tract bending and other features. We present the analysis of all-atom MD simulations of DNA oligomers containig the A-tract A₄T₄ sequence, and those containing the non-A-tract T₄A₄ , either as one copy or as two copies in phase. Each MD trajectory has been prolonged to 150 ns. In the course of the analysis, we confronted the problem of properly measuring the global bending of a DNA tract. We present a critical analysis of the existing methods and propose a new one, based on mathematically rigorous averaging of base-fixed coordinate frames. The study represents a stringent test of the reliability of the current Amber force field, and the proposed bending measurement method may be applied to other nucleic acids systems as well, for instance to ribosomal RNA motifs where the overall geometry plays an important functional role.

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