Abstract
The opening of a Watson-Crick double helix is required for crucial cellular processes, including replication, repair, and transcription. It has long been assumed that RNA or DNA base pairs are broken by the concerted symmetric movement of complementary nucleobases. By analyzing thousands of base-pair opening and closing events from molecular simulations, here, we uncover a systematic stepwise process driven by the asymmetric flipping-out probability of paired nucleobases. We demonstrate experimentally that such asymmetry strongly biases the unwinding efficiency of DNA helicases toward substrates that bear highly dynamic nucleobases, such as pyrimidines, on the displaced strand. Duplex substrates with identical thermodynamic stability are thus shown to be more easily unwound from one side than the other, in a quantifiable and predictable manner. Our results indicate a possible layer of gene regulation coded in the direction-dependent unwindability of the double helix.
Highlights
| | | | double helix nucleic acids simulations experiments unwindability different set of steric and torsional constraints and approximates the biological process of helix opening by helicases, as suggested by X-ray crystallography [16, 21] and single-molecule experiments [19, 22, 23]
How is the entwined embrace of doublestranded nucleic acids formed or disrupted? How does the energetics underlying this process influence nucleic-acid processing machineries? By combining simulations and experiments, our work addresses these questions and reveals that asymmetric base-pair dynamics drives the stepwise separation of nucleic acid duplexes, predicts the unwinding efficiency of helicases, and intimately relates the intrinsic dynamics of base pairs to the enzymatic mechanism evolved for their opening
We reveal that the general unzipping model stating the unwinding preference of helicases solely dependent on the thermodynamic stability of the substrate should be amended to include both the directionality of the helicase and the strand-specific nucleobase dynamics of the double helix
Summary
| | | | double helix nucleic acids simulations experiments unwindability different set of steric and torsional constraints and approximates the biological process of helix opening by helicases, as suggested by X-ray crystallography [16, 21] and single-molecule experiments [19, 22, 23]. The separation of ds nucleic acids is assumed to follow the classical zipper model [24], where base-pair opening occurs as a concerted process with an equivalence (or symmetry) between 2 complementary nucleobases This assumption has been largely based on the difficulty to observe and characterize the “invisible” intermediate states—for instance, those ss/ds junctions with only 1 of the 2 nucleobases flipped out [25,26,27]—which are too few and whose duration is too short for experimental determination. Our data suggest a layer of regulation of the genetic material encoded in the “unwindability” of the double helix
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