Asymmetric base-pair opening drives helicase unwinding dynamics

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.

Directional translocation resistance of Zika xrRNA

“…The xrRNA structure was represented with SMOG. The model retains the full atomistic details and has been validated for various molecular systems, including nucleic acids [23][24][25][26]. SMOG employs a native-centric force field that allows us to highlight structure-dependent properties while filtering out details more related to sequence or specific RNA-protein interactions.…”

“…The absolute temperature was calibrated similarly to ref. [25] by matching the experimental condition that mechanical unfolding of RNA helices [44,45] occur at about 15pN at 300K, see Supplementary Methods and Supplementary Table 1.…”

Directional translocation resistance of Zika xrRNA

“…The latter fact also rules out the helical asymmetry of nucleic acids, see e.g., refs. 23 , 34 , as a cause for xrRNAs directional resistance.…”

“…The absolute temperature was calibrated similarly to ref. 23 by matching the experimental condition that mechanical unfolding of RNA helices 42 , 43 occur at about 15 pN at 300 K, see Supplementary Methods and Supplementary Table 1 .…”

delta-Melt: Nucleic acid conformational penalties from melting experiments

“…As an initial test, we used delta-Melt to measure the conformational penalty associated with opening Watson-Crick A-T base pairs (bps) in DNA. Base opening is the elementary step that drives melting and annealing of nucleic acids, and their unwinding by helicases 6 . Measurements of imino proton exchange rates 7 have shown that Watson-Crick A-T bps transiently open to form exceptionally low-populated (population~0.001%) and short-lived (lifetime~0.1 s) conformations (Fig.…”