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. 2020 Mar 17;7:39. doi: 10.3389/fmolb.2020.00039

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Copyright © 2020 Mitchell, Hsu, Medrano, Zewde, Narkhede and Palermo.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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(A) Conformations adopted by the RNA:DNA hybrid, in the presence of an on-target DNA (left), including base pair mismatches “mm” at PAM distal ends (center) and within the heteroduplex (right). (B) Minor groove width measured at different levels of the RNA:DNA hybrid (i.e., from base pair bp20 to bp9) in the systems including “mm” at PAM distal ends (top panel) and within the heteroduplex (bottom panel). Data are compared with the on-target system. (C) Each graph reports the probability distribution (as violin plot) of the Propeller Twist angle for each base pair (bp) from PAM distal ends (bp19 to bp17) up to the middle of the RNA:DNA hybrid (bp16 to bp13), computed along the dynamics of each simulated system (reported on the x-axis). Regions of major and minor distortions are highlighted using boxes.