2021
DOI: 10.1016/j.bpj.2020.11.1484
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Supercoiling and Looping Promote DNA Base Accessibility and Coordination among Distant Sites

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“…Reiloff et al carried out coarse-grained MC simulations to show that the minimum size of stable DNA bubbles ranges from 12 to 20 bp and also explains the experimental observations of Zocchi and co-workers . Recently, Fogg et al studied the effect of supercoiling in DNA minicircles (336 BP long) and found that mechanical stress generated by negative supercoiling could disrupt BPs . Earlier atomistic simulations by Mitchell et al on small supercoiled stressed DNA minicircles revealed two distinct behaviors: (a) DNA writhing and denaturation induced by positive supercoiling and (b) kink and bubble formation induced by negative supercoiling. , Wong and Pettitt decoded the mechanism of DNA melting from 100 ns-long MD simulations of a 12 BP dsDNA at 400 K .…”
Section: Introductionmentioning
confidence: 94%
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“…Reiloff et al carried out coarse-grained MC simulations to show that the minimum size of stable DNA bubbles ranges from 12 to 20 bp and also explains the experimental observations of Zocchi and co-workers . Recently, Fogg et al studied the effect of supercoiling in DNA minicircles (336 BP long) and found that mechanical stress generated by negative supercoiling could disrupt BPs . Earlier atomistic simulations by Mitchell et al on small supercoiled stressed DNA minicircles revealed two distinct behaviors: (a) DNA writhing and denaturation induced by positive supercoiling and (b) kink and bubble formation induced by negative supercoiling. , Wong and Pettitt decoded the mechanism of DNA melting from 100 ns-long MD simulations of a 12 BP dsDNA at 400 K .…”
Section: Introductionmentioning
confidence: 94%
“…19 Recently, Fogg et al studied the effect of supercoiling in DNA minicircles (336 BP long) and found that mechanical stress generated by negative supercoiling could disrupt BPs. 20 Earlier atomistic simulations by Mitchell et al on small supercoiled stressed DNA minicircles revealed two distinct behaviors: (a) DNA writhing and denaturation induced by positive supercoiling and (b) kink and bubble formation induced by negative supercoiling. 21,22 Wong and Pettitt decoded the mechanism of DNA melting from 100 nslong MD simulations of a 12 BP dsDNA at 400 K. 23 They observed fraying from the ends accompanied by peeling of the two strands that eventually led to melting.…”
Section: Introductionmentioning
confidence: 99%