Wringing Out DNA

Lionnet, Timothée; Joubaud, Sylvain; Lavery, Richard; Bensimon, David; Croquette, Vincent

doi:10.1103/physrevlett.96.178102

Cited by 158 publications

(182 citation statements)

References 37 publications

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“…It is worth noting that in the region near the initial B-DNA structure ( Ͼ 9.5 Å), for which DNA is still in the entropic regime (F Յ 10 pN), we were also able to calculate (see supporting information for details) a twist͞stretch coupling constant of Ϫ15 nm. This finding agrees, both in sign and absolute value, with recent single molecule experiments indicating that, near the B form of DNA, an increase in twist leads to an increase in extension (33,34).…”

Section: Equilibrium Calculations Free Energy and Equilibrium Forces supporting

confidence: 80%

“…The calculation of the free energy profile in the vicinity of B-DNA has additionally provided an equilibrium twist-elongation dependence (see supporting information) that enabled the calculation, in the low-twist limit, of a negative twist-stretch coupling constant of Ϫ15 nm, in accord with recent experiments (33,34).…”

Section: Concluding Discussionmentioning

confidence: 55%

“…This is not totally unexpected, given twist-stretch coupling in DNA (33,34,38,39), and is in accord with the fact that stretching longitudinally undertwisted DNA induces a flipping out of bases that can activate homologous pairing in physiological conditions (15).…”

Section: Concluding Discussionmentioning

confidence: 62%

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On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension

Wereszczynski

Andricioaei

2006

Proc. Natl. Acad. Sci. U.S.A.

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A precise understanding of the flexibility of double stranded nucleic acids and the nature of their deformed conformations induced by external forces is important for a wide range of biological processes including transcriptional regulation, supercoil and catenane removal, and site-specific recombination. We present, at atomic resolution, a simulation of the dynamics involved in the transitions from B-DNA and A-RNA to Pauling (P) forms and to denatured states driven by application of external torque and tension. We then calculate the free energy profile along a B-to P-transition coordinate and from it, compute a reversible pathway, i.e., an isotherm of tension and torque pairs required to maintain P-DNA in equilibrium. The reversible isotherm maps correctly onto a phase diagram derived from single molecule experiments, and yields values of elongation, twist, and twist-stretch coupling in agreement with measured values. We also show that configurational entropy compensates significantly for the large electrostatic energy increase due to closer-packed P backbones. A similar set of simulations applied to RNA are used to predict a novel structure, P-RNA, with its associated free energy, equilibrium tension, torque and structural parameters, and to assign the location, on the phase-diagram,

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Section: Equilibrium Calculations Free Energy and Equilibrium Forces supporting

confidence: 80%

Section: Concluding Discussionmentioning

confidence: 55%

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On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension

Wereszczynski

Andricioaei

2006

Proc. Natl. Acad. Sci. U.S.A.

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“…4 B and C), in good agreement with previous measurements (38)(39)(40)(41). Our measurements suggest that dsRNA has a positive twist-stretch coupling equal to D RNA = -S RNA ·(dΔL/dN) RNA /(2π·k B T) = +11.5 ± 3.3 (assuming S RNA = 350 pN; SI Appendix, Materials and Methods), in contrast to the negative twist-stretch coupling of dsDNA (38)(39)(40)(41), D DNA = -17 ± 5.…”

Section: Resultssupporting

confidence: 82%

“…The linear elastic rod model has a fourth parameter, D, that describes the coupling between twist and stretch. We measured the twist-stretch coupling for dsRNA by monitoring changes in the extension upon over-and underwinding while holding the molecule at constant stretching forces that are large enough to suppress bending and writhe fluctuations (38,39) (Fig. 4A).…”

Section: Resultsmentioning

confidence: 99%

Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA

Lipfert

Skinner

Keegstra

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

174

258

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RNA plays myriad roles in the transmission and regulation of genetic information that are fundamentally constrained by its mechanical properties, including the elasticity and conformational transitions of the double-stranded (dsRNA) form. Although double-stranded DNA (dsDNA) mechanics have been dissected with exquisite precision, much less is known about dsRNA. Here we present a comprehensive characterization of dsRNA under external forces and torques using magnetic tweezers. We find that dsRNA has a forcetorque phase diagram similar to that of dsDNA, including plectoneme formation, melting of the double helix induced by torque, a highly overwound state termed "P-RNA," and a highly underwound, left-handed state denoted "L-RNA." Beyond these similarities, our experiments reveal two unexpected behaviors of dsRNA: Unlike dsDNA, dsRNA shortens upon overwinding, and its characteristic transition rate at the plectonemic buckling transition is two orders of magnitude slower than for dsDNA. Our results challenge current models of nucleic acid mechanics, provide a baseline for modeling RNAs in biological contexts, and pave the way for new classes of magnetic tweezers experiments to dissect the role of twist and torque for RNA-protein interactions at the single-molecule level.RNA | nucleic acids | magnetic tweezers | force | torque

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