DNA stretching and compression: large-scale simulations of double helical structures 1 1Edited by I. Tinoco

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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confidence: 99%

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

Wereszczynski

Andricioaei

2006

“…4D and SI Appendix, Materials and Methods). Interestingly, an all-atom, implicit-solvent model of dsDNA homopolymers found A-form dsDNA to unwind upon stretching whereas B-form dsDNA overwound when stretched close to its equilibrium conformation (47). Although these simulation results are in qualitative agreement with our findings for A-form dsRNA and B-form dsDNA, their simulation predicts un-and overwinding, respectively, by ∼3°per 0.1 nm, which corresponds to values of jDj ∼50, namely a factor of three to five larger in magnitude than the experimentally observed values for D RNA and D DNA .…”

Section: Discussionmentioning

confidence: 99%

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

Lipfert

Skinner

Keegstra

et al. 2014

175

258

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

“…The overstretching transition has been extensively studied; however, the nature of the overstretched state or states remains in dispute (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)15). Theoretical proposals of Lebrun and Lavery (16) have suggested that, because the base pairs in B-DNA are tilted with respect to the backbone, the nature of the overstretched structure would depend upon the ends to which force is applied.…”

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confidence: 99%

The structure of DNA overstretched from the 5′5′ ends differs from the structure of DNA overstretched from the 3′3′ ends

Danilowicz¹,

Limouse²,

Hatch³

et al. 2009

It has been suggested that the structure that results when doublestranded DNA (dsDNA) is pulled from the 3 3 ends differs from that which results when it is pulled from the 5 5 ends. In this work, we demonstrate, using phage dsDNA, that the overstretched states do indeed show different properties, suggesting that they correspond to different structures. For 3 3 pulling versus 5 5 pulling, the following differences are observed: (i) the forces at which half of the molecules in the ensemble have made a complete force-induced transition to single stranded DNA are 141 ؎ 3 pN and 122 ؎ 4 pN, respectively; (ii) the extension vs. force curve for overstretched DNA has a marked change in slope at 127 ؎ 3 pN for 3 3 and 110 ؎ 3 pN for 5 5 ; (iii) the hysteresis (H) in the extension vs. force curves at 150 mM NaCl is 0.3 ؎ 0.8 pN m for 3 3 versus 13 ؎ 8 pN for 5 5 ; and (iv) 3 3 and 5 5 molecules show different changes in hysteresis due to interactions with ␤-cyclodextrin, a molecule that is known to form stable host-guest complexes with rotated base pairs, and glyoxal that is known to bind stably to unpaired bases. These differences and additional findings are well-accommodated by the corresponding structures predicted on theoretical grounds.