Deciphering the mechanical properties of <scp>B‐DNA</scp> duplex

Dohnalová, Hana; Lankaš, Filip

doi:10.1002/wcms.1575

Cited by 19 publications

(33 citation statements)

References 271 publications

(696 reference statements)

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“…denoting equilibrium averages, so that ∆ n = 0. Small deformations from equilibrium are usually described within the harmonic approximation 2 , with an energy given by…”

Section: Introductionmentioning

confidence: 99%

Mechanical properties of nucleic acids and the non-local twistable wormlike chain model

Segers

Voorspoels

Sakaue

et al. 2022

The Journal of Chemical Physics

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We investigate the mechanical properties of double stranded RNA by means of all-atom simulations and compare its elastic behavior to that of DNA. Differently from DNA, which is characterized by a strong coupling between twist and roll degrees of freedom, such coupling is very weak in RNA. Both nucleic acids are characterized by couplings between distal sites, i.e.\ by interactions that go beyond nearest neighbors. These non-local couplings, both in RNA and DNA, are strong for tilt and twist degrees of freedom and weak for roll. We introduce and analyze a simple double stranded polymer model which clarifies the origin of the distal couplings. Overall, our results indicate that nucleic acid mechanics is well-described by a non-local Twistable Worm Like Chain (nlTWLC). Differently from its local counterpart, the nlTWLC is characterized by a length-scale-dependent elasticity: nucleic acids are mechanically softer at the scale of a few base pairs as compared to an asymptotic stiffer behavior.

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“…denoting equilibrium averages, so that ∆ n = 0. Small deformations from equilibrium are usually described within the harmonic approximation 2 , with an energy given by…”

Section: Introductionmentioning

confidence: 99%

Mechanical properties of nucleic acids and the non-local twistable wormlike chain model

Segers

Voorspoels

Sakaue

et al. 2022

The Journal of Chemical Physics

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“…MD simulations are widely used to study the structure and dynamics of dsDNA and other nucleic acids. It is possible to reproduce the dynamics and deformability of B-DNA (in also other regular forms of DNA) in quite good agreement with available experimental data. − However, so far, only very few simulation studies on ssDNA or folding of DNA structural motifs and on the process of dsDNA structure formation have been performed. An important prerequisite for successful simulations of dsDNA formation but also folding of more complicated DNA structures is a realistic description of nearest-neighbor effects in the underlying force field.…”

Section: Introductionmentioning

confidence: 64%

Nearest-Neighbor dsDNA Stability Analysis Using Alchemical Free-Energy Simulations

Rieger

Zacharias

2022

J. Phys. Chem. B

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The thermodynamic stability of double-stranded (ds)DNA depends on its sequence. It is influenced by the base pairing and stacking with neighboring bases along DNA molecules. Semiempirical schemes are available that allow us to predict the thermodynamic stability of DNA sequences based on empirically derived nearest-neighbor contributions of base pairs formed in the context of all possible nearest-neighbor base pairs. Current molecular dynamics (MD) simulations allow one to simulate the dynamics of DNA molecules in good agreement with experimentally obtained structures and available data on conformational flexibility. However, the suitability of current force field methods to reproduce dsDNA stability and its sequence dependence has been much less well tested. We have employed alchemical free-energy simulations of whole base pair transversions in dsDNA and in unbound single-stranded partner molecules. Such transversions change the sequence context but not the nucleotide content or base pairing in dsDNA and allow a direct comparison with the empirical nearest-neighbor dsDNA stability model. For the alchemical free-energy changes in the unbound single-stranded (ss)DNA partner molecules, we tested different setups assuming either complete unstacking or unrestrained simulations with partial stacking in the unbound ssDNA. The free-energy simulations predicted nearest-neighbor effects of similar magnitude, as observed experimentally but showed overall limited correlation with experimental data. An inaccurate description of stacking interactions and other possible reasons such as the neglect of electronic polarization effects are discussed. The results indicate the need to improve the realistic description of stacking interactions in current molecular mechanic force fields.

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“…Recently and thanks to the effort of the community, MD models has proven also powerful in quantitatively reproducing the conformations dynamics and mechanical response of DNA and RNA [65,66,67,15,68,69,70,71] (see section 3). This section shows how MD provides molecular insight into the interactions of RNA with ions.…”

Section: Rna Electrostatics At the Atomic Level: The Importance Of Th...mentioning

confidence: 99%

RNA multiscale simulations as an interplay of electrostatic, mechanical properties, and structures inside viruses

Cruz-León

Assenza

Poblete

et al. 2023

Preprint

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Multiscale simulations have broadened our understanding of RNA structure and function. Various methodologies have enabled the quantification of electrostatic and mechanical interactions of RNA at the nanometer scale. Atom-by-atom simulations, coarse-grained strategies, and continuum models of RNA and its environment provide physical insight and allow to interpret diverse experiments in a systematic way. In this chapter, we present and discuss recent advances in a set of methods to study nucleic acids at different scales. In particular, we introduce details of their parameterization, recent applications, and current limitations. We discuss the interaction of the proteinacous virus capsid, RNA with substrates, compare the properties of RNA and DNA and their interaction with the environment, and analyze the application of these methods to reconstruct the structure of the virus genome structure. Finally, the last lines are dedicated to future developments and challenges ahead.

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Deciphering the mechanical properties of B‐DNA duplex

Cited by 19 publications

References 271 publications

Mechanical properties of nucleic acids and the non-local twistable wormlike chain model

Mechanical properties of nucleic acids and the non-local twistable wormlike chain model

Nearest-Neighbor dsDNA Stability Analysis Using Alchemical Free-Energy Simulations

RNA multiscale simulations as an interplay of electrostatic, mechanical properties, and structures inside viruses

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