ArticleThe journal of physical chemistry. B2012
Multiscale modeling of double-helical DNA and RNA: a unification through Lie groups.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- A Study on the Bending Stiffness of a New DNA Origami Nano-Joint.Molecular biotechnology · 2021Article
- Black-Scholes Theory and Diffusion Processes on the Cotangent Bundle of the Affine Group.Entropy (Basel, Switzerland) · 2020Article
- Elasticity as the Basis of Allostery in DNA.The journal of physical chemistry. B · 2019Article
- Simulation Assisted Analysis of the Intrinsic Stiffness for Short DNA Molecules Imaged with Scanning Atomic Force Microscopy.PloS one · 2015Article
- Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutSα-DNA recognition complex.Journal of biomolecular structure & dynamics · 2014Article
- Destabilization of the MutSα's protein-protein interface due to binding to the DNA adduct induced by anticancer agent carboplatin via molecular dynamics simulations.Journal of molecular modeling · 2013Article
- Conformational Modeling of Continuum Structures in Robotics and Structural Biology: A Review.Advanced robotics : the international journal of the Robotics Society of JapanArticle
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Authors and funding
8 authors.
Funding
Abstract
Several different mechanical models of double-helical nucleic-acid structures that have been presented in the literature are reviewed here together with a new analysis method that provides a reconciliation between these disparate models. In all cases, terminology and basic results from the theory of Lie groups are used to describe rigid-body motions in a coordinate-free way, and when necessary, coordinates are introduced in a way in which simple equations result. We consider double-helical DNAs and RNAs which, in their unstressed referential state, have backbones that are either straight, slightly precurved, or bent by the action of a protein or other bound molecule. At the coarsest level, we consider worm-like chains with anisotropic bending stiffness. Then, we show how bi-rod models converge to this for sufficiently long filament lengths. At a finer level, we examine elastic networks of rigid bases and show how these relate to the coarser models. Finally, we show how results from molecular dynamics simulation at full atomic resolution (which is the finest scale considered here) and AFM experimental measurements (which is at the coarsest scale) relate to these models.
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