Literature DB >> 22658779

Recent developments in single-molecule DNA mechanics.

Zev Bryant1, Florian C Oberstrass, Aakash Basu.   

Abstract

Over the past two decades, measurements on individual stretched and twisted DNA molecules have helped define the basic elastic properties of the double helix and enabled real-time functional assays of DNA-associated molecular machines. Recently, new magnetic tweezers approaches for simultaneously measuring freely fluctuating twist and extension have begun to shed light on the structural dynamics of large nucleoprotein complexes. Related technical advances have facilitated direct measurements of DNA torque, contributing to a better understanding of abrupt structural transitions in mechanically stressed DNA. The new measurements have also been exploited in studies that hint at a developing synergistic relationship between single-molecule manipulation and structural DNA nanotechnology.
Copyright © 2012 Elsevier Ltd. All rights reserved.

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Year:  2012        PMID: 22658779      PMCID: PMC3726534          DOI: 10.1016/j.sbi.2012.04.007

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  52 in total

1.  Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA.

Authors:  Florian C Oberstrass; Louis E Fernandes; Zev Bryant
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-02       Impact factor: 11.205

2.  Energetics at the DNA supercoiling transition.

Authors:  Hergen Brutzer; Nicholas Luzzietti; Daniel Klaue; Ralf Seidel
Journal:  Biophys J       Date:  2010-04-07       Impact factor: 4.033

3.  Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments.

Authors:  Jan Lipfert; Jacob W J Kerssemakers; Tessa Jager; Nynke H Dekker
Journal:  Nat Methods       Date:  2010-10-17       Impact factor: 28.547

4.  Overstretching DNA at 65 pN does not require peeling from free ends or nicks.

Authors:  D Hern Paik; Thomas T Perkins
Journal:  J Am Chem Soc       Date:  2011-01-05       Impact factor: 15.419

5.  Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases.

Authors:  Sung Chul Ha; Ky Lowenhaupt; Alexander Rich; Yang-Gyun Kim; Kyeong Kyu Kim
Journal:  Nature       Date:  2005-10-20       Impact factor: 49.962

6.  Magnetic tweezers measurement of single molecule torque.

Authors:  Alfredo Celedon; Ilana M Nodelman; Bridget Wildt; Rohit Dewan; Peter Searson; Denis Wirtz; Gregory D Bowman; Sean X Sun
Journal:  Nano Lett       Date:  2009-04       Impact factor: 11.189

7.  Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules.

Authors:  Scott Forth; Christopher Deufel; Maxim Y Sheinin; Bryan Daniels; James P Sethna; Michelle D Wang
Journal:  Phys Rev Lett       Date:  2008-04-08       Impact factor: 9.161

8.  The folding cooperativity of a protein is controlled by its chain topology.

Authors:  Elizabeth A Shank; Ciro Cecconi; Jesse W Dill; Susan Marqusee; Carlos Bustamante
Journal:  Nature       Date:  2010-05-23       Impact factor: 49.962

9.  Direct observation of the binding state of the kinesin head to the microtubule.

Authors:  Nicholas R Guydosh; Steven M Block
Journal:  Nature       Date:  2009-08-19       Impact factor: 49.962

10.  Underwound DNA under tension: structure, elasticity, and sequence-dependent behaviors.

Authors:  Maxim Y Sheinin; Scott Forth; John F Marko; Michelle D Wang
Journal:  Phys Rev Lett       Date:  2011-09-01       Impact factor: 9.161

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  27 in total

1.  Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA.

Authors:  Jan Lipfert; Gary M Skinner; Johannes M Keegstra; Toivo Hensgens; Tessa Jager; David Dulin; Mariana Köber; Zhongbo Yu; Serge P Donkers; Fang-Chieh Chou; Rhiju Das; Nynke H Dekker
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-13       Impact factor: 11.205

2.  Thermodynamics of long supercoiled molecules: insights from highly efficient Monte Carlo simulations.

Authors:  Thibaut Lepage; François Képès; Ivan Junier
Journal:  Biophys J       Date:  2015-07-07       Impact factor: 4.033

3.  Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond.

Authors:  Stefanos K Nomidis; Enrico Skoruppa; Enrico Carlon; John F Marko
Journal:  Phys Rev E       Date:  2019-03       Impact factor: 2.529

4.  DNA elasticity from coarse-grained simulations: The effect of groove asymmetry.

Authors:  Enrico Skoruppa; Michiel Laleman; Stefanos K Nomidis; Enrico Carlon
Journal:  J Chem Phys       Date:  2017-06-07       Impact factor: 3.488

Review 5.  Supercoiling biases the formation of loops involved in gene regulation.

Authors:  Laura Finzi; David Dunlap
Journal:  Biophys Rev       Date:  2016-07-05

6.  Dynamics of active semiflexible polymers.

Authors:  A Ghosh; N S Gov
Journal:  Biophys J       Date:  2014-09-02       Impact factor: 4.033

7.  Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis.

Authors:  Korbinian Liebl; Tomas Drsata; Filip Lankas; Jan Lipfert; Martin Zacharias
Journal:  Nucleic Acids Res       Date:  2015-10-12       Impact factor: 16.971

8.  Multimodal Measurements of Single-Molecule Dynamics Using FluoRBT.

Authors:  Ivan E Ivanov; Paul Lebel; Florian C Oberstrass; Charles H Starr; Angelica C Parente; Athena Ierokomos; Zev Bryant
Journal:  Biophys J       Date:  2017-12-13       Impact factor: 4.033

9.  Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance.

Authors:  Maarten M van Oene; Seungkyu Ha; Tessa Jager; Mina Lee; Francesco Pedaci; Jan Lipfert; Nynke H Dekker
Journal:  Biophys J       Date:  2018-04-24       Impact factor: 4.033

10.  Torque spectroscopy of DNA: base-pair stability, boundary effects, backbending, and breathing dynamics.

Authors:  Florian C Oberstrass; Louis E Fernandes; Paul Lebel; Zev Bryant
Journal:  Phys Rev Lett       Date:  2013-04-25       Impact factor: 9.161

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