Literature DB >> 24843131

How molecular knots can pass through each other.

Benjamin Trefz1, Jonathan Siebert2, Peter Virnau3.   

Abstract

We propose a mechanism in which two molecular knots pass through each other and swap positions along a polymer strand. Associated free energy barriers in our simulations only amount to a few kBT, which may enable the interchange of knots on a single DNA strand.

Entities:  

Keywords:  diffusion; molecular dynamics

Mesh：

Substances：

Year:  2014        PMID： 24843131      PMCID： PMC4050568          DOI： 10.1073/pnas.1319376111

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  28 in total

1.  A deeply knotted protein structure and how it might fold.

Authors:  W R Taylor
Journal:  Nature       Date:  2000-08-24       Impact factor: 49.962

2.  Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. I. Statics.

Authors:  Jonathan D Halverson; Won Bo Lee; Gary S Grest; Alexander Y Grosberg; Kurt Kremer
Journal:  J Chem Phys       Date:  2011-05-28       Impact factor: 3.488

Review 3.  Biopolymer organization upon confinement.

Authors:  D Marenduzzo; C Micheletti; E Orlandini
Journal:  J Phys Condens Matter       Date:  2010-06-28       Impact factor: 2.333

4.  Statistical mechanics of supercoils and the torsional stiffness of the DNA double helix.

Authors:  A V Vologodskii; V V Anshelevich; A V Lukashin; M D Frank-Kamenetskii
Journal:  Nature       Date:  1979-07-26       Impact factor: 49.962

5.  Knotting of a DNA chain during ring closure.

Authors:  S Y Shaw; J C Wang
Journal:  Science       Date:  1993-04-23       Impact factor: 47.728

6.  Influence of a knot on the strength of a polymer strand.

Authors:  A M Saitta; P D Soper; E Wasserman; M L Klein
Journal:  Nature       Date:  1999-05-06       Impact factor: 49.962

7.  Knotted vs. unknotted proteins: evidence of knot-promoting loops.

Authors:  Raffaello Potestio; Cristian Micheletti; Henri Orland
Journal:  PLoS Comput Biol       Date:  2010-07-29       Impact factor: 4.475

Review 8.  The potential and challenges of nanopore sequencing.

Authors:  Daniel Branton; David W Deamer; Andre Marziali; Hagan Bayley; Steven A Benner; Thomas Butler; Massimiliano Di Ventra; Slaven Garaj; Andrew Hibbs; Xiaohua Huang; Stevan B Jovanovich; Predrag S Krstic; Stuart Lindsay; Xinsheng Sean Ling; Carlos H Mastrangelo; Amit Meller; John S Oliver; Yuriy V Pershin; J Michael Ramsey; Robert Riehn; Gautam V Soni; Vincent Tabard-Cossa; Meni Wanunu; Matthew Wiggin; Jeffery A Schloss
Journal:  Nat Biotechnol       Date:  2008-10       Impact factor: 54.908

9.  Knot-controlled ejection of a polymer from a virus capsid.

Authors:  Richard Matthews; A A Louis; J M Yeomans
Journal:  Phys Rev Lett       Date:  2009-02-23       Impact factor: 9.161

10.  Statistics of knots, geometry of conformations, and evolution of proteins.

Authors:  Rhonald C Lua; Alexander Y Grosberg
Journal:  PLoS Comput Biol       Date:  2006-05-19       Impact factor: 4.475
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  8 in total

1.  Simulations of knotting of DNA during genome mapping.

Authors:  Aashish Jain; Kevin D Dorfman
Journal:  Biomicrofluidics       Date:  2017-04-11       Impact factor: 2.800

2.  Enhanced electrostatic force microscopy reveals higher-order DNA looping mediated by the telomeric protein TRF2.

Authors:  Parminder Kaur; Dong Wu; Jiangguo Lin; Preston Countryman; Kira C Bradford; Dorothy A Erie; Robert Riehn; Patricia L Opresko; Hong Wang
Journal:  Sci Rep       Date:  2016-02-09       Impact factor: 4.379

3.  A nanofluidic knot factory based on compression of single DNA in nanochannels.

Authors:  Susan Amin; Ahmed Khorshid; Lili Zeng; Philip Zimny; Walter Reisner
Journal:  Nat Commun       Date:  2018-04-17       Impact factor: 14.919

4.  Securing a Supramolecular Architecture by Tying a Stopper Knot.

Authors:  David A Leigh; Lucian Pirvu; Fredrik Schaufelberger; Daniel J Tetlow; Liang Zhang
Journal:  Angew Chem Int Ed Engl       Date:  2018-05-27       Impact factor: 15.336

5.  Complex DNA knots detected with a nanopore sensor.

Authors:  Rajesh Kumar Sharma; Ishita Agrawal; Liang Dai; Patrick S Doyle; Slaven Garaj
Journal:  Nat Commun       Date:  2019-10-02       Impact factor: 14.919

6.  Investigation of Ring and Star Polymers in Confined Geometries: Theory and Simulations.

Authors:  Joanna Halun; Pawel Karbowniczek; Piotr Kuterba; Zoriana Danel
Journal:  Entropy (Basel)       Date:  2021-02-19       Impact factor: 2.738

7.  Knot formation of dsDNA pushed inside a nanochannel.

Authors:  Jan Rothörl; Sarah Wettermann; Peter Virnau; Aniket Bhattacharya
Journal:  Sci Rep       Date:  2022-03-29       Impact factor: 4.996

8.  Epigenetic Transitions and Knotted Solitons in Stretched Chromatin.

Authors:  D Michieletto; E Orlandini; D Marenduzzo
Journal:  Sci Rep       Date:  2017-11-07       Impact factor: 4.379
  8 in total

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