Literature DB >> 11031608

Tightness of random knotting.

V Katritch1, W K Olson, A Vologodskii, J Dubochet, A Stasiak.   

Abstract

Long polymers in solution frequently adopt knotted configurations. To understand the physical properties of knotted polymers, it is important to find out whether the knots formed at thermodynamic equilibrium are spread over the whole polymer chain or rather are localized as tight knots. We present here a method to analyze the knottedness of short linear portions of simulated random chains. Using this method, we observe that knot-determining domains are usually very tight, so that, for example, the preferred size of the trefoil-determining portions of knotted polymer chains corresponds to just seven freely jointed segments.

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Year:  2000        PMID: 11031608     DOI: 10.1103/physreve.61.5545

Source DB:  PubMed          Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics        ISSN: 1063-651X


  22 in total

1.  Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots.

Authors:  Alessandro Flammini; Amos Maritan; Andrzej Stasiak
Journal:  Biophys J       Date:  2004-08-23       Impact factor: 4.033

2.  Topologically driven swelling of a polymer loop.

Authors:  Nathan T Moore; Rhonald C Lua; Alexander Y Grosberg
Journal:  Proc Natl Acad Sci U S A       Date:  2004-08-31       Impact factor: 11.205

3.  Conservation of complex knotting and slipknotting patterns in proteins.

Authors:  Joanna I Sułkowska; Eric J Rawdon; Kenneth C Millett; Jose N Onuchic; Andrzej Stasiak
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-08       Impact factor: 11.205

4.  DNA knots reveal a chiral organization of DNA in phage capsids.

Authors:  Javier Arsuaga; Mariel Vazquez; Paul McGuirk; Sonia Trigueros; De Witt Sumners; Joaquim Roca
Journal:  Proc Natl Acad Sci U S A       Date:  2005-06-15       Impact factor: 11.205

5.  Scaling behavior of random knots.

Authors:  Akos Dobay; Jacques Dubochet; Kenneth Millett; Pierre-Edouard Sottas; Andrzej Stasiak
Journal:  Proc Natl Acad Sci U S A       Date:  2003-04-29       Impact factor: 11.205

6.  Simulations of knotting in confined circular DNA.

Authors:  C Micheletti; D Marenduzzo; E Orlandini; D W Sumners
Journal:  Biophys J       Date:  2008-07-11       Impact factor: 4.033

7.  Tightening of DNA knots by supercoiling facilitates their unknotting by type II DNA topoisomerases.

Authors:  Guillaume Witz; Giovanni Dietler; Andrzej Stasiak
Journal:  Proc Natl Acad Sci U S A       Date:  2011-02-14       Impact factor: 11.205

8.  How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation.

Authors:  Eric J Rawdon; Julien Dorier; Dusan Racko; Kenneth C Millett; Andrzej Stasiak
Journal:  Nucleic Acids Res       Date:  2016-04-22       Impact factor: 16.971

9.  Sequence-specific size, structure, and stability of tight protein knots.

Authors:  Joachim Dzubiella
Journal:  Biophys J       Date:  2009-02       Impact factor: 4.033

Review 10.  Theoretical models of DNA topology simplification by type IIA DNA topoisomerases.

Authors:  Alexander Vologodskii
Journal:  Nucleic Acids Res       Date:  2009-04-21       Impact factor: 16.971

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