Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation

Biophysical Journal
H MerlitzJ Langowski

Abstract

A Brownian dynamics (BD) model described in the accompanying paper (Klenin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the simulation of linear and circular DNA, and other wormlike chain polyelectrolytes. Biophys. J. 74:000-000) has been used for computing the end-to-end distance distribution function, the cyclization probability, and the cyclization kinetics of linear DNA fragments between 120 and 470 basepairs with optional insertion of DNA bends. Protein-mediated DNA loop formation was modeled by varying the reaction distance for cyclization between 0 and 10 nm. The low cyclization probability of DNA fragments shorter than the Kuhn length (300 bp) is enhanced by several orders of magnitude when the cyclization is mediated by a protein bridge of 10 nm diameter, and/or when the DNA is bent. From the BD trajectories, end-to-end collision frequencies were computed. Typical rates for loop formation of linear DNAs are 1.3 x 10(3) s(-1) (235 bp) and 4.8 x 10(2) s(-1) (470 bp), while the insertion of a 120 degree bend in the center increases this rate to 3.0 x 10(4) s(-1) (235 bp) and 5.5 x 10(3) s(-1) (470 bp), respectively. The duration of each encounter is between 0.05 and 0.5 micros for these DNAs. T...Continue Reading

References

Oct 20, 1992·Journal of Molecular Biology·A V VologodskiiN R Cozzarelli
Jan 1, 1992·Annual Review of Biochemistry·R Schleif
Feb 20, 1992·Journal of Molecular Biology·T Schlick, W K Olson
Mar 1, 1992·Microbiological Reviews·K S Matthews
Dec 1, 1991·Proceedings of the National Academy of Sciences of the United States of America·L Frappier, M O'Donnell
Jun 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·M AffolterW J Gehring
Feb 5, 1991·Journal of Molecular Biology·K V KleninM D Frank-Kamenetskii
Jul 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·W SuH Echols
Jan 1, 1990·Progress in Nucleic Acid Research and Molecular Biology·G R Bellomy, M T Record
Aug 22, 1986·Science·M C Mossing, M T Record
Jan 1, 1988·Annual Review of Biophysics and Biophysical Chemistry·P J Hagerman
Jul 5, 1987·Journal of Molecular Biology·J A BorowiecJ D Gralla
Aug 1, 1981·Proceedings of the National Academy of Sciences of the United States of America·D ShoreR L Baldwin
Nov 15, 1983·Journal of Molecular Biology·D Shore, R L Baldwin
Aug 1, 1995·Trends in Biochemical Sciences·Y YangW K Olson
Sep 23, 1994·Journal of Molecular Biology·P ZhangW K Olson
Nov 1, 1993·Molecular and Cellular Biology·P A BeachyS C Ekker
Oct 7, 1993·Nature·Y KimP B Sigler
Dec 1, 1995·Trends in Biochemical Sciences·K RippeJ Langowski
Apr 1, 1996·Current Opinion in Structural Biology·W K Olson
Aug 1, 1996·Biophysical Journal·G Chirico, J Langowski
Feb 1, 1996·Trends in Biochemical Sciences·J LangowskiY Yang
Apr 5, 1997·Biopolymers·J A Martino, W K Olson
Mar 28, 1997·Journal of Molecular Biology·V V RybenkovN R Cozzarelli
Jun 1, 1997·Computer Applications in the Biosciences : CABIOS·L EhrlichJ Langowski

❮ Previous
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Citations

Oct 1, 2006·Journal of Biological Physics·Seth BlumbergJens-Christian Meiners
May 14, 1999·Current Opinion in Structural Biology·I Lafontaine, R Lavery
Dec 12, 2001·Trends in Biochemical Sciences·K Rippe
Aug 2, 2012·Quarterly Reviews of Biophysics·Jonathan M FoggLynn Zechiedrich
Jul 27, 2006·Proceedings of the National Academy of Sciences of the United States of America·Gregory J GemmenDouglas E Smith
Aug 27, 2009·Proceedings of the National Academy of Sciences of the United States of America·Alexander GansenClaus A M Seidel
Oct 6, 2000·Journal of Biomolecular Structure & Dynamics·D LiuC Bai
Jul 3, 2009·Physical Biology·Kevin B TowlesPhilip C Nelson
Jul 13, 2006·Nucleic Acids Research·Francesco VanziFrancesco Saverio Pavone
Mar 24, 2006·The European Physical Journal. E, Soft Matter·J-F AllemandG Lia
Jan 8, 2016·The Journal of Physical Chemistry. B·Zhong-Ru XieYinghao Wu
Mar 5, 2016·The Journal of Physical Chemistry Letters·Qian Wang, B Montgomery Pettitt
Jan 15, 2008·Biophysical Journal·Neeraj J AgrawalPrashant K Purohit
May 5, 2004·Journal of Molecular Biology·Michelle L EmbletonStephen E Halford
Sep 17, 2013·Annals of the New York Academy of Sciences·Fabian ErdelKarsten Rippe
Aug 6, 2015·Biophysical Journal·Peter J MulliganAndrew J Spakowitz
Oct 16, 2007·Seminars in Cell & Developmental Biology·Jörg Langowski, Dieter W Heermann
May 6, 2004·Molecular Cell·Timothy E Cloutier, Jonathan Widom
Sep 4, 2007·Biophysical Journal·Sachin GoyalN C Perkins
Sep 12, 2006·Biophysical Journal·Gregory J GemmenDouglas E Smith
Nov 18, 2010·Biophysical Journal·Irina V DobrovolskaiaGaurav Arya
Oct 8, 1999·Biophysical Journal·P E SottasJ Dubochet
Jun 28, 2003·Biophysical Journal·Andreas Hanke, Ralf Metzler
Mar 18, 2006·The Journal of Chemical Physics·Changbong Hyeon, D Thirumalai
Aug 31, 2004·The Journal of Chemical Physics·Konstantin V Klenin, Jorg Langowski
Oct 16, 2004·The Journal of Chemical Physics·Steven P MielkeCraig J Benham
Aug 13, 2004·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·A BalaeffK Schulten
Jun 4, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Steven P MielkeCraig J Benham
Jul 22, 2018·BMC Biophysics·Giuseppe ChiricoKatalin Tóth
Oct 10, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Philipp M Diesinger, Dieter W Heermann
Feb 21, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Nicolas Douarche, Simona Cocco
Feb 27, 2018·Biophysical Journal·Maddalena ColliniGiuseppe Chirico
Aug 19, 2021·BMC Bioinformatics·Kalyani Dhusia, Yinghao Wu
Mar 13, 2012·Journal of Chemical Theory and Computation·Nicolas ClauvelinIrwin Tobias

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