Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel

Macromolecules
Jeffrey G ReifenbergerKevin D Dorfman

Abstract

We report experimental data on the unfolding of human and E. coli genomic DNA molecules shortly after injection into a 45 nm nanochannel. The unfolding dynamics are deterministic, consistent with previous experiments and modeling in larger channels, and do not depend on the biological origin of the DNA. The measured entropic unfolding force per friction per unit contour length agrees with that predicted by combining the Odijk excluded volume with numerical calculations of the Kirkwood diffusivity of confined DNA. The time scale emerging from our analysis has implications for genome mapping in nanochannels, especially as the technology moves towards longer DNA, by setting a lower bound for the delay time before making a measurement.

References

Aug 11, 2005·Physical Review Letters·Walter ReisnerRobert H Austin
Feb 21, 2006·Physical Review Letters·Christian Hermann RecciusH G Craighead
Jun 17, 2006·The European Physical Journal. E, Soft Matter·M Kenward, G W Slater
Dec 6, 2006·The Journal of Chemical Physics·Theo Odijk
Dec 19, 2006·Nucleic Acids Research·Ming XiaoPui-Yan Kwok
Feb 14, 2007·Proceedings of the National Academy of Sciences of the United States of America·Kyubong JoDavid C Schwartz
Aug 7, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Yingzi YangGerhard Gompper
Oct 9, 2007·Biophysical Journal·Colin Echeverría AitkenJoseph D Puglisi
Oct 13, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Axel Arnold, Suckjoon Jun
May 8, 2008·Nano Letters·Chih-Chen HsiehPatrick S Doyle
Jun 17, 2008·The Journal of Chemical Physics·Ce ZhangJohan R C van der Maarel
Jul 23, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Theo Odijk
Oct 11, 2008·Nano Letters·Stephen L LevyHarold G Craighead
Feb 10, 2009·The Journal of Physical Chemistry. B·Peter CifraTomás Bleha
Mar 18, 2009·Nano Letters·Fredrik PerssonAnders Kristensen
Dec 17, 2009·The Journal of Chemical Physics·Peter Cifra
Jan 15, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Theodore W BurkhardtGerhard Gompper
Aug 24, 2011·Macromolecules·Yanwei WangKevin D Dorfman
Sep 15, 2012·Reports on Progress in Physics·Walter ReisnerRobert H Austin
Sep 26, 2012·Physical Review Letters·Douglas R TreeKevin D Dorfman
Feb 23, 2013·Current Opinion in Biotechnology·Michal Levy-Sakin, Yuval Ebenstein
Dec 7, 2013·Biomicrofluidics·Douglas R TreeKevin D Dorfman
Dec 18, 2013·ACS Nano·Michal Levy-SakinYuval Ebenstein
Dec 19, 2013·Macromolecules·Douglas R TreeKevin D Dorfman
Jan 24, 2015·Physical Review Letters·Ahmed KhorshidWalter Reisner
Feb 16, 2015·The Journal of Chemical Physics·Wesley F ReinhartKevin D Dorfman
May 21, 2015·The Analyst·Jeffrey G ReifenbergerHan Cao
Jun 13, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·E Werner, B Mehlig
Jul 15, 2015·Macromolecules·Abhiram Muralidhar, Kevin D Dorfman
Jan 14, 2016·Biomicrofluidics·Julian SheatsKevin D Dorfman
Oct 6, 2016·Nature·Jeong-Sun SeoChanghoon Kim
Nov 1, 2016·Biomicrofluidics·Aashish JainKevin D Dorfman
Aug 12, 2017·Biomicrofluidics·Aashish Jain, Kevin D Dorfman
Jan 13, 2018·Physical Review Letters·E WernerB Mehlig
Mar 14, 2016·Polymers·Abhiram MuralidharKevin D Dorfman

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Citations

Dec 12, 2018·Small·Saroj Dangi, Robert Riehn
Mar 27, 2018·Biomicrofluidics·E WernerB Mehlig
Sep 17, 2018·The Journal of Chemical Physics·Aditya Bikram BhandariKevin D Dorfman
Dec 12, 2018·The Journal of Chemical Physics·Jens KrogTobias Ambjörnsson

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