Theoretical study of sequence-dependent nanopore unzipping of DNA

Biophysical Journal
U Bockelmann, V Viasnoff

Abstract

We theoretically investigate the unzipping of DNA electrically driven through a nanometer-size pore. Taking the DNA base sequence explicitly into account, the unpairing and translocation process is described by a biased random walk in a one-dimensional energy landscape determined by the sequential basepair opening. Distributions of translocation times are numerically calculated as a function of applied voltage and temperature. We show that varying these two parameters changes the dynamics from a predominantly diffusive behavior to a dynamics governed by jumps over local energy barriers. The work suggests experimentally studying sequence effects, by comparing the average value and standard deviation of the statistical distribution of translocation times.

References

Nov 26, 1996·Proceedings of the National Academy of Sciences of the United States of America·J J KasianowiczD W Deamer
Oct 29, 1997·Proceedings of the National Academy of Sciences of the United States of America·B Essevaz-RouletF Heslot
Mar 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SantaLucia
Feb 3, 2000·Proceedings of the National Academy of Sciences of the United States of America·A MellerD Branton
Sep 6, 2000·Physical Review Letters·D K Lubensky, D R Nelson
Sep 8, 2000·Physical Review Letters·N L GoddardA Libchaber
Feb 28, 2002·Biophysical Journal·U BockelmannF Heslot
Feb 8, 2003·Proceedings of the National Academy of Sciences of the United States of America·Claudia DanilowiczMara Prentiss
Jul 15, 2003·Physical Review Letters·Alexis F Sauer-BudgeDaniel Branton
Mar 11, 2004·The European Physical Journal. E, Soft Matter·S CoccoR Monasson
May 14, 2004·Annual Review of Biophysics and Biomolecular Structure·John SantaLucia, Donald Hicks
Jun 11, 2004·Biophysical Journal·Yariv KafriDavid R Nelson
Sep 7, 2004·Biophysical Journal·Jérôme MathéAmit Meller
Oct 6, 2005·Physical Biology·Ulrich GerlandTerence Hwa
Oct 15, 2005·Physical Biology·Greg LakatosGren N Patey
Dec 31, 2005·Physical Review Letters·Ralf Bundschuh, Ulrich Gerland
Apr 12, 2006·Physical Review Letters·Silvina MatysiakCecilia Clementi
Sep 13, 2006·The Journal of Chemical Physics·Stanislav Kotsev, Anatoly B Kolomeisky
Feb 22, 2007·Annual Review of Biophysics and Biomolecular Structure·Murugappan Muthukumar

❮ Previous
Next ❯

Citations

Oct 7, 2008·European Biophysics Journal : EBJ·Virgile ViasnoffUlrich Bockelmann
Jun 14, 2012·Journal of the American Chemical Society·Qian JinHenry S White
Jul 1, 2011·Journal of the Royal Society, Interface·Ulrich F Keyser
Aug 18, 2012·The European Physical Journal. E, Soft Matter·M BrutM Djafari Rouhani
Jun 30, 2011·Nanoscale Research Letters·Waseem AsgharSamir Muzaffar Iqbal
Sep 16, 2009·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Henk VocksGerard T Barkema
Feb 23, 2011·Journal of Physics. Condensed Matter : an Institute of Physics Journal·V ViasnoffU Bockelmann
Jun 2, 2018·European Biophysics Journal : EBJ·Oleksii Zdorevskyi, Sergey N Volkov
Mar 5, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Kaifu LuoAniket Bhattacharya
Sep 28, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Kaifu Luo, Ralf Metzler

❮ Previous
Next ❯

Related Concepts

Related Feeds

Bacteriophage: Phage Therapy

Phage therapy uses bacterial viruses (bacteriophages) to treat bacterial infections and is widely being recognized as an alternative to antibiotics. Here is the latest research.