Theoretical study of sequence-dependent nanopore unzipping of DNA

被引:23
作者
Bockelmann, U. [1 ]
Viasnoff, V. [1 ]
机构
[1] Ecole Super Phys & Chim Ind Ville Paris, Ctr Natl Rech Sci, Paris, France
关键词
D O I
10.1529/biophysj.107.111732
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
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.
引用
收藏
页码:2716 / 2724
页数:9
相关论文
共 36 条
  • [1] Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules
    Akeson, M
    Branton, D
    Kasianowicz, JJ
    Brandin, E
    Deamer, DW
    [J]. BIOPHYSICAL JOURNAL, 1999, 77 (06) : 3227 - 3233
  • [2] Imaging α-hemolysin with molecular dynamics:: Ionic conductance, osmotic permeability, and the electrostatic potential map
    Aksimentiev, A
    Schulten, K
    [J]. BIOPHYSICAL JOURNAL, 2005, 88 (06) : 3745 - 3761
  • [3] Recognizing a single base in an individual DNA strand:: A step toward DNA sequencing in nanopores
    Ashkenasy, N
    Sánchez-Quesada, J
    Bayley, H
    Ghadiri, MR
    [J]. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2005, 44 (09) : 1401 - 1404
  • [4] Dynamics of the DNA duplex formation studied by single molecule force measurements
    Bockelmann, U
    Thomen, P
    Heslot, F
    [J]. BIOPHYSICAL JOURNAL, 2004, 87 (05) : 3388 - 3396
  • [5] Unzipping DNA with optical tweezers: high sequence sensitivity and force flips
    Bockelmann, U
    Thomen, P
    Essevaz-Roulet, B
    Viasnoff, V
    Heslot, F
    [J]. BIOPHYSICAL JOURNAL, 2002, 82 (03) : 1537 - 1553
  • [6] Molecular stick-slip motion revealed by opening DNA with piconewton forces
    Bockelmann, U
    EssevazRoulet, B
    Heslot, F
    [J]. PHYSICAL REVIEW LETTERS, 1997, 79 (22) : 4489 - 4492
  • [7] ANOMALOUS DIFFUSION IN DISORDERED MEDIA - STATISTICAL MECHANISMS, MODELS AND PHYSICAL APPLICATIONS
    BOUCHAUD, JP
    GEORGES, A
    [J]. PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, 1990, 195 (4-5): : 127 - 293
  • [8] Coupled dynamics of RNA folding and nanopore translocation
    Bundschuh, R
    Gerland, U
    [J]. PHYSICAL REVIEW LETTERS, 2005, 95 (20)
  • [9] Slow nucleic acid unzipping kinetics from sequence-defined barriers
    Cocco, S
    Marko, JF
    Monasson, R
    [J]. EUROPEAN PHYSICAL JOURNAL E, 2003, 10 (02) : 153 - 161
  • [10] DNA unzipped under a constant force exhibits multiple metastable intermediates
    Danilowicz, C
    Coljee, VW
    Bouzigues, C
    Lubensky, DK
    Nelson, DR
    Prentiss, M
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (04) : 1694 - 1699