Sequence dependence of DNA translocation through a nanopore.
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases A and C, which have been shown previously to have different interactions with the pore. We study DNA with repeating blocks A(n)C(n) for various values of n and find that the translocation time depends strongly on the block length 2n as well as on the orientation of which base enters the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through a nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences is contained in the periodicity of the residence time of the individual nucleotides inside the pore.
Luo
Kaifu
K
Laboratory of Physics, Helsinki University of Technology, P.O. Box 1100, FIN-02015 TKK, Espoo, Finland. luokaifu@yahoo.com
Ala-Nissila
Tapio
T
Ying
See-Chen
SC
Bhattacharya
Aniket
A
D000465:Algorithms; D004247:DNA / Q000737:chemistry*; D006460:Hemolysin Proteins / Q000737:chemistry; D007700:Kinetics; D008954:Models, Biological; D053758:Nanoparticles; D017711:Nonlinear Dynamics; D014178:Translocation, Genetic
D006460:Hemolysin Proteins; D004247:DNA