Unzipping Kinetics of Double-Stranded DNA in a Nanopore

Sauer-Budge, Alexis F.; Nyamwanda, Jacqueline A.; Lubensky, David K.; Branton, Daniel

doi:10.1103/physrevlett.90.238101

Cited by 290 publications

(352 citation statements)

References 34 publications

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“…This prevents fluorescence when the DNA is away from the pore. When the ds-DNA is pulled into, for instance, an ␣-hemolysin pore, the double strand has to unzip into single strands ͑Sauer- Budge et al, 2003;Mathé et al, 2004. This pulls the fluorescent tag away from its quencher and allows the tag, and thus the base in the original strand, to be detected via optical means.…”

Section: B Optical Detectionmentioning

confidence: 99%

Colloquium: Physical approaches to DNA sequencing and detection

2008

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With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, a revolutionary sequencing method is needed for the cost-effective and rapid interrogation of individual genomes. This capability is likely to be provided by a physical approach to probing DNA at the single-nucleotide level. This is in sharp contrast to current techniques and instruments that probe ͑through chemical elongation, electrophoresis, and optical detection͒ length differences and terminating bases of strands of DNA. Several physical approaches to DNA detection have the potential to deliver fast and low-cost sequencing. Central to these approaches is the concept of nanochannels or nanopores, which allow for the spatial confinement of DNA molecules. In addition to their possible impact in medicine and biology, the methods offer ideal test beds to study open scientific issues and challenges in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale. This Colloquium emphasizes the physics behind these methods and ideas, critically describes their advantages and drawbacks, and discusses future research opportunities in the field.

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Section: B Optical Detectionmentioning

confidence: 99%

Colloquium: Physical approaches to DNA sequencing and detection

2008

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“…6 In addition to its biological relevance, the translocation dynamics is also a challenging topic in polymer physics. Accordingly, the polymer translocation has attracted a considerable number of experimental, [7][8][9][10][11][12][13][14] theoretical, [15][16][17][18][19][20][21][22][23][24][25][26][27][28] and numerical studies. [29][30][31][32][33][34][35][36] The translocation of a polymer through a nanopore faces a large entropic barrier due to the loss of a great number of available configurations.…”

Section: Introductionmentioning

confidence: 99%

Polymer translocation through a nanopore: A two-dimensional Monte Carlo study

Luo

Ala-Nissilä

Ying

2006

The Journal of Chemical Physics

118

144

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Polymer translocation through a nanopore induced by adsorption: Monte Carlo simulation of a coarse-grained model J. Chem. Phys. 121, 6042 (2004); 10.1063/1.1785776 This article is copyrighted as indicated in the article. Reuse of AIP content is subject to the terms at: http://scitation. We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional fluctuating bond model with single-segment Monte Carlo moves. To overcome the entropic barrier without artificial restrictions, we consider a polymer which is initially placed in the middle of the pore and study the escape time required for the polymer to completely exit the pore on either end. We find numerically that scales with the chain length N as ϳ N 1+2 , where is the Flory exponent. This is the same scaling as predicted for the translocation time of a polymer which passes through the nanopore in one direction only. We examine the interplay between the pore length L and the radius of gyration R g . For L Ӷ R g , we numerically verify that asymptotically ϳ N 1+2 . For L ӷ R g , we find ϳ N. In addition, we numerically find the scaling function describing crossover between short and long pores. We also show that has a minimum as a function of L for longer chains when the radius of gyration along the pore direction R ʈ Ϸ L. Finally, we demonstrate that the stiffness of the polymer does not change the scaling behavior of translocation dynamics for single-segment dynamics.

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“…Each base (nucleotide) is estimated to have an effective charge of 0:094e from Ref. [7], leading to an effective charge of a bead being 0:282e. Thus, F 0:5 corresponds to a voltage of about 187.9 mV across the pore within the range of experimental parameters [1,2,4 -6].…”

mentioning

confidence: 99%

“…Similar experiments have been done recently using solid state nanopores with more precisely controlled dimensions. Triggered by these experiments and potential technological applications [1,2], such as rapid DNA sequencing, gene therapy, and controlled drug delivery, the translocation of biopolymers through a nanopore has become the subject of intensive experimental [3][4][5][6][7][8] and theoretical [8][9][10][11][12][13][14][15][16][17][18][19][20][21] studies. A particular important question is if DNA translocation through a nanopore can be used to determine the detailed sequence structure of the molecule [2 -4,18].…”

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confidence: 99%

Sequence Dependence of DNA Translocation through a Nanopore

et al. 2008

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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.

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Unzipping Kinetics of Double-Stranded DNA in a Nanopore

Cited by 290 publications

References 34 publications

Colloquium: Physical approaches to DNA sequencing and detection

Colloquium: Physical approaches to DNA sequencing and detection

Polymer translocation through a nanopore: A two-dimensional Monte Carlo study

Sequence Dependence of DNA Translocation through a Nanopore

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