Literature DB >> 18836709

Probing DNA base pairing energy profiles using a nanopore.

Virgile Viasnoff1, Nicolas Chiaruttini, Ulrich Bockelmann.   

Abstract

We experimentally show that the voltage driven unzipping of long DNA duplexes by an alpha-hemolysin pore is sensitive to the shape of the base pairing energy landscape. Two sequences of equal global stability were investigated. The sequence with an homogeneous base pairing profile translocates faster than the one with alternative weak and strong regions. We could qualitatively account for theses observations by theoretically describing the voltage driven translocation as a biased random walk of the unzipping fork in the sequence dependent energy landscape.

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Year:  2008        PMID： 18836709     DOI： 10.1007/s00249-008-0372-2

Source DB:  PubMed          Journal:  Eur Biophys J        ISSN： 0175-7571            Impact factor:   1.733


  28 in total

1.  Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel.

Authors:  W Vercoutere; S Winters-Hilt; H Olsen; D Deamer; D Haussler; M Akeson
Journal:  Nat Biotechnol       Date:  2001-03       Impact factor: 54.908

2.  Discrimination among individual Watson-Crick base pairs at the termini of single DNA hairpin molecules.

Authors:  Wenonah A Vercoutere; Stephen Winters-Hilt; Veronica S DeGuzman; David Deamer; Sam E Ridino; Joseph T Rodgers; Hugh E Olsen; Andre Marziali; Mark Akeson
Journal:  Nucleic Acids Res       Date:  2003-02-15       Impact factor: 16.971

3.  Rapid nanopore discrimination between single polynucleotide molecules.

Authors:  A Meller; L Nivon; E Brandin; J Golovchenko; D Branton
Journal:  Proc Natl Acad Sci U S A       Date:  2000-02-01       Impact factor: 11.205

4.  Nanopore unzipping of individual DNA hairpin molecules.

Authors:  Jérôme Mathé; Hasina Visram; Virgile Viasnoff; Yitzhak Rabin; Amit Meller
Journal:  Biophys J       Date:  2004-09-03       Impact factor: 4.033

Review 5.  Analysis of thermal melting curves.

Authors:  Jean-Louis Mergny; Laurent Lacroix
Journal:  Oligonucleotides       Date:  2003

6.  First passage times of driven DNA hairpin unzipping.

Authors:  Greg Lakatos; Tom Chou; Birger Bergersen; Gren N Patey
Journal:  Phys Biol       Date:  2005-09-12       Impact factor: 2.583

7.  Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins.

Authors:  Olga K Dudko; Jérôme Mathé; Attila Szabo; Amit Meller; Gerhard Hummer
Journal:  Biophys J       Date:  2007-03-23       Impact factor: 4.033

8.  A Monte Carlo algorithm to study polymer translocation through nanopores. I. Theory and numerical approach.

Authors:  Michel G Gauthier; Gary W Slater
Journal:  J Chem Phys       Date:  2008-02-14       Impact factor: 3.488

9.  Theoretical study of sequence-dependent nanopore unzipping of DNA.

Authors:  U Bockelmann; V Viasnoff
Journal:  Biophys J       Date:  2008-01-04       Impact factor: 4.033

10.  Characterization of individual polynucleotide molecules using a membrane channel.

Authors:  J J Kasianowicz; E Brandin; D Branton; D W Deamer
Journal:  Proc Natl Acad Sci U S A       Date:  1996-11-26       Impact factor: 11.205
View more
  10 in total

1.  DNA translocation and unzipping through a nanopore: some geometrical effects.

Authors:  J Muzard; M Martinho; J Mathé; U Bockelmann; V Viasnoff
Journal:  Biophys J       Date:  2010-05-19       Impact factor: 4.033

2.  Structural destabilization of DNA duplexes containing single-base lesions investigated by nanopore measurements.

Authors:  Qian Jin; Aaron M Fleming; Yun Ding; Cynthia J Burrows; Henry S White
Journal:  Biochemistry       Date:  2013-10-31       Impact factor: 3.162

3.  Mimicking DNA stretching with the Static Mode method: shear stress versus transverse pulling stress.

Authors:  M Brut; A Estève; G Landa; M Djafari Rouhani
Journal:  Eur Phys J E Soft Matter       Date:  2012-08-21       Impact factor: 1.890

4.  Electrical Current Signatures of DNA Base Modifications in Single Molecules Immobilized in the α-Hemolysin Ion Channel.

Authors:  Anna H Wolna; Aaron M Fleming; Na An; Lidong He; Henry S White; Cynthia J Burrows
Journal:  Isr J Chem       Date:  2013-06-01       Impact factor: 3.333

5.  Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments.

Authors:  Swati Bhattacharya; L Muzard; L Payet; Jerome Mathé; Ulrich Bockelmann; Aleksei Aksimentiev; Virgile Viasnoff
Journal:  J Phys Chem C Nanomater Interfaces       Date:  2011-02-21       Impact factor: 4.126

6.  Sequence-specific single-molecule analysis of 8-oxo-7,8-dihydroguanine lesions in DNA based on unzipping kinetics of complementary probes in ion channel recordings.

Authors:  Anna E P Schibel; Aaron M Fleming; Qian Jin; Na An; Jin Liu; Charles P Blakemore; Henry S White; Cynthia J Burrows
Journal:  J Am Chem Soc       Date:  2011-08-29       Impact factor: 15.419

7.  Quantitative analysis of the nanopore translocation dynamics of simple structured polynucleotides.

Authors:  Severin Schink; Stephan Renner; Karen Alim; Vera Arnaut; Friedrich C Simmel; Ulrich Gerland
Journal:  Biophys J       Date:  2012-01-03       Impact factor: 4.033

8.  Unzipping kinetics of duplex DNA containing oxidized lesions in an α-hemolysin nanopore.

Authors:  Qian Jin; Aaron M Fleming; Cynthia J Burrows; Henry S White
Journal:  J Am Chem Soc       Date:  2012-06-25       Impact factor: 15.419

9.  Interactions of the human telomere sequence with the nanocavity of the α-hemolysin ion channel reveal structure-dependent electrical signatures for hybrid folds.

Authors:  Na An; Aaron M Fleming; Cynthia J Burrows
Journal:  J Am Chem Soc       Date:  2013-05-29       Impact factor: 15.419

10.  Internal vs fishhook hairpin DNA: unzipping locations and mechanisms in the α-hemolysin nanopore.

Authors:  Yun Ding; Aaron M Fleming; Henry S White; Cynthia J Burrows
Journal:  J Phys Chem B       Date:  2014-11-03       Impact factor: 2.991
  10 in total

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