Single-stranded DNA within nanopores: Conformational dynamics and implications for sequencing; A molecular dynamics simulation study

Biophysical Journal

Volumn 103, Issue 5, 2012, Pages 1028-1036

  Guy, Andrew T ^a   Piggot, Thomas J ^a   Khalid, Syma ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; HEMOLYSIN; SINGLE STRANDED DNA;

ARTICLE; CHEMISTRY; CONFORMATION; DNA SEQUENCE; ELECTRICITY; GENETICS; METABOLISM; MOLECULAR DYNAMICS; MOVEMENT (PHYSIOLOGY); NANOPORE; NUCLEOTIDE SEQUENCE; PROTEIN SECONDARY STRUCTURE; REPRODUCIBILITY;

BACTERIAL PROTEINS; BASE SEQUENCE; DNA, SINGLE-STRANDED; ELECTRICITY; HEMOLYSIN PROTEINS; MOLECULAR DYNAMICS SIMULATION; MOVEMENT; NANOPORES; NUCLEIC ACID CONFORMATION; PROTEIN STRUCTURE, SECONDARY; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

STAPHYLOCOCCUS AUREUS;

EID: 84865770620     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2012.08.012     Document Type: Article

References (36)

1. D.J.F. du Plessis, N. Nouwen, and A.J.M. Driessen The Sec translocase Biochim. Biophys. Acta 1808 2011 851 865
2. S.R. Carmody, and S.R. Wente mRNA nuclear export at a glance J. Cell Sci. 122 2009 1933 1937
3. H. Bayley, and P.S. Cremer Stochastic sensors inspired by biology Nature 413 2001 226 230
4. C. Dekker Solid-state nanopores Nat. Nanotechnol. 2 2007 209 215
5. J.J. Kasianowicz, and E. Brandin D.W. Deamer Characterization of individual polynucleotide molecules using a membrane channel Proc. Natl. Acad. Sci. USA 93 1996 13770 13773
6. L. Song, and M.R. Hobaugh J.E. Gouaux Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore Science 274 1996 1859 1866
7. J. Clarke, and H.-C. Wu H. Bayley Continuous base identification for single-molecule nanopore DNA sequencing Nat. Nanotechnol. 4 2009 265 270
8. G. Maglia, and M.R. Restrepo H. Bayley Enhanced translocation of single DNA molecules through α-hemolysin nanopores by manipulation of internal charge Proc. Natl. Acad. Sci. USA 105 2008 19720 19725
9. S. Bhattacharya, and I.M. Derrington A. Aksimentiev Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence ACS Nano. 2012 10.1021/nn3019943 published online
10. M. Rincon-Restrepo, and E. Mikhailova G. Maglia Controlled translocation of individual DNA molecules through protein nanopores with engineered molecular brakes Nano Lett. 11 2011 746 750
11. Y. Astier, O. Braha, and H. Bayley Toward single molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5′-monophosphates by using an engineered protein nanopore equipped with a molecular adapter J. Am. Chem. Soc. 128 2006 1705 1710
12. M.C. Murphy, and I. Rasnik T. Ha Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy Biophys. J. 86 2004 2530 2537
13. P.J. Bond, and A.T. Guy S. Khalid Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation Biochemistry 50 2011 3777 3783
14. S. Khalid, and M.J. Hannon P.M. Rodger Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove Chemistry 12 2006 3493 3506
15. R. García-Fandiño, and M.S. Sansom Designing biomimetic pores based on carbon nanotubes Proc. Natl. Acad. Sci. USA 109 2012 6939 6944
16. J. Mathé, and A. Aksimentiev A. Meller Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel Proc. Natl. Acad. Sci. USA 102 2005 12377 12382
17. U. Mirsaidov, and J. Comer G. Timp Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix Nanotechnology 21 2010 395501
18. H. Martin, and S. Jha P. Coveney Determination of free energy profiles for the translocation of polynucleotides through α-hemolysin nanopores using non-equilibrium molecular dynamics simulations J. Chem. Theory Comput. 5 2009 2135 2148
19. D.B. Wells, V. Abramkina, and A. Aksimentiev Exploring transmembrane transport through α-hemolysin with grid-steered molecular dynamics J. Chem. Phys. 127 2007 125101
20. J. Wang, P. Cieplak, and P. Kollman How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21 2000 1049 1074
21. A. Pérez, and I. Marchán M. Orozco Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers Biophys. J. 92 2007 3817 3829
22. S.E. Feller, and A.D. MacKerell An improved empirical potential energy function for molecular simulations of phospholipids J. Phys. Chem. B 104 2000 7510 7515
23. C. Oostenbrink, and A. Villa W.F. van Gunsteren A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6 J. Comput. Chem. 25 2004 1656 1676
24. H.R. Drew, and R.M. Wing R.E. Dickerson Structure of a B-DNA dodecamer: conformation and dynamics Proc. Natl. Acad. Sci. USA 78 1981 2179 2183
25. B. Hess, and C. Kutzner E. Lindahl GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 2008 435 447
26. D.A. Case, and T.A. Darden B.P. Roberts Amber 11 2010 University of California San Francisco, CA
27. T. Darden, D. York, and L. Pedersen Particle mesh Ewald - an n.log(n) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
28. O.F. Lange, D. van der Spoel, and B.L. de Groot Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data Biophys. J. 99 2010 647 655
29. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38 27-28
30. H. Rozenberg, and D. Rabinovich Z. Shakked Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets Proc. Natl. Acad. Sci. USA 95 1998 15194 15199
31. X. Daura, and K. Gademann A.E. Mark Peptide folding: when simulation meets experiment Angew. Chem. Int. Ed. 38 1999 236 240
32. C.G. Ricci, and A.S. de Andrade P.A. Netz Molecular dynamics of DNA: comparison of force fields and terminal nucleotide definitions J. Phys. Chem. B 114 2010 9882 9893
33. A. Sali, and T.L. Blundell Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234 1993 779 815
34. G. Zheng, X.J. Lu, and W.K. Olson Web 3DNA - a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures Nucleic Acids Res. 37 Web Server issue 2009 W240-6
35. P. Bjelkmar, and P. Larsson E. Lindahl Implementation of the CHARMM force field in GROMACS: analysis of protein stability effects from correction maps, virtual interaction sites, and water models J. Chem. Theory Comput. 6 2010 459 466
36. A. Rich The rise of single-molecule DNA biochemistry Proc. Natl. Acad. Sci. USA 95 1998 13999 14000