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Volumn 749, Issue , 2011, Pages 317-358

Modeling Nanopores for Sequencing DNA

Author keywords

Bionanotechnology; Computer simulations; Membrane proteins; Molecular dynamics; Nucleic acids; Transmembrane transport

Indexed keywords

DNA; HEMOLYSIN;

EID: 84855168500     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-142-0_22     Document Type: Chapter
Times cited : (23)

References (41)
  • 3
    • 38749105770 scopus 로고    scopus 로고
    • Detection of DNA sequence using an alternating electric field in a nanopore capacitor
    • Sigalov, G., Comer, J., Timp, G., and Aksimentiev, A. (2008) Detection of DNA sequence using an alternating electric field in a nanopore capacitor Nano Lett 8, 56–63.
    • (2008) Nano Lett , vol.8 , pp. 56-63
    • Sigalov, G.1    Comer, J.2    Timp, G.3    Aksimentiev, A.4
  • 4
    • 35648963025 scopus 로고    scopus 로고
    • Progress toward ultrafast DNA sequencing using solid-state nanopores
    • Soni, G. V. and Meller, A. (2007) Progress toward ultrafast DNA sequencing using solid-state nanopores Clinical Chemistry 53, 1996–2001.
    • (2007) Clinical Chemistry , vol.53 , pp. 1996-2001
    • Soni, G.V.1    Meller, A.2
  • 5
    • 0036929209 scopus 로고    scopus 로고
    • A Fast in Silico Simulation of Ion Flux through the Large-Pore Channel Proteins
    • Bransburg-Zabary, S., Nachliel, E., and Gutman, M. (2002) A Fast in Silico Simulation of Ion Flux through the Large-Pore Channel Proteins Biophys J 83, 3001–3011.
    • (2002) Biophys J , vol.83 , pp. 3001-3011
    • Bransburg-Zabary, S.1    Nachliel, E.2    Gutman, M.3
  • 6
    • 4444234147 scopus 로고    scopus 로고
    • Microscopic kinetics of DNA translocation through synthetic nanopores
    • Aksimentiev, A., Heng, J. B., Timp, G., and Schulten, K. (2004) Microscopic kinetics of DNA translocation through synthetic nanopores Biophys J 87, 2086–2097.
    • (2004) Biophys J , vol.87 , pp. 2086-2097
    • Aksimentiev, A.1    Heng, J.B.2    Timp, G.3    Schulten, K.4
  • 7
    • 22244445788 scopus 로고    scopus 로고
    • Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability and the electrostatic potential map
    • Aksimentiev, A. and Schulten, K. (2005) Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability and the electrostatic potential map Biophys J 88, 3745–3761.
    • (2005) Biophys J , vol.88 , pp. 3745-3761
    • Aksimentiev, A.1    Schulten, K.2
  • 8
    • 50849102996 scopus 로고    scopus 로고
    • Electro-osmotic screening of the dna charge in a nanopore
    • Luan, B. and Aksimentiev, A. (2008) Electro-osmotic screening of the dna charge in a nanopore Phys Rev E 78, 021912.
    • (2008) Phys Rev E , vol.78
    • Luan, B.1    Aksimentiev, A.2
  • 10
    • 34848830419 scopus 로고    scopus 로고
    • Exploring transmembrane transport through a-hemolysin with grid-steered molecular dynamics
    • Wells, D. B., Abramkina, V., and Aksimentiev, A. (2007) Exploring transmembrane transport through a-hemolysin with grid-steered molecular dynamics J Chem Phys 127, 125101.
    • (2007) J Chem Phys , vol.127
    • Wells, D.B.1    Abramkina, V.2    Aksimentiev, A.3
  • 11
    • 85139097177 scopus 로고    scopus 로고
    • VMD User Guide. URL: http://www.ks.uiuc. edu/Research/vmd/current/ug/ug.html.
    • VMD User Guide. URL: http://www.ks.uiuc. edu/Research/vmd/current/ug/ug.html.
  • 12
    • 85139174379 scopus 로고    scopus 로고
    • VMD Tutorial. URL: http://www.ks.uiuc. edu/Trai ni ng/Tutori al s/vmd/tutori al-html/index.html.
    • VMD Tutorial. URL: http://www.ks.uiuc. edu/Trai ni ng/Tutori al s/vmd/tutori al-html/index.html.
  • 14
    • 85139088506 scopus 로고    scopus 로고
    • NAMD User Guide. URL: http://www. ks.uiuc.edu/Research/namd/current/ug/.
    • NAMD User Guide. URL: http://www. ks.uiuc.edu/Research/namd/current/ug/.
  • 15
    • 85139147728 scopus 로고    scopus 로고
    • NAMD Tutorial. URL: http://www.ks.uiuc. edu/Tr ai ni ng/Tut or i al s/namd/namd-tutorial-unix-html/index.html.
    • NAMD Tutorial. URL: http://www.ks.uiuc. edu/Tr ai ni ng/Tut or i al s/namd/namd-tutorial-unix-html/index.html.
  • 16
    • 85139133129 scopus 로고    scopus 로고
    • NAMD Tutorial. URL: http://www.ks.uiuc. edu/Tr ai ni ng/Tut or i al s/namd/namd-tutorial-win-html/index.html.
    • NAMD Tutorial. URL: http://www.ks.uiuc. edu/Tr ai ni ng/Tut or i al s/namd/namd-tutorial-win-html/index.html.
  • 17
    • 67849110013 scopus 로고    scopus 로고
    • 3D-DART: A DNA structure modelling server
    • van Dijk, M. and Bonvin, A. M. J. J. (2009) 3D-DART: a DNA structure modelling server Nucl Acids Res 37, W235–W239.
    • (2009) Nucl Acids Res , vol.37 , pp. W235-W239
    • van Dijk, M.1    Bonvin, A.M.J.J.2
  • 18
    • 58849087632 scopus 로고    scopus 로고
    • Microscopic mechanics of hairpin DNA translocation through synthetic nanopores
    • Comer, J., Dimitrov, V., Zhao, Q., Timp, G., and Aksimentiev, A. (2009) Microscopic mechanics of hairpin DNA translocation through synthetic nanopores Biophys J 96, 593–608.
    • (2009) Biophys J , vol.96 , pp. 593-608
    • Comer, J.1    Dimitrov, V.2    Zhao, Q.3    Timp, G.4    Aksimentiev, A.5
  • 21
    • 33751266937 scopus 로고    scopus 로고
    • Water-silica force field for simulating nanodevices
    • Cruz-Chu, E. R., Aksimentiev, A., and Schulten, K. (2006) Water-silica force field for simulating nanodevices J Phys Chem B 110, 21497–21508.
    • (2006) J Phys Chem B , vol.110 , pp. 21497-21508
    • Cruz-Chu, E.R.1    Aksimentiev, A.2    Schulten, K.3
  • 23
    • 11944254490 scopus 로고
    • Force fields for silicas and aluminophosphates based on ab initio calculations
    • van Beest, B. W. H., Kramer, G. J., and van Santen, R. A. (1990) Force fields for silicas and aluminophosphates based on ab initio calculations Phys Rev Lett 64, 1955–1958.
    • (1990) Phys Rev Lett , vol.64 , pp. 1955-1958
    • van Beest, B.W.H.1    Kramer, G.J.2    van Santen, R.A.3
  • 24
    • 0001497255 scopus 로고    scopus 로고
    • Cooling-rate effects in amorphous silica: A computer-simulation study
    • Vollmayr, K., Kob, W., and Binder, K. (1996) Cooling-rate effects in amorphous silica: A computer-simulation study Phys Rev B 54, 15808–15827.
    • (1996) Phys Rev B , vol.54 , pp. 15808-15827
    • Vollmayr, K.1    Kob, W.2    Binder, K.3
  • 25
    • 65349156366 scopus 로고    scopus 로고
    • Ionic current rectification through silica nanopores
    • Cruz-Chu, E. R., Aksimentiev, A., and Schulten, K. (2009) Ionic current rectification through silica nanopores J Phys Chem C 113, 1850–1862.
    • (2009) J Phys Chem C , vol.113 , pp. 1850-1862
    • Cruz-Chu, E.R.1    Aksimentiev, A.2    Schulten, K.3
  • 26
    • 0030059225 scopus 로고    scopus 로고
    • Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force
    • Grubmüller, H., Heymann, B., and Tavan, P. (1996) Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force Science 271, 997–999.
    • (1996) Science , vol.271 , pp. 997-999
    • Grubmüller, H.1    Heymann, B.2    Tavan, P.3
  • 27
    • 1542289939 scopus 로고    scopus 로고
    • Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase
    • Aksimentiev, A., Balabin, I. A., Fillingame, R. H., and Schulten, K. (2004) Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase Biophys J 86, 1332–1344.
    • (2004) Biophys J , vol.86 , pp. 1332-1344
    • Aksimentiev, A.1    Balabin, I.A.2    Fillingame, R.H.3    Schulten, K.4
  • 29
    • 34247494251 scopus 로고    scopus 로고
    • Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope
    • Kim, M., McNally, B., Murata, K., and Meller, A. (2007) Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope Nanotechnology 18, 205302.
    • (2007) Nanotechnology , vol.18
    • Kim, M.1    McNally, B.2    Murata, K.3    Meller, A.4
  • 30
    • 0032762996 scopus 로고    scopus 로고
    • Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and poly-uridylic acid as homopolymers or as segments within singe RNA molecules
    • Akeson, M., Branton, D., Kasianowicz, J. J., Brandin, E., and Deamer, D. W. (1999) Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and poly-uridylic acid as homopolymers or as segments within singe RNA molecules Biophys J 77, 3227–3233.
    • (1999) Biophys J , vol.77 , pp. 3227-3233
    • Akeson, M.1    Branton, D.2    Kasianowicz, J.J.3    Brandin, E.4    Deamer, D.W.5
  • 32
    • 0035107270 scopus 로고    scopus 로고
    • Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel
    • Vercoutere, W., Winters-Hilt, S., Olsen, H., Deamer, D., Haussler, D., and Akeson, M. (2001) Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel Nature Biotech 19, 248–252.
    • (2001) Nature Biotech , vol.19 , pp. 248-252
    • Vercoutere, W.1    Winters-Hilt, S.2    Olsen, H.3    Deamer, D.4    Haussler, D.5    Akeson, M.6
  • 34
    • 3042736845 scopus 로고    scopus 로고
    • A nanosensor for transmembrane capture and identification of single nucleic acid molecules
    • Nakane, J., Wiggin, M., and Marziali, A. (2004) A nanosensor for transmembrane capture and identification of single nucleic acid molecules Biophys J 87, 615–621.
    • (2004) Biophys J , vol.87 , pp. 615-621
    • Nakane, J.1    Wiggin, M.2    Marziali, A.3
  • 35
    • 14844290867 scopus 로고    scopus 로고
    • Recognizing a single base in an individual DNA strand: A step toward DNA sequencing in nanopores
    • Ashkenasy, N., Sánchez-Quesada, J., Bayley, H., and Ghadiri, M. R. (2005) Recognizing a single base in an individual DNA strand: A step toward DNA sequencing in nanopores Angew Chem Int Ed Engl 44, 1401–1404.
    • (2005) Angew Chem Int Ed Engl , vol.44 , pp. 1401-1404
    • Ashkenasy, N.1    Sánchez-Quesada, J.2    Bayley, H.3    Ghadiri, M.R.4
  • 36
    • 31044443423 scopus 로고    scopus 로고
    • Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor
    • Gracheva, M. E., Xiong, A., Leburton, J.-P., Aksimentiev, A., Schulten, K., and Timp, G. (2006) Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor Nanotechnology 17, 622–633.
    • (2006) Nanotechnology , vol.17 , pp. 622-633
    • Gracheva, M.E.1    Xiong, A.2    Leburton, J.-P.3    Aksimentiev, A.4    Schulten, K.5    Timp, G.6
  • 37
    • 33746625243 scopus 로고    scopus 로고
    • Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor
    • Gracheva, M. E., Aksimentiev, A., and Leburton, J.-P. (2006) Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor Nanotechnology 17, 3160–3165.
    • (2006) Nanotechnology , vol.17 , pp. 3160-3165
    • Gracheva, M.E.1    Aksimentiev, A.2    Leburton, J.-P.3
  • 38
    • 38349169632 scopus 로고    scopus 로고
    • A Single-Molecule Nanopore Device Detects DNA Polymerase Activity with Single-Nucleotide Resolution
    • Cockroft, S., Chu, J., Amorin, M., and Ghadiri, M. (2008) A Single-Molecule Nanopore Device Detects DNA Polymerase Activity with Single-Nucleotide Resolution J Am Chem Soc 130, 818–820.
    • (2008) J am Chem Soc , vol.130 , pp. 818-820
    • Cockroft, S.1    Chu, J.2    Amorin, M.3    Ghadiri, M.4
  • 39
    • 0030465241 scopus 로고    scopus 로고
    • Characterization of individual polynucleotide molecules using a membrane channel
    • Kasianowicz, J. J., Brandin, E., Branton, D., and Deamer, D. W. (1996) Characterization of individual polynucleotide molecules using a membrane channel Proc Natl Acad Sci USA 93, 13770–13773.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 13770-13773
    • Kasianowicz, J.J.1    Brandin, E.2    Branton, D.3    Deamer, D.W.4
  • 41
    • 24644451580 scopus 로고    scopus 로고
    • Orientation discrimination of single stranded DNA inside the a-hemolysin membrane channel
    • Mathé, J., Aksimentiev, A., Nelson, D. R., Schulten, K., and Meller, A. (2005) Orientation discrimination of single stranded DNA inside the a-hemolysin membrane channel Proc Natl Acad Sci USA 102, 12377–12382.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 12377-12382
    • Mathé, J.1    Aksimentiev, A.2    Nelson, D.R.3    Schulten, K.4    Meller, A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.