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Volumn 34, Issue 22, 2006, Pages 6425-6437

Sequence-dependent gating of an ion channel by DNA hairpin molecules

Author keywords

[No Author keywords available]

Indexed keywords

HEMOLYSIN; ION CHANNEL;

EID: 33845913010     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl754     Document Type: Article
Times cited : (41)

References (59)
  • 1
    • 0036280690 scopus 로고    scopus 로고
    • Accurate representation of B-DNA double helical structure with implicit solvent and counterions
    • Wang,L., Hingerty,B.E., Srinivasan,A.R., Olson,W.K. and Broyde,S. (2002) Accurate representation of B-DNA double helical structure with implicit solvent and counterions. Biophys. J., 83, 382-406.
    • (2002) Biophys. J. , vol.83 , pp. 382-406
    • Wang, L.1    Hingerty, B.E.2    Srinivasan, A.R.3    Olson, W.K.4    Broyde, S.5
  • 3
    • 0037106324 scopus 로고    scopus 로고
    • Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG
    • Ng,H.-L. and Dickerson,R.E. (2002) Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG. Nucleic Acids Res., 30, 4061-4067.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4061-4067
    • Ng, H.-L.1    Dickerson, R.E.2
  • 4
    • 0038725129 scopus 로고    scopus 로고
    • Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and P-31 chemical shift anisotropy
    • Wu,Z.G., Delaglio,F., Tjandra,N., Zhurkin,V.B. and Bax,A. (2003) Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and P-31 chemical shift anisotropy. J. Biomol. NMR, 26, 297-315.
    • (2003) J. Biomol. NMR , vol.26 , pp. 297-315
    • Wu, Z.G.1    Delaglio, F.2    Tjandra, N.3    Zhurkin, V.B.4    Bax, A.5
  • 6
    • 0002459355 scopus 로고
    • Thermal denaturation of DNA molecules: A comparison of theory with experiment
    • Wartell,R.M. and Benight,A.S. (1985) Thermal denaturation of DNA molecules: A comparison of theory with experiment. Phys. Rep., 126, 67-107.
    • (1985) Phys. Rep. , vol.126 , pp. 67-107
    • Wartell, R.M.1    Benight, A.S.2
  • 7
    • 0033527321 scopus 로고    scopus 로고
    • Melting studies of short DNA hairpins: Influence of loop sequence and adjoining base pair identity on hairpin thermodynamics
    • Vallone,P.M., Paner,T.M., Hilario,J., Lane,M.J., Faldasz,B.D. and Benight,A.S. (1999) Melting studies of short DNA hairpins: Influence of loop sequence and adjoining base pair identity on hairpin thermodynamics. Biopolymers, 50, 425-442.
    • (1999) Biopolymers , vol.50 , pp. 425-442
    • Vallone, P.M.1    Paner, T.M.2    Hilario, J.3    Lane, M.J.4    Faldasz, B.D.5    Benight, A.S.6
  • 8
    • 0024290403 scopus 로고
    • Influence of dangling thymidine residues on the stability and structure of two DNA duplexes
    • Senior,M., Jones,R.A. and Breslauer,K.J. (1988) Influence of dangling thymidine residues on the stability and structure of two DNA duplexes. Biochemistry, 27, 3879-3885.
    • (1988) Biochemistry , vol.27 , pp. 3879-3885
    • Senior, M.1    Jones, R.A.2    Breslauer, K.J.3
  • 9
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia,J., Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 1460-1465
    • SantaLucia Jr., J.1
  • 10
    • 0032555119 scopus 로고    scopus 로고
    • Kinetics of conformational fluctuations in DNA hairpin-loops
    • Bonnet,G., Krichevsky,O. and Libchaber,A. (1998) Kinetics of conformational fluctuations in DNA hairpin-loops. Proc. Natl Acad. Sci. USA, 95, 8602-8606.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 8602-8606
    • Bonnet, G.1    Krichevsky, O.2    Libchaber, A.3
  • 11
    • 33845890413 scopus 로고
    • Helix formation by d(TA) oligomers. 3. Electrostatic effects
    • Elson,E.L., Scheffler,I.E. and Baldwin,R.L. (1970) Helix formation by d(TA) oligomers. 3. Electrostatic effects. J. Mol. Biol., 30, 17-37.
    • (1970) J. Mol. Biol. , vol.30 , pp. 17-37
    • Elson, E.L.1    Scheffler, I.E.2    Baldwin, R.L.3
  • 15
    • 0038637695 scopus 로고    scopus 로고
    • Single-strand stacking free energy from DNA beacon kinetics
    • Aalberts,D.P., Parman,J.M. and Goddard,N.L. (2003) Single-strand stacking free energy from DNA beacon kinetics. Biophys. J., 84, 3212-3217.
    • (2003) Biophys. J. , vol.84 , pp. 3212-3217
    • Aalberts, D.P.1    Parman, J.M.2    Goddard, N.L.3
  • 16
    • 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. Nat. Biotechnol., 19, 248-252.
    • (2001) Nat. Biotechnol. , vol.19 , pp. 248-252
    • Vercoutere, W.1    Winters-Hilt, S.2    Olsen, H.3    Deamer, D.4    Haussler, D.5    Akeson, M.6
  • 18
    • 0032762996 scopus 로고    scopus 로고
    • Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single 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 polyuridylic acid as homopolymers or as segments within single 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
  • 19
    • 0035831563 scopus 로고    scopus 로고
    • Voltage-driven DNA translocations through a nanopore
    • Meller,A., Nivon,L. and Branton,D. (2001) Voltage-driven DNA translocations through a nanopore. Phys. Rev. Lett., 86, 3435-3439.
    • (2001) Phys. Rev. Lett. , vol.86 , pp. 3435-3439
    • Meller, A.1    Nivon, L.2    Branton, D.3
  • 21
    • 0036797062 scopus 로고    scopus 로고
    • Characterization of nucleic acids by nanopore analysis
    • Deamer,D.W. and Branton,D. (2002) Characterization of nucleic acids by nanopore analysis. Acc. Chem. Res., 35, 817-825.
    • (2002) Acc. Chem. Res. , vol.35 , pp. 817-825
    • Deamer, D.W.1    Branton, D.2
  • 22
    • 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
  • 25
    • 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
  • 26
    • 0037306228 scopus 로고    scopus 로고
    • Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules
    • Winters-Hilt,S., Vercoutere,W., DeGuzman,V.S., Deamer,D., Akeson,M. and Haussler,D. (2003) Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules. Biophys. J., 84, 967-976.
    • (2003) Biophys. J. , vol.84 , pp. 967-976
    • Winters-Hilt, S.1    Vercoutere, W.2    DeGuzman, V.S.3    Deamer, D.4    Akeson, M.5    Haussler, D.6
  • 27
    • 0030447720 scopus 로고    scopus 로고
    • Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore
    • [see comments]
    • Song,L., Hobaugh,M.R., Shustak,C., Cheley,S., Bayley,H. and Gouaux,J.E. (1996) Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore [see comments]. Science, 274, 1859-1866.
    • (1996) Science , vol.274 , pp. 1859-1866
    • Song, L.1    Hobaugh, M.R.2    Shustak, C.3    Cheley, S.4    Bayley, H.5    Gouaux, J.E.6
  • 30
    • 0034930381 scopus 로고    scopus 로고
    • Sequence-specific detection of individual DNA strands using engineered nanopores
    • Howorka,S., Cheley,S. and Bayley,H. (2001) Sequence-specific detection of individual DNA strands using engineered nanopores. Nat. Biotechnol., 19, 636-639.
    • (2001) Nat. Biotechnol. , vol.19 , pp. 636-639
    • Howorka, S.1    Cheley, S.2    Bayley, H.3
  • 33
    • 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
  • 34
    • 14844318136 scopus 로고    scopus 로고
    • Nanopore unzipping of individual DNA hairpin molecules
    • Mathe,J., Visram,H., Viasnoff,V., Rabin,Y. and Meller,A. (2004) Nanopore unzipping of individual DNA hairpin molecules. Biophys. J., 87, 3205-3212.
    • (2004) Biophys. J. , vol.87 , pp. 3205-3212
    • Mathe, J.1    Visram, H.2    Viasnoff, V.3    Rabin, Y.4    Meller, A.5
  • 35
    • 0032941774 scopus 로고    scopus 로고
    • Water transport by the bacterial channel alpha-hemolysin
    • Paula,S., Akeson,M. and Deamer,D. (1999) Water transport by the bacterial channel alpha-hemolysin. Biochim. Biophys. Acta, 1418, 117-126.
    • (1999) Biochim. Biophys. Acta , vol.1418 , pp. 117-126
    • Paula, S.1    Akeson, M.2    Deamer, D.3
  • 36
    • 15244338641 scopus 로고    scopus 로고
    • Ion permeation through the alpha-hemolysin channel: Theoretical studies based on brownian dynamics and Poisson-Nernst-Plank Electrodiffusion Theory
    • Noskov,S.Y., Im,W. and Roux,B. (2004) Ion permeation through the alpha-hemolysin channel: Theoretical studies based on brownian dynamics and Poisson-Nernst-Plank Electrodiffusion Theory. Biophys. J., 87, 2299-2309.
    • (2004) Biophys. J. , vol.87 , pp. 2299-2309
    • Noskov, S.Y.1    Im, W.2    Roux, B.3
  • 37
    • 0032845645 scopus 로고    scopus 로고
    • Driven polymer translocation through a narrow pore
    • Lubensky,D.K. and Nelson,D.R. (1999) Driven polymer translocation through a narrow pore. Biophys. J., 77, 1824-1838.
    • (1999) Biophys. J. , vol.77 , pp. 1824-1838
    • Lubensky, D.K.1    Nelson, D.R.2
  • 38
    • 0000102029 scopus 로고    scopus 로고
    • Polymer translocation through a hole
    • Muthukumar,M. (1999) Polymer translocation through a hole. J. Chem. Phys., 111, 10371-10374.
    • (1999) J. Chem. Phys. , vol.111 , pp. 10371-10374
    • Muthukumar, M.1
  • 39
    • 33645765294 scopus 로고    scopus 로고
    • Simulation of polymer translocation through protein channels
    • Muthukumar,M. and Kong,C.Y. (2006) Simulation of polymer translocation through protein channels. Proc. Natl Acad. Sci. USA, 103, 5273-5278.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 5273-5278
    • Muthukumar, M.1    Kong, C.Y.2
  • 40
    • 84990946704 scopus 로고    scopus 로고
    • Single-stranded DNA translocation through a nanopore: A master equation approach
    • Flomenbom,O. and Klafter,J. (2003) Single-stranded DNA translocation through a nanopore: A master equation approach. Phys. Rev. E, 68, 041910-041917.
    • (2003) Phys. Rev. E , vol.68 , pp. 041910-041917
    • Flomenbom, O.1    Klafter, J.2
  • 41
    • 9744225875 scopus 로고    scopus 로고
    • Electrophoresis of a bead-rod chain through a narrow slit: A brownian dynamics study
    • Kim,S.H., Panwar,A.S., Kumar,S., Ahn,K.H. and Lee,S.J. (2004) Electrophoresis of a bead-rod chain through a narrow slit: A brownian dynamics study. J. Chem. Phys., 121, 9116-9122.
    • (2004) J. Chem. Phys. , vol.121 , pp. 9116-9122
    • Kim, S.H.1    Panwar, A.S.2    Kumar, S.3    Ahn, K.H.4    Lee, S.J.5
  • 42
    • 33645150902 scopus 로고    scopus 로고
    • Dynamics of polymer translocation through nanopores: Theory meets experiment
    • Matysiak,S., Montesi,A., Pasquali,M., Kolomeisky,A.B. and Clementi,C. (2006) Dynamics of polymer translocation through nanopores: Theory meets experiment. Phys. Rev. Lett., 96, 118101-118104.
    • (2006) Phys. Rev. Lett. , vol.96 , pp. 118101-118104
    • Matysiak, S.1    Montesi, A.2    Pasquali, M.3    Kolomeisky, A.B.4    Clementi, C.5
  • 43
    • 0035902469 scopus 로고    scopus 로고
    • Force and kinetic barriers to unzipping of the DNA double helix
    • Cocco,S., Monasson,R. and Marko,J.F. (2001) Force and kinetic barriers to unzipping of the DNA double helix. Proc. Natl Acad. Sci. USA, 98, 8608-8613.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 8608-8613
    • Cocco, S.1    Monasson, R.2    Marko, J.F.3
  • 44
    • 0001660217 scopus 로고
    • Influence of loop residues on the relative stabilities of DNA hairpin structures
    • Senior,M.M., Jones,R.A. and Breslauer,K.J. (1988) Influence of loop residues on the relative stabilities of DNA hairpin structures. Proc. Natl Acad. Sci. USA, 85, 6242-6246
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 6242-6246
    • Senior, M.M.1    Jones, R.A.2    Breslauer, K.J.3
  • 45
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 46
    • 0001774017 scopus 로고
    • Fitting and Statistical Analysis of Single Channel Records
    • In Sakmann,B. and Neher,E. (eds), Plenum Press, NY
    • Colquhoun,D. and Sigworth,F.J. (1983) Fitting and Statistical Analysis of Single Channel Records. In Sakmann,B. and Neher,E. (eds), Single Channel Recording. Plenum Press, NY, pp. 191-263.
    • (1983) Single Channel Recording , pp. 191-263
    • Colquhoun, D.1    Sigworth, F.J.2
  • 48
    • 0019438921 scopus 로고
    • The internal dynamics of globular proteins
    • Karplus,M. and McCammon,J.A. (1981) The internal dynamics of globular proteins. CRC Crit. Rev. Biochem., 9, 293-349.
    • (1981) CRC Crit. Rev. Biochem. , vol.9 , pp. 293-349
    • Karplus, M.1    McCammon, J.A.2
  • 49
    • 0025048105 scopus 로고
    • Molecular dynamics simulations in biology
    • Karplus,M. and Petsko,G.A. (1990) Molecular dynamics simulations in biology. Nature, 347, 631-639.
    • (1990) Nature , vol.347 , pp. 631-639
    • Karplus, M.1    Petsko, G.A.2
  • 50
    • 10344245541 scopus 로고    scopus 로고
    • On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation
    • Allen,T.W., Andersen,O.S. and Roux,B. (2004) On the importance of atomic fluctuations, protein flexibility, and solvent in ion permeation. J. Gen. Physiol., 124, 679-690.
    • (2004) J. Gen. Physiol. , vol.124 , pp. 679-690
    • Allen, T.W.1    Andersen, O.S.2    Roux, B.3
  • 51
    • 0034934258 scopus 로고    scopus 로고
    • Configurational diffusion down a folding tunnel describes the dynamics of DNA hairpins
    • Ansari,A., Kuznetsov,S.V. and Shen,Y.-Q. (2001) Configurational diffusion down a folding tunnel describes the dynamics of DNA hairpins. Proc Natl Acad. Sci. USA, 98, 7771-7776.
    • (2001) Proc Natl Acad. Sci. USA , vol.98 , pp. 7771-7776
    • Ansari, A.1    Kuznetsov, S.V.2    Shen, Y.-Q.3
  • 52
    • 16344374747 scopus 로고    scopus 로고
    • Dynamics of DNA duplex formation studied by single molecule force measurements
    • Bockelmann,U., Thomen,P. and Heslot,F. (2004) Dynamics of DNA duplex formation studied by single molecule force measurements. Biophys. J., 87, 3388-3396.
    • (2004) Biophys. J. , vol.87 , pp. 3388-3396
    • Bockelmann, U.1    Thomen, P.2    Heslot, F.3
  • 55
    • 0022504362 scopus 로고
    • Ionic channels formed by Staphylococcus aureus alpha-toxin: Voltage-dependent inhibition by divalent and tri-valent cations
    • Menestrina,G. (1986) Ionic channels formed by Staphylococcus aureus alpha-toxin: Voltage-dependent inhibition by divalent and tri-valent cations. J. Membr. Biol., 90, 177-190.
    • (1986) J. Membr. Biol. , vol.90 , pp. 177-190
    • Menestrina, G.1
  • 56
    • 0035169385 scopus 로고    scopus 로고
    • Prolonged residence time of a noncovalent molecular adapter, beta-cyclodextrin, within the lumen of mutant alpha-hemolysin pores
    • Gu,L.Q., Cheley,S. and Bayley,H. (2001) Prolonged residence time of a noncovalent molecular adapter, beta-cyclodextrin, within the lumen of mutant alpha-hemolysin pores. J. Gen. Physiol., 118, 481-493.
    • (2001) J. Gen. Physiol. , vol.118 , pp. 481-493
    • Gu, L.Q.1    Cheley, S.2    Bayley, H.3
  • 58
    • 33644874826 scopus 로고    scopus 로고
    • LGICdb: A manually curated sequence database after the genomes
    • Donizelli,M., Djite,M.-A. and Le Novère,N. (2006) LGICdb: A manually curated sequence database after the genomes. Nucleic Acids Res., 34, D267-D269.
    • (2006) Nucleic Acids Res. , vol.34
    • Donizelli, M.1    Djite, M.-A.2    Le Novère, N.3
  • 59
    • 1642383081 scopus 로고    scopus 로고
    • Mechanisms of channel gating of the ligand-gated ion channel superfamily inferred from protein structure
    • Absalom,N.L., Lewis,T.M. and Schofield,P.R. (2004) Mechanisms of channel gating of the ligand-gated ion channel superfamily inferred from protein structure. J. Exp. Physiol., 89, 145-153.
    • (2004) J. Exp. Physiol. , vol.89 , pp. 145-153
    • Absalom, N.L.1    Lewis, T.M.2    Schofield, P.R.3


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