메뉴 건너뛰기




Volumn 5, Issue 12, 2011, Pages 9345-9353

Nanopore analysis of individual RNA/antibiotic complexes

Author keywords

A site; antibiotics; drug discovery; molecular dynamics; rRNA; single molecule

Indexed keywords

A-SITE; AMINOGLYCOSIDE ANTIBIOTICS; AMINOGLYCOSIDES; BINDING ISOTHERMS; DRUG DISCOVERY; ION CURRENTS; IONIC CURRENT; LABEL FREE; MOLECULAR DYNAMICS SIMULATIONS; RRNA; SILICON NITRIDE MEMBRANE; SINGLE-MOLECULE; SOLID-STATE MEMBRANES;

EID: 84555163558     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn203764j     Document Type: Article
Times cited : (71)

References (53)
  • 3
    • 65549105556 scopus 로고    scopus 로고
    • Mechanisms of RNA-Mediated Disease
    • ORourke, J. R.; Swanson, M. S. Mechanisms of RNA-Mediated Disease J. Biol. Chem. 2009, 284, 7419-7423
    • (2009) J. Biol. Chem. , vol.284 , pp. 7419-7423
    • Orourke, J.R.1    Swanson, M.S.2
  • 4
    • 76349090175 scopus 로고    scopus 로고
    • RNAs Coming of Age as a Drug Target
    • Vicens, Q. RNAs Coming of Age as a Drug Target J. Incl. Phenom. Macrocycl. Chem. 2009, 65, 171-188
    • (2009) J. Incl. Phenom. Macrocycl. Chem. , vol.65 , pp. 171-188
    • Vicens, Q.1
  • 5
    • 77749291830 scopus 로고    scopus 로고
    • Targeting RNA
    • Borman, S. Targeting RNA Chem. Eng. News 2009, 87, 63-66
    • (2009) Chem. Eng. News , vol.87 , pp. 63-66
    • Borman, S.1
  • 6
    • 34147214716 scopus 로고    scopus 로고
    • Multiple molecular mechanisms for multidrug resistance transporters
    • DOI 10.1038/nature05630, PII NATURE05630
    • Higgins, C. F. Multiple Molecular Mechanisms for Multidrug Resistance Transporters Nature 2007, 446, 749-757 (Pubitemid 46582024)
    • (2007) Nature , vol.446 , Issue.7137 , pp. 749-757
    • Higgins, C.F.1
  • 7
    • 0034886697 scopus 로고    scopus 로고
    • Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site
    • DOI 10.1016/S0969-2126(01)00629-3, PII S0969212601006293
    • Vicens, Q.; Westhof, E. Crystal Structure of Paromomycin Docked into the Eubacterial Ribosomal Decoding A-Site Structure 2001, 9, 647-658 (Pubitemid 32772887)
    • (2001) Structure , vol.9 , Issue.8 , pp. 647-658
    • Vicens, Q.1    Westhof, E.2
  • 8
    • 33747894350 scopus 로고    scopus 로고
    • A-site model RNAs
    • DOI 10.1016/j.biochi.2006.04.020, PII S0300908406001209, The Ribosomal Decoding Site and Antibiotics
    • Hermann, T. A-Site Model RNAs Biochimie 2006, 88, 1021-1026 (Pubitemid 44291881)
    • (2006) Biochimie , vol.88 , Issue.8 , pp. 1021-1026
    • Hermann, T.1
  • 9
    • 33747891811 scopus 로고    scopus 로고
    • The Ribosomal A-Site as an Inspiration for the Design of RNA Binders
    • Tor, Y. The Ribosomal A-Site as an Inspiration for the Design of RNA Binders Biochimie 2006, 88, 1045-1051
    • (2006) Biochimie , vol.88 , pp. 1045-1051
    • Tor, Y.1
  • 10
    • 61449249034 scopus 로고    scopus 로고
    • Exploring RNA-Ligand Interactions
    • Tor, Y. Exploring RNA-Ligand Interactions. Pure & Appl. Chem. 2009, 81, 263-272.
    • (2009) Pure & Appl. Chem. , vol.81 , pp. 263-272
    • Tor, Y.1
  • 11
    • 0023238983 scopus 로고
    • Interaction of antibiotics with functional sites in 16S ribosomal RNA
    • DOI 10.1038/327389a0
    • Moazed, D.; Noller, H. F. Interaction of Antibiotics with Functional Sites in 16S Ribosomal-RNA Nature 1987, 327, 389-394 (Pubitemid 17075811)
    • (1987) Nature , vol.327 , Issue.6121 , pp. 389-394
    • Moazed, D.1    Noller, H.F.2
  • 12
    • 0037229886 scopus 로고    scopus 로고
    • Comparison of X-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex
    • DOI 10.1016/S0969-2126(02)00934-6, PII S0969212602009346
    • Lynch, S. R.; Gonzalez, R. L.; Puglisi, J. D. Comparison of X-Ray Crystal Structure of the 30S Subunit-Antibiotic Complex with NMR Structure of Decoding Site Oligonucleotide-Paromomycin Complex Structure 2003, 11, 43-53 (Pubitemid 36071495)
    • (2003) Structure , vol.11 , Issue.1 , pp. 43-53
    • Lynch, S.R.1    Gonzalez Jr., R.L.2    Puglisi, J.D.3
  • 13
    • 68349114868 scopus 로고    scopus 로고
    • Selection of Small Peptides, Inhibitors of Translation
    • Llano-Sotelo, B.; Klepacki, D.; Mankin, A. S. Selection of Small Peptides, Inhibitors of Translation J. Mol. Biol. 2009, 391, 813-819
    • (2009) J. Mol. Biol. , vol.391 , pp. 813-819
    • Llano-Sotelo, B.1    Klepacki, D.2    Mankin, A.S.3
  • 14
    • 0028138280 scopus 로고
    • Interactions of a small RNA with antibiotic and RNA ligands of the 30S subunit
    • DOI 10.1038/370659a0
    • Purohit, P.; Stern, S. Interactions of a Small RNA with Antibiotic and RNA Ligands of the 30S Subunit Nature 1994, 370, 659-662 (Pubitemid 24270688)
    • (1994) Nature , vol.370 , Issue.6491 , pp. 659-662
    • Purohit, P.1    Stern, S.2
  • 15
    • 33947200641 scopus 로고    scopus 로고
    • Conformational flexibility of ribosomal decoding-site RNA monitored by fluorescent pteridine base analogues
    • DOI 10.1016/j.tet.2006.08.106, PII S0040402007001718, Flourescent Nucleoside Analogs: Synthesis, Properties and Applications
    • Parsons, J.; Hermann, T. Conformational Flexibility of Ribosomal Decoding-Site RNA Monitored by Fluorescent Pteridine Base Analogues Tetrahedron 2007, 63, 3548-3552 (Pubitemid 46428350)
    • (2007) Tetrahedron , vol.63 , Issue.17 , pp. 3548-3552
    • Parsons, J.1    Hermann, T.2
  • 16
    • 33947234581 scopus 로고    scopus 로고
    • Use of 2-aminopurine as a fluorescent tool for characterizing antibiotic recognition of the bacterial rRNA A-site
    • DOI 10.1016/j.tet.2006.08.107, PII S0040402007001731, Flourescent Nucleoside Analogs: Synthesis, Properties and Applications
    • Barbieri, C. M.; Kaul, M.; Pilch, D. S. Use of 2-Aminopurine as a Fluorescent Tool for Characterizing Antibiotic Recognition of the Bacterial rRNA A-Site Tetrahedron 2007, 63, 3567-3574 (Pubitemid 46428352)
    • (2007) Tetrahedron , vol.63 , Issue.17 , pp. 3567-3574
    • Barbieri, C.M.1    Kaul, M.2    Pilch, D.S.3
  • 18
    • 1642347123 scopus 로고    scopus 로고
    • Fluorescence-Based Approach for Detecting and Characterizing Antibiotic-Induced Conformational Changes in Ribosomal RNA: Comparing Aminoglycoside Binding to Prokaryotic and Eukaryotic Ribosomal RNA Sequences
    • DOI 10.1021/ja030568i
    • Kaul, M.; Barbieri, C. M.; Pilch, D. S. Fluorescence-Based Approach for Detecting and Characterizing Antibiotic-Induced Conformational Changes in Ribosomal RNA: Comparing Aminoglycoside Binding to Prokaryotic and Eukaryotic Ribosomal RNA Sequences J. Am. Chem. Soc. 2004, 126, 3447-3453 (Pubitemid 38366734)
    • (2004) Journal of the American Chemical Society , vol.126 , Issue.11 , pp. 3447-3453
    • Kaul, M.1    Barbieri, C.M.2    Pilch, D.S.3
  • 19
    • 34247395439 scopus 로고    scopus 로고
    • Monitoring aminoglycoside-induced conformational changes in 16S rRNA through acrylamide quenching
    • DOI 10.1016/j.bmc.2007.03.025, PII S0968089607002155
    • Chao, P. W.; Chow, C. S. Monitoring Aminoglycoside-Induced Conformational Changes in 16S rRNA through Acrylamide Quenching Bioorg. Med. Chem. 2007, 15, 3825-3831 (Pubitemid 46635134)
    • (2007) Bioorganic and Medicinal Chemistry , vol.15 , Issue.11 , pp. 3825-3831
    • Chao, P.-W.1    Chow, C.S.2
  • 20
    • 33847298021 scopus 로고    scopus 로고
    • Fluorescent Pyrimidine Ribonucleotide: Synthesis, Enzymatic Incorporation, and Utilization
    • Srivatsan, S. G.; Tor, Y. Fluorescent Pyrimidine Ribonucleotide: Synthesis, Enzymatic Incorporation, and Utilization J. Am. Chem. Soc. 2007, 129, 2044-2053
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 2044-2053
    • Srivatsan, S.G.1    Tor, Y.2
  • 21
    • 72249111306 scopus 로고    scopus 로고
    • FRET Enabled Real Time Detection of RNA-Small Molecule Binding
    • Xie, Y.; Dix, A. V.; Tor, Y. FRET Enabled Real Time Detection of RNA-Small Molecule Binding J. Am. Chem. Soc. 2009, 131, 17605-17614
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 17605-17614
    • Xie, Y.1    Dix, A.V.2    Tor, Y.3
  • 22
    • 0028465092 scopus 로고
    • Counting polymers moving through a single ion channel
    • DOI 10.1038/370279a0
    • Bezrukov, S. M.; Vodyanoy, I.; Parsegian, V. A. Counting Polymers Moving through a Single-Ion Channel Nature 1994, 370, 279-281 (Pubitemid 24250118)
    • (1994) Nature , vol.370 , Issue.6487 , pp. 279-281
    • Bezrukov, S.M.1    Vodyanoy, I.2    Parsegian, V.A.3
  • 24
    • 0033594410 scopus 로고    scopus 로고
    • Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter
    • DOI 10.1038/19491
    • Gu, L. Q.; Braha, O.; Conlan, S.; Cheley, S.; Bayley, H. Stochastic Sensing of Organic Analytes by a Pore-Forming Protein Containing a Molecular Adapter Nature 1999, 398, 686-690 (Pubitemid 29197642)
    • (1999) Nature , vol.398 , Issue.6729 , pp. 686-690
    • Gu, L.-Q.1    Braha, O.2    Conlan, S.3    Cheley, S.4    Bayley, H.5
  • 25
    • 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.; Deamer, D. W. Microsecond Time-Scale Discrimination among Polycytidylic Acid, Polyadenylic Acid, and Polyuridylic Acid as Homopolymers or as Segments within Single RNA Molecules Biophys. J. 1999, 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
  • 26
    • 32244449078 scopus 로고    scopus 로고
    • Toward single molecule DNA sequencing: Direct identification of ribonucleoside and deoxyribonucleoside 5′-monophosphates by using an engineered protein nanopore equipped with a molecular adapter
    • DOI 10.1021/ja057123+
    • Astier, Y.; Braha, O.; Bayley, H. 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. 2006, 128, 1705-1710 (Pubitemid 43214885)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.5 , pp. 1705-1710
    • Astier, Y.1    Braha, O.2    Bayley, H.3
  • 27
  • 28
    • 78149415469 scopus 로고    scopus 로고
    • Rapid Electronic Detection of Probe-Specific MicroRNAs Using Thin Nanopore Sensors
    • Wanunu, M.; Dadosh, T.; Ray, V.; Jin, J.; McReynolds, L.; Drndic, M. Rapid Electronic Detection of Probe-Specific MicroRNAs Using Thin Nanopore Sensors Nat. Nanotechnol. 2010, 5, 807-814
    • (2010) Nat. Nanotechnol. , vol.5 , pp. 807-814
    • Wanunu, M.1    Dadosh, T.2    Ray, V.3    Jin, J.4    McReynolds, L.5    Drndic, M.6
  • 29
    • 70350649035 scopus 로고    scopus 로고
    • Single-Molecule Bonds Characterized by Solid-State Nanopore Force Spectroscopy
    • Tabard-Cossa, V.; Wiggin, M.; Trivedi, D.; Jetha, N. N.; Dwyer, J. R.; Marziali, A. Single-Molecule Bonds Characterized by Solid-State Nanopore Force Spectroscopy ACS Nano 2009, 3, 3009-3014
    • (2009) ACS Nano , vol.3 , pp. 3009-3014
    • Tabard-Cossa, V.1    Wiggin, M.2    Trivedi, D.3    Jetha, N.N.4    Dwyer, J.R.5    Marziali, A.6
  • 30
    • 74849140157 scopus 로고    scopus 로고
    • Detection of Local Protein Structures along DNA Using Solid-State Nanopores
    • Kowalczyk, S. W.; Hall, A. R.; Dekker, C. Detection of Local Protein Structures along DNA Using Solid-State Nanopores Nano Lett. 2010, 10, 324-328
    • (2010) Nano Lett. , vol.10 , pp. 324-328
    • Kowalczyk, S.W.1    Hall, A.R.2    Dekker, C.3
  • 32
    • 33746287457 scopus 로고    scopus 로고
    • Label-free affinity assays by rapid detection of immune complexes in submicrometer pores
    • DOI 10.1002/anie.200502862
    • Uram, J. D.; Ke, K.; Hunt, A. J.; Mayer, M. Label-Free Affinity Assays by Rapid Detection of Immune Complexes in Submicrometer Pores Angew. Chem., Int. Ed. 2006, 45, 2281-2285 (Pubitemid 44105163)
    • (2006) Angewandte Chemie - International Edition , vol.45 , Issue.14 , pp. 2281-2285
    • Uram, J.D.1    Ke, K.2    Hunt, A.J.3    Mayer, M.4
  • 33
    • 33747166710 scopus 로고    scopus 로고
    • Submicrometer pore-based characterization and quantification of antibody-virus interactions
    • DOI 10.1002/smll.200600006
    • Uram, J. D.; Ke, K.; Hunt, A. J.; Mayer, M. Submicrometer Pore-Based Characterization and Quantification of Antibody-Virus Interactions Small 2006, 2, 967-972 (Pubitemid 44230993)
    • (2006) Small , vol.2 , Issue.8-9 , pp. 967-972
    • Uram, J.D.1    Ke, K.2    Hunt, A.J.3    Mayer, M.4
  • 35
    • 72849121316 scopus 로고    scopus 로고
    • DNA Profiling Using Solid-State Nanopores: Detection of DNA-Binding Molecules
    • Wanunu, M.; Sutin, J.; Meller, A. DNA Profiling Using Solid-State Nanopores: Detection of DNA-Binding Molecules Nano Lett. 2009, 9, 3498-3502
    • (2009) Nano Lett. , vol.9 , pp. 3498-3502
    • Wanunu, M.1    Sutin, J.2    Meller, A.3
  • 36
    • 33748882391 scopus 로고    scopus 로고
    • Ribosomal RNA recognition by aminoglycoside antibiotics
    • DOI 10.1007/b100447, DNA Binders and Related Subjects
    • Pilch, D. S.; Kaul, M.; Barbieri, C. M. Ribosomal RNA Recognition by Aminoglycoside Antibiotics. In DNA Binders and Related Subjects; Springer-Verlag: Berlin, 2005; Vol. 253, pp 179-204. (Pubitemid 44420843)
    • (2005) Topics in Current Chemistry , vol.253 , pp. 179-204
    • Pilch, D.S.1    Kaul, M.2    Barbieri, C.M.3
  • 37
    • 58149299894 scopus 로고    scopus 로고
    • DNA Translocation Governed by Interactions with Solid-State Nanopores
    • Wanunu, M.; Sutin, J.; McNally, B.; Chow, A.; Meller, A. DNA Translocation Governed by Interactions with Solid-State Nanopores Biophys. J. 2008, 95, 4716-4725
    • (2008) Biophys. J. , vol.95 , pp. 4716-4725
    • Wanunu, M.1    Sutin, J.2    McNally, B.3    Chow, A.4    Meller, A.5
  • 39
    • 58849087632 scopus 로고    scopus 로고
    • Microscopic Mechanics of Hairpin DNA Translocation through Synthetic Nanopores
    • Comer, J.; Dimitrov, V.; Zhao, Q.; Timp, G.; Aksimentiev, A. Microscopic Mechanics of Hairpin DNA Translocation through Synthetic Nanopores Biophys. J. 2009, 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
  • 41
    • 33846823909 scopus 로고
    • Particle Mesh Ewald - An N.LOG(N) Method for Ewald Sums in Large Systems
    • Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald-An N.LOG(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 42
    • 0035449971 scopus 로고    scopus 로고
    • Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations
    • DOI 10.1063/1.1389854
    • Batcho, P. F.; Case, D. A.; Schlick, T. Optimized Particle-Mesh Ewald/Multiple-Time Step Integration for Molecular Dynamics Simulations J. Chem. Phys. 2001, 115, 4003-4018 (Pubitemid 32841402)
    • (2001) Journal of Chemical Physics , vol.115 , Issue.9 , pp. 4003-4018
    • Batcho, P.F.1    Case, D.A.2    Schlick, T.3
  • 43
    • 48749148224 scopus 로고
    • RATTLE - A Velocity Version of the SHAKE Algorithm for Molecular-Dynamics Calculations
    • Andersen, H. C. RATTLE-A Velocity Version of the SHAKE Algorithm for Molecular-Dynamics Calculations J. Comput. Phys. 1983, 52, 24-34
    • (1983) J. Comput. Phys. , vol.52 , pp. 24-34
    • Andersen, H.C.1
  • 44
    • 84986440341 scopus 로고
    • SETTLE - An Analytical Version of the SHAKE and RATTLE Algorithm for Rigid Water Models
    • Miyamoto, S.; Kollman, P. A. SETTLE-An Analytical Version of the SHAKE and RATTLE Algorithm for Rigid Water Models J. Comput. Chem. 1992, 13, 952-962
    • (1992) J. Comput. Chem. , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 45
    • 0041784950 scopus 로고    scopus 로고
    • All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
    • MacKerell, A. D. et al. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.1
  • 47
    • 57449090256 scopus 로고    scopus 로고
    • Molecular Dynamics Study of the Ribosomal A-Site
    • Romanowska, J.; Setny, P.; Trylska, J. Molecular Dynamics Study of the Ribosomal A-Site J. Phys. Chem. B 2008, 112, 15227-15243
    • (2008) J. Phys. Chem. B , vol.112 , pp. 15227-15243
    • Romanowska, J.1    Setny, P.2    Trylska, J.3
  • 48
    • 36449003554 scopus 로고
    • Constant-Pressure Molecular-Dynamics Algorithms
    • Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant-Pressure Molecular-Dynamics Algorithms J. Chem. Phys. 1994, 101, 4177-4189
    • (1994) J. Chem. Phys. , vol.101 , pp. 4177-4189
    • Martyna, G.J.1    Tobias, D.J.2    Klein, M.L.3
  • 49
    • 4444234147 scopus 로고    scopus 로고
    • Microscopic kinetics of DNA translocation through synthetic nanopores
    • DOI 10.1529/biophysj.104.042960
    • Aksimentiev, A.; Heng, J. B.; Timp, G.; Schulten, K. Microscopic Kinetics of DNA Translocation through Synthetic Nanopores Biophys. J. 2004, 87, 2086-2097 (Pubitemid 39172203)
    • (2004) Biophysical Journal , vol.87 , Issue.3 , pp. 2086-2097
    • Aksimentiev, A.1    Heng, J.B.2    Timp, G.3    Schulten, K.4
  • 50
    • 0029825658 scopus 로고    scopus 로고
    • Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic
    • DOI 10.1126/science.274.5291.1367
    • Fourmy, D.; Recht, M. I.; Blanchard, S. C.; Puglisi, J. D. Structure of the A-Site of Escherichia coli 16S Ribosomal RNA Complexed with an Aminoglycoside Antibiotic Science 1996, 274, 1367-1371 (Pubitemid 26391459)
    • (1996) Science , vol.274 , Issue.5291 , pp. 1367-1371
    • Fourmy, D.1    Recht, M.I.2    Blanchard, S.C.3    Puglisi, J.D.4
  • 52
    • 22244445788 scopus 로고    scopus 로고
    • Imaging α-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability, and the electrostatic potential map
    • DOI 10.1529/biophysj.104.058727
    • Aksimentiev, A.; Schulten, K. Imaging α-Hemolysin with Molecular Dynamics: Ionic Conductance, Osmotic Permeability, and the Electrostatic Potential Map Biophys. J. 2005, 88, 3745-3761 (Pubitemid 40991090)
    • (2005) Biophysical Journal , vol.88 , Issue.6 , pp. 3745-3761
    • Aksimentiev, A.1    Schulten, K.2
  • 53
    • 77953677764 scopus 로고    scopus 로고
    • Deciphering Ionic Current Signatures of DNA Transport through a Nanopore
    • Aksimentiev, A. Deciphering Ionic Current Signatures of DNA Transport through a Nanopore Nanoscale 2010, 2, 468-483
    • (2010) Nanoscale , vol.2 , pp. 468-483
    • Aksimentiev, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.