메뉴 건너뛰기




Volumn , Issue , 2013, Pages 181-213

Fluorescence resonance energy transfer as a tool to investigate RNA structure and folding

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84979155898     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1515/9783110284959.181     Document Type: Chapter
Times cited : (5)

References (103)
  • 1
    • 84981779372 scopus 로고
    • Zwischenmolekulare Energiewanderung und Fluoreszenz
    • Forster T. Zwischenmolekulare Energiewanderung und Fluoreszenz. Ann Phys. 1948; 437:55-75.
    • (1948) Ann Phys , vol.437 , pp. 55-75
    • Forster, T.1
  • 3
    • 0036738673 scopus 로고    scopus 로고
    • Specific labeling of polypeptides at amino-terminal cysteine residues using Cy5-benzyl thioester
    • Schuler B, Pannell LK. Specific labeling of polypeptides at amino-terminal cysteine residues using Cy5-benzyl thioester. Bioconjug Chem. 2002;13:1039-43.
    • (2002) Bioconjug Chem , vol.13 , pp. 1039-1043
    • Schuler, B.1    Pannell, L.K.2
  • 4
    • 0034647205 scopus 로고    scopus 로고
    • Intein-mediated synthesis of proteins containing carbohydrates and other molecular probes
    • Tolbert TJ, Wong, CH. Intein-mediated synthesis of proteins containing carbohydrates and other molecular probes. J Am Chem Soc. 2000;122:5421-8.
    • (2000) J am Chem Soc , vol.122 , pp. 5421-5428
    • Tolbert, T.J.1    Wong, C.H.2
  • 6
    • 33645325418 scopus 로고    scopus 로고
    • Efficient incorporation of unnatural amino acids into proteins in Escherichia coli
    • Ryu Y Schultz PG. Efficient incorporation of unnatural amino acids into proteins in Escherichia coli. Nat Methods. 2006;3:263-5.
    • (2006) Nat Methods , vol.3 , pp. 263-265
    • Ryu Y Schultz, P.G.1
  • 7
    • 0037422608 scopus 로고    scopus 로고
    • Addition of the keto functional group to the genetic code of Escherichia coli
    • Wang L, Zhang Z, Brock A, Schultz PG. Addition of the keto functional group to the genetic code of Escherichia coli. Proc Natl Acad Sci U S A. 2003;100:56-61.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 56-61
    • Wang, L.1    Zhang, Z.2    Brock, A.3    Schultz, P.G.4
  • 8
    • 0037936779 scopus 로고    scopus 로고
    • Merging fluorescence resonance energy transfer and expressed protein ligation to analyze protein-protein interactions
    • Scheibner KA, Zhang Z, Cole PA. Merging fluorescence resonance energy transfer and expressed protein ligation to analyze protein-protein interactions. Anal Biochem. 2003;317:226-32.
    • (2003) Anal Biochem , vol.317 , pp. 226-232
    • Scheibner, K.A.1    Zhang, Z.2    Cole, P.A.3
  • 9
    • 0032568924 scopus 로고    scopus 로고
    • Expressed protein ligation, a novel method for studying protein-protein interactions in transcription
    • Severinov K, Muir TW. Expressed protein ligation, a novel method for studying protein-protein interactions in transcription. J Biol Chem. 1998;273:16205-9.
    • (1998) J Biol Chem , vol.273 , pp. 16205-16209
    • Severinov, K.1    Muir, T.W.2
  • 10
    • 0026538940 scopus 로고
    • Initiator oligonucleotides for the combination of chemical and enzymatic RNA synthesis
    • Pitulle C, Kleineidam RG, Sproat B, Krupp G. Initiator oligonucleotides for the combination of chemical and enzymatic RNA synthesis. Gene. 1992;112:101-5.
    • (1992) Gene , vol.112 , pp. 101-105
    • Pitulle, C.1    Kleineidam, R.G.2    Sproat, B.3    Krupp, G.4
  • 11
    • 0026680843 scopus 로고
    • Site-specific modification of pre-mRNA: The 2'-hydroxyl groups at the splice sites
    • Moore MJ, Sharp PA. Site-specific modification of pre-mRNA: the 2'-hydroxyl groups at the splice sites. Science. 1992;256:992-7.
    • (1992) Science , vol.256 , pp. 992-997
    • Moore, M.J.1    Sharp, P.A.2
  • 12
    • 0034131335 scopus 로고    scopus 로고
    • Joining of RNAs by splinted ligation
    • Moore MJ, Query CC. Joining of RNAs by splinted ligation. Methods Enzymol. 2000;317:109-23.
    • (2000) Methods Enzymol , vol.317 , pp. 109-123
    • Moore, M.J.1    Query, C.C.2
  • 13
    • 12844274892 scopus 로고    scopus 로고
    • Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization
    • Smith GJ, et al. Efficient fluorescence labeling of a large RNA through oligonucleotide hybridization. RNA. 2005;11:234-9.
    • (2005) RNA , vol.11 , pp. 234-239
    • Smith, G.J.1
  • 14
    • 0026687952 scopus 로고
    • Fluorescence resonance energy transfer and nucleic acids
    • Clegg RM. Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 1992;211:353-88.
    • (1992) Methods Enzymol , vol.211 , pp. 353-388
    • Clegg, R.M.1
  • 16
    • 0016502735 scopus 로고
    • Distribution of end-to-end distances of oligopeptides in solution as estimated by energy transfer
    • Haas E, et al. Distribution of end-to-end distances of oligopeptides in solution as estimated by energy transfer. Proc Natl Acad Sci U S A. 1975;72:1807-11.
    • (1975) Proc Natl Acad Sci U S A , vol.72 , pp. 1807-1811
    • Haas, E.1
  • 17
    • 77954641162 scopus 로고    scopus 로고
    • Accurate single-molecule FRET studies using multiparameter fluorescence detection
    • Sisamakis E, et al. Accurate single-molecule FRET studies using multiparameter fluorescence detection. Methods Enzymol. 2010;475:455-514.
    • (2010) Methods Enzymol , vol.475 , pp. 455-514
    • Sisamakis, E.1
  • 18
    • 77957157863 scopus 로고    scopus 로고
    • Single-molecule FRET of protein-nucleic acid and protein-protein complexes: Surface passivation and immobilization
    • Lamichhane R, et al. Single-molecule FRET of protein-nucleic acid and protein-protein complexes: surface passivation and immobilization. Methods. 2010;52:192-200.
    • (2010) Methods , vol.52 , pp. 192-200
    • Lamichhane, R.1
  • 19
    • 0037461520 scopus 로고    scopus 로고
    • Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules
    • Kapanidis AN, Weiss S. Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules. J Chem Phys. 2002;117:10953-64.
    • (2002) J Chem Phys , vol.117 , pp. 10953-10964
    • Kapanidis, A.N.1    Weiss, S.2
  • 20
    • 33750295496 scopus 로고    scopus 로고
    • Nonblinking and long-lasting single-molecule fluorescence imaging
    • Rasnik I, McKinney SA, Ha T. Nonblinking and long-lasting single-molecule fluorescence imaging. Nat Methods. 2006;3:891-3.
    • (2006) Nat Methods , vol.3 , pp. 891-893
    • Rasnik, I.1    Mc Kinney, S.A.2    Ha, T.3
  • 21
    • 84862975911 scopus 로고    scopus 로고
    • Conformational changes of DEAD-box helicases monitored by single molecule fluorescence resonance energy transfer
    • Andreou AZ, Klostermeier D. Conformational changes of DEAD-box helicases monitored by single molecule fluorescence resonance energy transfer. Methods Enzymol. 2012;511:75-109.
    • (2012) Methods Enzymol , vol.511 , pp. 75-109
    • Andreou, A.Z.1    Klostermeier, D.2
  • 22
    • 38649106732 scopus 로고    scopus 로고
    • Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase
    • Theissen B, et al. Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase. Proc Natl Acad Sci U S A. 2008;105:548-53.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 548-553
    • Theissen, B.1
  • 23
    • 69449106505 scopus 로고    scopus 로고
    • The DNA gate of Bacillus subtilis gyrase is predominantly in the closed conformation during the DNA supercoiling reaction
    • Gubaev A, Hilbert M, Klostermeier D. The DNA gate of Bacillus subtilis gyrase is predominantly in the closed conformation during the DNA supercoiling reaction. Proc Natl Acad Sci U S A. 2009;106:13278-83.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 13278-13283
    • Gubaev, A.1    Hilbert, M.2    Klostermeier, D.3
  • 24
    • 22144492905 scopus 로고    scopus 로고
    • Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation
    • Lee NK, et al. Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophys J. 2005;88:2939-53.
    • (2005) Biophys J , vol.88 , pp. 2939-2953
    • Lee, N.K.1
  • 25
    • 33645765585 scopus 로고    scopus 로고
    • Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes
    • Margeat E, et al. Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes. Biophys J. 2006;90:1419-31.
    • (2006) Biophys J , vol.90 , pp. 1419-1431
    • Margeat, E.1
  • 26
    • 0033514435 scopus 로고    scopus 로고
    • Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism
    • Ha T, et al. Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism. Proc Natl Acad Sci U S A. 1999;96:893-8.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 893-898
    • Ha, T.1
  • 27
    • 33847682952 scopus 로고
    • Correction of fluorescence spectra and measurement of fluorescence quantum efficiency
    • Parker CA, Rees WT. Correction of fluorescence spectra and measurement of fluorescence quantum efficiency. Analyst. 1960;85:587-600.
    • (1960) Analyst , vol.85 , pp. 587-600
    • Parker, C.A.1    Rees, W.T.2
  • 28
    • 0001433022 scopus 로고    scopus 로고
    • Fluorescence quantum yields and their relation to lifetimes of rhodamine 6G and fluorescein in nine solvents: Improved absolute standards for quantum yields
    • Magde D, Wong R, Seybold PG. Fluorescence quantum yields and their relation to lifetimes of rhodamine 6G and fluorescein in nine solvents: improved absolute standards for quantum yields. Photochem Photobiol. 2002;75:327-34.
    • (2002) Photochem Photobiol , vol.75 , pp. 327-334
    • Magde, D.1    Wong, R.2    Seybold, P.G.3
  • 29
    • 0018464261 scopus 로고
    • The orientational freedom of molecular probes. The orientation factor in intramolecular energy transfer
    • Dale RE, Eisinger J, Blumberg WE. The orientational freedom of molecular probes. The orientation factor in intramolecular energy transfer. Biophys J. 1979;26:161-93.
    • (1979) Biophys J , vol.26 , pp. 161-193
    • Dale, R.E.1    Eisinger, J.2    Blumberg, W.E.3
  • 30
    • 0026640565 scopus 로고
    • Orientation factor in steady-state and time-resolved resonance energy transfer measurements
    • Wu P, Brand L. Orientation factor in steady-state and time-resolved resonance energy transfer measurements. Biochemistry. 1992;31:7939-47.
    • (1992) Biochemistry , vol.31 , pp. 7939-7947
    • Wu, P.1    Brand, L.2
  • 31
    • 0036177565 scopus 로고    scopus 로고
    • Kappa-squared: From nuisance to new sense
    • van der Meer BW. Kappa-squared: from nuisance to new sense. J Biotechnol. 2002;82:181-96.
    • (2002) J Biotechnol , vol.82 , pp. 181-196
    • Van Der Meer, B.W.1
  • 32
    • 34250335726 scopus 로고    scopus 로고
    • Fretting about FRET: Correlation between kappa and R
    • VanBeek DB, et al. Fretting about FRET: correlation between kappa and R. Biophys J. 2007;92:4168-78.
    • (2007) Biophys J , vol.92 , pp. 4168-4178
    • Vanbeek, D.B.1
  • 33
    • 0018267881 scopus 로고
    • Effect of the orientation of donor and acceptor on the probability of energy transfer involving electronic transitions of mixed polarization
    • Haas E, Katchalski-Katzir E, Steinberg IZ. Effect of the orientation of donor and acceptor on the probability of energy transfer involving electronic transitions of mixed polarization. Biochemistry. 1978;17:5064-70.
    • (1978) Biochemistry , vol.17 , pp. 5064-5070
    • Haas, E.1    Katchalski-Katzir, E.2    Steinberg, I.Z.3
  • 34
    • 14244270749 scopus 로고    scopus 로고
    • Time-resolved fluorescence resonance energy transfer studies of DNA bending in double-stranded oligonucleotides and in DNA-protein complexes
    • Parkhurst LJ, et al. Time-resolved fluorescence resonance energy transfer studies of DNA bending in double-stranded oligonucleotides and in DNA-protein complexes. Biopolymers. 2001;61:180-200.
    • (2001) Biopolymers , vol.61 , pp. 180-200
    • Parkhurst, L.J.1
  • 35
    • 0000823855 scopus 로고
    • Determination of distance distribution from time domain fluorometry
    • Albaugh S, Steiner RF. Determination of distance distribution from time domain fluorometry. J Phys Chem. 1989;93:8013-16.
    • (1989) J Phys Chem , vol.93 , pp. 8013-8016
    • Albaugh, S.1    Steiner, R.F.2
  • 36
    • 0035909052 scopus 로고    scopus 로고
    • Tertiary structure stability of the hairpin rlbozyme In Its natural and minimal forms: Different energetic contributions from a ribose zipper motif
    • Klostermeier D, Millar DP. Tertiary structure stability of the hairpin rlbozyme In Its natural and minimal forms: different energetic contributions from a ribose zipper motif. Biochemistry. 2001;40:11211-18.
    • (2001) Biochemistry , vol.40 , pp. 11211-11218
    • Klostermeier, D.1    Millar, D.P.2
  • 37
    • 2442519939 scopus 로고    scopus 로고
    • Time-resolved fluorescence resonance energy transfer: A versatile tool for the analysis of nucleic acids
    • Klostermeier D, Millar DP. Time-resolved fluorescence resonance energy transfer: a versatile tool for the analysis of nucleic acids. Biopolymers. 2001;61:159-79.
    • (2001) Biopolymers , vol.61 , pp. 159-179
    • Klostermeier, D.1    Millar, D.P.2
  • 38
    • 34548096938 scopus 로고    scopus 로고
    • Theory of photon statistics in single-molecule Forster resonance energy transfer
    • Gopich I, Szabo A. Theory of photon statistics in single-molecule Forster resonance energy transfer. J Chem Phys. 2005;122:14707.
    • (2005) J Chem Phys , vol.122 , pp. 14707
    • Gopich, I.1    Szabo, A.2
  • 39
    • 33646377416 scopus 로고    scopus 로고
    • Separating structural heterogeneities from stochastic variations in fluorescence resonance energy transfer distributions via photon distribution analysis
    • Antonik M, et al. Separating structural heterogeneities from stochastic variations in fluorescence resonance energy transfer distributions via photon distribution analysis. J Phys Chem B. 2006;110:6970-8.
    • (2006) J Phys Chem B , vol.110 , pp. 6970-6978
    • Antonik, M.1
  • 40
    • 33751349660 scopus 로고    scopus 로고
    • Shot-noise limited single-molecule FRET histograms: Comparison between theory and experiments
    • Nir E, et al. Shot-noise limited single-molecule FRET histograms: comparison between theory and experiments. J Phys Chem B. 2006;110:22103-24.
    • (2006) J Phys Chem B , vol.110 , pp. 22103-22124
    • Nir, E.1
  • 41
    • 0028672799 scopus 로고
    • Maximum entropy method of data analysis in time-resolved spectroscopy
    • Brochon JC. Maximum entropy method of data analysis in time-resolved spectroscopy. Methods Enzymol. 1994;240:262-311.
    • (1994) Methods Enzymol , vol.240 , pp. 262-311
    • Brochon, J.C.1
  • 42
    • 79851509342 scopus 로고    scopus 로고
    • Three-dimensional molecular modeling with single molecule FRET
    • Brunger AT, et al. Three-dimensional molecular modeling with single molecule FRET. J Struct Biol. 2010;173:497-505.
    • (2010) J Struct Biol , vol.173 , pp. 497-505
    • Brunger, A.T.1
  • 43
    • 56149121056 scopus 로고    scopus 로고
    • A nano-positioning system for macromolecular structural analysis
    • Muschielok A, et al. A nano-positioning system for macromolecular structural analysis. Nat Methods. 2008;5:965-71.
    • (2008) Nat Methods , vol.5 , pp. 965-971
    • Muschielok, A.1
  • 44
    • 57449089390 scopus 로고    scopus 로고
    • Single-molecule FRET measures bends and kinks in DNA
    • Wozniak AK, et al. Single-molecule FRET measures bends and kinks in DNA. Proc Natl Acad Sci U S A. 2008;105:18337-42.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 18337-18342
    • Wozniak, A.K.1
  • 45
    • 79952255056 scopus 로고    scopus 로고
    • Accurate distance determination of nucleic acids via Forster resonance energy transfer: Implications of dye linker length and rigidity
    • Sindbert S, et al. Accurate distance determination of nucleic acids via Forster resonance energy transfer: implications of dye linker length and rigidity. J Am Chem Soc., 2011;133:2463-80.
    • (2011) J am Chem Soc. , vol.133 , pp. 2463-2480
    • Sindbert, S.1
  • 46
    • 0032439514 scopus 로고    scopus 로고
    • Folding of branched RNA species
    • Lilley DM. Folding of branched RNA species. Biopolymers. 1998;48:101-12.
    • (1998) Biopolymers , vol.48 , pp. 101-112
    • Lilley, D.M.1
  • 47
    • 0023498897 scopus 로고
    • Self-cleavage of RNA in the replication of viroids and virusoids
    • Symons RH, et al. Self-cleavage of RNA in the replication of viroids and virusoids. J Cell Sci Suppl. 1987;7:303-18.
    • (1987) J Cell Sci Suppl , vol.7 , pp. 303-318
    • Symons, R.H.1
  • 48
    • 0023663396 scopus 로고
    • Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites
    • Forster AC, Symons RH. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell. 1987;49:211-20.
    • (1987) Cell , vol.49 , pp. 211-220
    • Forster, A.C.1    Symons, R.H.2
  • 49
    • 0027973506 scopus 로고
    • A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements [erratum appears in Science. 1995;267:1581]
    • Tuschl T, et al. A three-dimensional model for the hammerhead ribozyme based on fluorescence measurements [erratum appears in Science. 1995;267:1581]. Science. 1994;266:785-9.
    • (1994) Science , vol.266 , pp. 785-789
    • Tuschl, T.1
  • 50
    • 0029073091 scopus 로고
    • The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage
    • Scott WG, Finch JT, Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 1995;81:991-1002.
    • (1995) Cell , vol.81 , pp. 991-1002
    • Scott, W.G.1    Finch, J.T.2    Klug, A.3
  • 51
    • 0031463467 scopus 로고    scopus 로고
    • Ion-induced folding ofthe hammerhead ribozyme: A fluorescence resonance energy transfer study
    • Bassi GS, et al. Ion-induced folding ofthe hammerhead ribozyme: a fluorescence resonance energy transfer study. EMBO J. 1997;16:7481-9.
    • (1997) EMBO J , vol.16 , pp. 7481-7489
    • Bassi, G.S.1
  • 52
    • 0023055382 scopus 로고
    • Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA
    • Buzayan JM, Hampel A, Bruening G. Nucleotide sequence and newly formed phosphodiester bond of spontaneously ligated satellite tobacco ringspot virus RNA. Nucleic Acids Res. 1986;14:9729-43.
    • (1986) Nucleic Acids Res , vol.14 , pp. 9729-9743
    • Buzayan, J.M.1    Hampel, A.2    Bruening, G.3
  • 53
    • 0028848490 scopus 로고
    • Catalytic properties of hairpin ribozymes derived from chicory yellow mottle virus and arabis mosaic virus satellite RNAs
    • DeYoung M, et al. Catalytic properties of hairpin ribozymes derived from chicory yellow mottle virus and arabis mosaic virus satellite RNAs. Biochemistry. 1995;34:15785-91.
    • (1995) Biochemistry , vol.34 , pp. 15785-15791
    • Deyoung, M.1
  • 54
    • 0034708334 scopus 로고    scopus 로고
    • Structure and function of the hairpin ribozyme
    • Fedor MJ. Structure and function of the hairpin ribozyme. J Mol Biol. 2000;297:269-91.
    • (2000) J Mol Biol , vol.297 , pp. 269-291
    • Fedor, M.J.1
  • 55
    • 0032535607 scopus 로고    scopus 로고
    • Folding of the four-way RNA junction of the hairpin ribozyme
    • Walter F, Murchie AIH, Lilley DMJ. Folding of the four-way RNA junction of the hairpin ribozyme. Biochemistry. 1998;37:17629-36.
    • (1998) Biochemistry , vol.37 , pp. 17629-17636
    • Walter, F.1    Murchie, A.2    Lilley, D.M.J.3
  • 56
    • 0032061318 scopus 로고    scopus 로고
    • Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops
    • Murchie AI, et al. Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Mol Cell. 1998;1:873-81.
    • (1998) Mol Cell , vol.1 , pp. 873-881
    • Murchie, A.I.1
  • 57
    • 0032491204 scopus 로고    scopus 로고
    • Structure and activity of the hairpin ribozyme in its natural junction conformation: Effect of metal ions
    • Walter F, et al. Structure and activity of the hairpin ribozyme in its natural junction conformation: effect of metal ions. Biochemistry. 1998;37:14195-203.
    • (1998) Biochemistry , vol.37 , pp. 14195-14203
    • Walter, F.1
  • 58
    • 0035848837 scopus 로고    scopus 로고
    • Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis [see comments]
    • Rupert PB, Ferre-D'Amare AR. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis [see comments]. Nature. 2001;410:780-6.
    • (2001) Nature , vol.410 , pp. 780-786
    • Rupert, P.B.1    Ferre-D’amare, A.R.2
  • 59
    • 0034545071 scopus 로고    scopus 로고
    • The folding of the hairpin ribozyme: Dependence on the loops and the junction
    • Zhao ZY, et al. The folding of the hairpin ribozyme: dependence on the loops and the junction. RNA. 2000;6:1833-46.
    • (2000) RNA , vol.6 , pp. 1833-1846
    • Zhao, Z.Y.1
  • 60
    • 36949051443 scopus 로고
    • Assembly mapping of 30S ribosomal proteins from E. Coli
    • Mizushima S, Nomura M. Assembly mapping of 30S ribosomal proteins from E. coli. Nature. 1970;226:1214-18.
    • (1970) Nature , vol.226 , pp. 1214-1218
    • Mizushima, S.1    Nomura, M.2
  • 61
    • 0032559410 scopus 로고    scopus 로고
    • Protein and Mg2+-induced conformational changes in the S15 binding site of 16 S ribosomal RNA
    • 2+-induced conformational changes in the S15 binding site of 16 S ribosomal RNA. J Mol Biol. 1998;275:453-64.
    • (1998) J Mol Biol , vol.275 , pp. 453-464
    • Orr, J.W.1    Hagerman, P.J.2    Williamson, J.R.3
  • 62
    • 0037006790 scopus 로고    scopus 로고
    • Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules
    • Kim HD, et al. Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. Proc Natl Acad Sci U S A. 2002;99:4284-9.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 4284-4289
    • Kim, H.D.1
  • 63
    • 2542601493 scopus 로고    scopus 로고
    • A three-fluorophore FRET assay for high-throughput screening of small-molecule inhibitors of ribosome assembly
    • Klostermeier D, et al. A three-fluorophore FRET assay for high-throughput screening of small-molecule inhibitors of ribosome assembly. Nucleic Acids Res. 2004;32:2707-15.
    • (2004) Nucleic Acids Res , vol.32 , pp. 2707-2715
    • Klostermeier, D.1
  • 64
    • 0033529972 scopus 로고    scopus 로고
    • Ligand-induced conformational changes observed in single RNA molecules
    • Ha T, et al. Ligand-induced conformational changes observed in single RNA molecules. Proc Natl Acad Sci U S A. 1999;96:9077-82.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 9077-9082
    • Ha, T.1
  • 65
    • 0037123763 scopus 로고    scopus 로고
    • Views of transcription initiation
    • Young BA, Gruber TM, Gross CA. Views of transcription initiation. Cell. 2002;109:417-20.
    • (2002) Cell , vol.109 , pp. 417-420
    • Young, B.A.1    Gruber, T.M.2    Gross, C.A.3
  • 66
  • 67
    • 0035943446 scopus 로고    scopus 로고
    • Translocation of sigma(70) with RNA polymerase during transcription: Fluorescence resonance energy transfer assay for movement relative to DNA
    • Mukhopadhyay J, et al. Translocation of sigma(70) with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell. 2001;106:453-63.
    • (2001) Cell , vol.106 , pp. 453-463
    • Mukhopadhyay, J.1
  • 68
    • 27644579628 scopus 로고    scopus 로고
    • Retention of transcription initiation factor sigma70 in transcription elongation: Single-molecule analysis
    • Kapanidis AN, et al. Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis. Mol Cell. 2005;20:347-56.
    • (2005) Mol Cell , vol.20 , pp. 347-356
    • Kapanidis, A.N.1
  • 69
    • 18344371347 scopus 로고    scopus 로고
    • Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex
    • Mekler V, et al. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell. 2002;108:599-614.
    • (2002) Cell , vol.108 , pp. 599-614
    • Mekler, V.1
  • 70
    • 0033578701 scopus 로고    scopus 로고
    • Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution
    • Zhang G, et al. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell. 1999;98:811-24.
    • (1999) Cell , vol.98 , pp. 811-824
    • Zhang, G.1
  • 71
    • 0030271890 scopus 로고    scopus 로고
    • Crystal structure of a sigma 70 subunit fragment from E. Coli RNA polymerase
    • Malhotra A, Severinova E, Darst SA. Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell. 1996;87:127-36.
    • (1996) Cell , vol.87 , pp. 127-136
    • Malhotra, A.1    Severinova, E.2    Darst, S.A.3
  • 72
    • 0035222927 scopus 로고    scopus 로고
    • Site-specific protein-DNA photocrosslinking. Analysis of bacterial transcription initiation complexes
    • Naryshkin N, et al. Site-specific protein-DNA photocrosslinking. Analysis of bacterial transcription initiation complexes. Methods Mol Biol. 2001;148:337-61.
    • (2001) Methods Mol Biol , vol.148 , pp. 337-361
    • Naryshkin, N.1
  • 73
    • 0032979707 scopus 로고    scopus 로고
    • Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction
    • Walter NG, Burke JM, Millar DP. Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction. Nat Struct Biol. 1999;6:544-9.
    • (1999) Nat Struct Biol , vol.6 , pp. 544-549
    • Walter, N.G.1    Burke, J.M.2    Millar, D.P.3
  • 74
    • 0034711046 scopus 로고    scopus 로고
    • Helical junctions as determinants for RNA folding: Origin of tertiary structure stability of the hairpin ribozyme
    • Klostermeier D, Millar DP. Helical junctions as determinants for RNA folding: origin of tertiary structure stability of the hairpin ribozyme. Biochemistry. 2000;39:12970-8.
    • (2000) Biochemistry , vol.39 , pp. 12970-12978
    • Klostermeier, D.1    Millar, D.P.2
  • 75
    • 0037016023 scopus 로고    scopus 로고
    • Energetics of hydrogen bond networks in RNA: Hydrogen bonds surrounding G+1 and U42 are the major determinants for tertiary structure stability of the hairpin ribozyme
    • Klostermeier D, Millar DP. Energetics of hydrogen bond networks in RNA: hydrogen bonds surrounding G+1 and U42 are the major determinants for tertiary structure stability of the hairpin ribozyme. Biochemistry. 2002;41:14095-102.
    • (2002) Biochemistry , vol.41 , pp. 14095-14102
    • Klostermeier, D.1    Millar, D.P.2
  • 76
    • 23744470902 scopus 로고    scopus 로고
    • Single-molecule RNA folding
    • Bokinsky G, Zhuang X. Single-molecule RNA folding. Acc Chem Res. 2005;38:566-73.
    • (2005) Acc Chem Res , vol.38 , pp. 566-573
    • Bokinsky, G.1    Zhuang, X.2
  • 77
    • 0042925420 scopus 로고    scopus 로고
    • Single-molecule transition-state analysis of RNA folding
    • Bokinsky G, et al. Single-molecule transition-state analysis of RNA folding. Proc Natl Acad Sci U S A. 2003;100:9302-7.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 9302-9307
    • Bokinsky, G.1
  • 78
    • 0025367254 scopus 로고
    • Self-splicing of group I introns
    • Cech TR. Self-splicing of group I introns. Annu Rev Biochem. 1990;59:543-68.
    • (1990) Annu Rev Biochem , vol.59 , pp. 543-568
    • Cech, T.R.1
  • 80
    • 29244449617 scopus 로고    scopus 로고
    • An obligate intermediate along the slow folding pathway of a group II intron ribozyme
    • Su LJ, Waldsich C, Pyle AM. An obligate intermediate along the slow folding pathway of a group II intron ribozyme. Nucleic Acids Res. 2005;33:6674-87.
    • (2005) Nucleic Acids Res , vol.33 , pp. 6674-6687
    • Su, L.J.1    Waldsich, C.2    Pyle, A.M.3
  • 81
    • 52949084315 scopus 로고    scopus 로고
    • Single-molecule studies of group II intron ribozymes
    • Steiner M, et al. Single-molecule studies of group II intron ribozymes. Proc Natl Acad Sci U S A. 2008;105:13853-88.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 13853-13888
    • Steiner, M.1
  • 82
    • 33845738802 scopus 로고    scopus 로고
    • Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity
    • Halls C, et al. Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity. J Mol Biol. 2007;365:835-55.
    • (2007) J Mol Biol , vol.365 , pp. 835-855
    • Halls, C.1
  • 83
    • 70350089113 scopus 로고    scopus 로고
    • The mechanism of ATP-dependent RNA unwinding by DEAD box proteins
    • Hilbert M, Karow AR, Klostermeier D. The mechanism of ATP-dependent RNA unwinding by DEAD box proteins. Biol Chem. 2009;390:1237-50.
    • (2009) Biol Chem , vol.390 , pp. 1237-1250
    • Hilbert, M.1    Karow, A.R.2    Klostermeier, D.3
  • 84
    • 78049234242 scopus 로고    scopus 로고
    • Single-molecule analysis of Mss116-mediated group II intron folding
    • Karunatilaka KS, et al. Single-molecule analysis of Mss116-mediated group II intron folding. Nature. 2010;467:935-9.
    • (2010) Nature , vol.467 , pp. 935-939
    • Karunatilaka, K.S.1
  • 85
    • 23744455796 scopus 로고    scopus 로고
    • Alternating-laser excitation of single molecules
    • Kapanidis AN, et al. Alternating-laser excitation of single molecules. Acc Chem Res. 2005;38:523-33.
    • (2005) Acc Chem Res , vol.38 , pp. 523-533
    • Kapanidis, A.N.1
  • 86
    • 33751212468 scopus 로고    scopus 로고
    • Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism
    • Kapanidis AN, et al. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science. 2006;314:1144-7.
    • (2006) Science , vol.314 , pp. 1144-1147
    • Kapanidis, A.N.1
  • 87
    • 77956926253 scopus 로고    scopus 로고
    • A structural model for the DEAD box helicase YxiN in solution: Localization of the RNA-binding domain
    • Karow AR, Klostermeier D. A structural model for the DEAD box helicase YxiN in solution: localization of the RNA-binding domain. J Mol Biol. 2010;402:629-37.
    • (2010) J Mol Biol , vol.402 , pp. 629-637
    • Klostermeier, A.R.D.1
  • 88
    • 77956715760 scopus 로고    scopus 로고
    • Structure of the RNA binding domain of a DEAD-box helicase bound to its ribosomal RNA target reveals a novel mode of recognition by an RNA recognition motif
    • Hardin JW, Hu YX, McKay DB. Structure of the RNA binding domain of a DEAD-box helicase bound to its ribosomal RNA target reveals a novel mode of recognition by an RNA recognition motif. J Mol Biol. 2010;402:412-27.
    • (2010) J Mol Biol , vol.402 , pp. 412-427
    • Hardin, J.W.1    Hu, Y.X.2    Mc Kay, D.B.3
  • 89
    • 38349173560 scopus 로고    scopus 로고
    • Single-molecule tracking of mRNA exiting from RNA polymerase II
    • Andrecka J, et al. Single-molecule tracking of mRNA exiting from RNA polymerase II. Proc Natl Acad Sci U S A. 2007;105:135-40.
    • (2007) Proc Natl Acad Sci U S A , vol.105 , pp. 135-140
    • Andrecka, J.1
  • 90
    • 73049092277 scopus 로고    scopus 로고
    • Nano positioningsystem reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex
    • Andrecka J, et al. Nano positioningsystem reveals the course of upstream and nontemplate DNA within the RNA polymerase II elongation complex. Nucleic Acids Res. 2009;37:5803-9.
    • (2009) Nucleic Acids Res , vol.37 , pp. 5803-5809
    • Andrecka, J.1
  • 91
    • 84860334486 scopus 로고    scopus 로고
    • Dynamic architecture of a minimal RNA polymerase II open promoter complex
    • Treutlein B, et al. Dynamic architecture of a minimal RNA polymerase II open promoter complex. Mol Cell. 2012;46:136-46.
    • (2012) Mol Cell , vol.46 , pp. 136-146
    • Treutlein, B.1
  • 92
    • 4143071283 scopus 로고    scopus 로고
    • Single-molecule three-color FRET
    • Hohng S, Joo C, Ha T. Single-molecule three-color FRET. Biophys J. 2004;87:1328-37.
    • (2004) Biophys J , vol.87 , pp. 1328-1337
    • Joo Ha, S.C.T.1
  • 93
    • 0041810129 scopus 로고    scopus 로고
    • Triple FRET: A tool for studying long-range molecular interactions
    • Haustein E, Jahnz M, Schwille P. Triple FRET: a tool for studying long-range molecular interactions. ChemPhysChem. 2003;4:745-8.
    • (2003) Chemphyschem , vol.4 , pp. 745-748
    • Jahnz Schwille, E.M.P.1
  • 94
    • 78650272919 scopus 로고    scopus 로고
    • Single-molecule four-color FRET
    • Lee J, et al. Single-molecule four-color FRET. Angew Chem Int Ed Engl. 2010;49:9922-5.
    • (2010) Angew Chem Int Ed Engl , vol.49 , pp. 9922-9925
    • Lee, J.1
  • 95
    • 77957689889 scopus 로고    scopus 로고
    • Monitoring multiple distances within a single molecule usingswitchable FRET
    • Uphoff S, et al. Monitoring multiple distances within a single molecule usingswitchable FRET. Nat Methods. 2010;7:831-6.
    • (2010) Nat Methods , vol.7 , pp. 831-836
    • Uphoff, S.1
  • 96
    • 2942650138 scopus 로고    scopus 로고
    • Fluorescence-aided molecule sorting: Analysis of structure and interactions by alternating-laser excitation of single molecules
    • Kapanidis AN, et al. Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules. Proc Natl Acad Sci U S A. 2004;101:8936-41.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 8936-8941
    • Kapanidis, A.N.1
  • 97
    • 0037474152 scopus 로고    scopus 로고
    • Zero-mode waveguides for single-molecule analysis at high concentrations
    • Levene MJ, et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science. 2003;299:682-6.
    • (2003) Science , vol.299 , pp. 682-686
    • Levene, M.J.1
  • 98
    • 79551680953 scopus 로고    scopus 로고
    • Dynamics of the translational machinery
    • Petrov A, et al. Dynamics of the translational machinery. Curr Opin Struct Biol. 2011;21:137-45.
    • (2011) Curr Opin Struct Biol , vol.21 , pp. 137-145
    • Petrov, A.1
  • 99
    • 84857698151 scopus 로고    scopus 로고
    • Manipulating protein conformations by single-molecule AFM-FRET nanoscopy
    • He Y et al. Manipulating protein conformations by single-molecule AFM-FRET nanoscopy. ACS Nano. 2012;6:1221-9.
    • (2012) ACS Nano , vol.6 , pp. 1221-1229
    • He, Y.1
  • 100
    • 79953292607 scopus 로고    scopus 로고
    • Ultrahigh-resolution optical trap with single-fluorophore sensitivity
    • Comstock MJ, Ha T, Chemla YR. Ultrahigh-resolution optical trap with single-fluorophore sensitivity. Nat Methods. 2011;8:335-40.
    • (2011) Nat Methods , vol.8 , pp. 335-340
    • Comstock, M.J.1    Ha, T.2    Chemla, Y.R.3
  • 101
    • 77954580825 scopus 로고    scopus 로고
    • Force-fluorescence spectroscopy at the single-molecule level
    • Zhou R, Schlierf M, Ha T. Force-fluorescence spectroscopy at the single-molecule level. Methods Enzymol. 2010;475:405-26.
    • (2010) Methods Enzymol , vol.475 , pp. 405-426
    • Schlierf Ha, R.M.T.1
  • 102
    • 35348897239 scopus 로고    scopus 로고
    • Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction
    • Hohng S, et al. Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction. Science. 2007;318:279-83.
    • (2007) Science , vol.318 , pp. 279-283
    • Hohng, S.1
  • 103
    • 23144441755 scopus 로고    scopus 로고
    • Biocompatible force sensor with optical readout and dimensions of 6 nm3
    • 3. Nano Lett. 2005;5:1509-14.
    • (2005) Nano Lett , vol.5 , pp. 1509-1514
    • Shroff, H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.