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Volumn 105, Issue 9, 2008, Pages 3315-3320

Monitoring RNA transcription in real time by using surface plasmon resonance

Author keywords

Elongation complex dissociation; Intrinsic termination; Kinetic modeling; RNA polymerase binding; Sigma release

Indexed keywords

RNA POLYMERASE; BACTERIAL RNA; DNA DIRECTED RNA POLYMERASE; SIGMA FACTOR;

EID: 42149126654     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0712074105     Document Type: Article
Times cited : (28)

References (38)
  • 1
    • 0031008221 scopus 로고    scopus 로고
    • Basic mechanisms of transcript elongation and its regulation
    • Uptain SM, Kane CM, Chamberlin MJ (1997) Basic mechanisms of transcript elongation and its regulation. Annu Rev Biochem 66:117-172.
    • (1997) Annu Rev Biochem , vol.66 , pp. 117-172
    • Uptain, S.M.1    Kane, C.M.2    Chamberlin, M.J.3
  • 2
    • 0032836135 scopus 로고    scopus 로고
    • Transcription elongation and human disease
    • Conaway JW, Conaway RC (1999) Transcription elongation and human disease. Annu Rev Biochem 68:301-319.
    • (1999) Annu Rev Biochem , vol.68 , pp. 301-319
    • Conaway, J.W.1    Conaway, R.C.2
  • 3
    • 0028804889 scopus 로고
    • Control of rRNA transcription in Escherichia coli
    • Condon C, Squires C, Squires CL (1995) Control of rRNA transcription in Escherichia coli. Microbiol Rev 59:623-645.
    • (1995) Microbiol Rev , vol.59 , pp. 623-645
    • Condon, C.1    Squires, C.2    Squires, C.L.3
  • 4
    • 14644407528 scopus 로고    scopus 로고
    • Thinking quantitatively about transcriptional regulation
    • Greive SJ, von Hippel PH (2005) Thinking quantitatively about transcriptional regulation. Nat Rev Mol Cell Biol 6:221-232.
    • (2005) Nat Rev Mol Cell Biol , vol.6 , pp. 221-232
    • Greive, S.J.1    von Hippel, P.H.2
  • 5
    • 0033179498 scopus 로고    scopus 로고
    • Transcriptional pause, arrest and termination sites for RNA polymerase II in mammalian N- and c-myc genes
    • Keene RG, Mueller A, Landick R, London L (1999) Transcriptional pause, arrest and termination sites for RNA polymerase II in mammalian N- and c-myc genes. Nucleic Acids Res 27:3173-3182.
    • (1999) Nucleic Acids Res , vol.27 , pp. 3173-3182
    • Keene, R.G.1    Mueller, A.2    Landick, R.3    London, L.4
  • 6
    • 33646556092 scopus 로고    scopus 로고
    • Pause sites promote transcriptional termination of mammalian RNA polymerase II
    • Gromak N, West S, Proudfoot NJ (2006) Pause sites promote transcriptional termination of mammalian RNA polymerase II. Mol Cell Biol 26:3986-3996.
    • (2006) Mol Cell Biol , vol.26 , pp. 3986-3996
    • Gromak, N.1    West, S.2    Proudfoot, N.J.3
  • 7
    • 0025976369 scopus 로고
    • Transcript elongation and termination are competitive kinetic processes
    • von Hippel PH, Yager TD (1991) Transcript elongation and termination are competitive kinetic processes. Proc Natl Acad Sci USA 88:2307-2311.
    • (1991) Proc Natl Acad Sci USA , vol.88 , pp. 2307-2311
    • von Hippel, P.H.1    Yager, T.D.2
  • 8
    • 0031558773 scopus 로고    scopus 로고
    • Regulation of the elongation-termination decision at intrinsic terminators by antitermination protein N of phage (lambda)
    • Rees W, Weitzel S, Das A, von Hippel P (1997) Regulation of the elongation-termination decision at intrinsic terminators by antitermination protein N of phage (lambda). J Mol Biol 273:17.
    • (1997) J Mol Biol , vol.273 , pp. 17
    • Rees, W.1    Weitzel, S.2    Das, A.3    von Hippel, P.4
  • 9
    • 0028091898 scopus 로고
    • Stability of Escherichia coli transcription complexes near an intrinsic terminator
    • Wilson K, von Hippel P (1994) Stability of Escherichia coli transcription complexes near an intrinsic terminator. J Mol Biol 244:36-51.
    • (1994) J Mol Biol , vol.244 , pp. 36-51
    • Wilson, K.1    von Hippel, P.2
  • 10
    • 0037058904 scopus 로고    scopus 로고
    • Reaction pathways in transcript elongation
    • von Hippel PH, Pasman Z (2002) Reaction pathways in transcript elongation. Biophys Chem 101-102:401-423.
    • (2002) Biophys Chem , vol.101-102 , pp. 401-423
    • von Hippel, P.H.1    Pasman, Z.2
  • 11
    • 0028020630 scopus 로고
    • Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate
    • McDowell JC, Roberts JW, Jin DJ, Gross C (1994) Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate. Science 266:822-825.
    • (1994) Science , vol.266 , pp. 822-825
    • McDowell, J.C.1    Roberts, J.W.2    Jin, D.J.3    Gross, C.4
  • 13
    • 0018622529 scopus 로고
    • A quantitative assay for bacterial RNA polymerases
    • Chamberlin MJ, Nierman WC, Wiggs J, Neff N (1979) A quantitative assay for bacterial RNA polymerases. J Biol Chem 254:10061-10069.
    • (1979) J Biol Chem , vol.254 , pp. 10061-10069
    • Chamberlin, M.J.1    Nierman, W.C.2    Wiggs, J.3    Neff, N.4
  • 14
    • 0019412155 scopus 로고
    • Pausing and termination of transcription within the early region of bacteriophage T7 DNA in vitro
    • Kassavetis GA, Chamberlin MJ (1981) Pausing and termination of transcription within the early region of bacteriophage T7 DNA in vitro. J Biol Chem 256:2777-2786.
    • (1981) J Biol Chem , vol.256 , pp. 2777-2786
    • Kassavetis, G.A.1    Chamberlin, M.J.2
  • 15
    • 0025867008 scopus 로고
    • Transcription by single molecules of RNA polymerase observed by light microscopy
    • Schafer DA, Gelles J, Sheetz MP, Landick R (1991) Transcription by single molecules of RNA polymerase observed by light microscopy. Nature 352:444-448.
    • (1991) Nature , vol.352 , pp. 444-448
    • Schafer, D.A.1    Gelles, J.2    Sheetz, M.P.3    Landick, R.4
  • 16
    • 0033539658 scopus 로고    scopus 로고
    • Nonequilibrium mechanism of transcription termination from observations of singleRNApolymerase molecules
    • Yin H, Artsimovitch I, Landick R, Gelles J (1999) Nonequilibrium mechanism of transcription termination from observations of singleRNApolymerase molecules. Proc Natl Acad Sci USA 96:13124-13129.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 13124-13129
    • Yin, H.1    Artsimovitch, I.2    Landick, R.3    Gelles, J.4
  • 17
    • 0034737593 scopus 로고    scopus 로고
    • Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase
    • Davenport RJ, Wuite GJ, Landick R, Bustamante C (2000) Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase. Science 287:2497-2500.
    • (2000) Science , vol.287 , pp. 2497-2500
    • Davenport, R.J.1    Wuite, G.J.2    Landick, R.3    Bustamante, C.4
  • 18
    • 0038756088 scopus 로고    scopus 로고
    • Cooperation between RNA polymerase molecules in transcription elongation
    • Epshtein V, Nudler E (2003) Cooperation between RNA polymerase molecules in transcription elongation Science 300:801-805.
    • (2003) Science , vol.300 , pp. 801-805
    • Epshtein, V.1    Nudler, E.2
  • 19
    • 0345047725 scopus 로고    scopus 로고
    • Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking
    • Neuman KC, Abbondanzieri EA, Landick R, Gelles J, Block SM (2003) Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell 115:437-447.
    • (2003) Cell , vol.115 , pp. 437-447
    • Neuman, K.C.1    Abbondanzieri, E.A.2    Landick, R.3    Gelles, J.4    Block, S.M.5
  • 20
    • 0346258014 scopus 로고    scopus 로고
    • Backtracking by single RNA polymerase molecules observed at near-base-pair resolution
    • Shaevitz JW, Abbondanzieri EA, Landick R, Block SM (2003) Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature 426:684-687.
    • (2003) Nature , vol.426 , pp. 684-687
    • Shaevitz, J.W.1    Abbondanzieri, E.A.2    Landick, R.3    Block, S.M.4
  • 21
    • 0026084789 scopus 로고
    • A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli
    • Yager TD, von Hippel PH (1991) A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli. Biochemistry 30:1097-1118.
    • (1991) Biochemistry , vol.30 , pp. 1097-1118
    • Yager, T.D.1    von Hippel, P.H.2
  • 22
    • 0037177866 scopus 로고    scopus 로고
    • Transcription termination: Primary intermediates and secondary adducts
    • Kashlev M, Komissarova N (2002) Transcription termination: Primary intermediates and secondary adducts. J Biol Chem 277:14501-14508.
    • (2002) J Biol Chem , vol.277 , pp. 14501-14508
    • Kashlev, M.1    Komissarova, N.2
  • 23
    • 0036863659 scopus 로고    scopus 로고
    • Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination
    • Komissarova N, Becker J, Solter S, Kireeva M, Kashlev M (2002) Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol Cell 10:1151-1162.
    • (2002) Mol Cell , vol.10 , pp. 1151-1162
    • Komissarova, N.1    Becker, J.2    Solter, S.3    Kireeva, M.4    Kashlev, M.5
  • 24
    • 41249091442 scopus 로고    scopus 로고
    • Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework
    • Datta K, von Hippel PH (2008) Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework. J Biol Chem 283:3537-3549.
    • (2008) J Biol Chem , vol.283 , pp. 3537-3549
    • Datta, K.1    von Hippel, P.H.2
  • 25
    • 0023711743 scopus 로고
    • Transcription termination in Escherichia coli. Measurement of the rate of enzyme release from Rho-independent terminators
    • Arndt KM, Chamberlin MJ (1988) Transcription termination in Escherichia coli. Measurement of the rate of enzyme release from Rho-independent terminators J Mol Biol 202:271-285.
    • (1988) J Mol Biol , vol.202 , pp. 271-285
    • Arndt, K.M.1    Chamberlin, M.J.2
  • 26
    • 0026527507 scopus 로고
    • Termination efficiency at rho-dependent terminators depends on kinetic coupling between RNA polymerase and rho
    • Jin DJ, Burgess RR, Richardson JP, Gross CA (1992) Termination efficiency at rho-dependent terminators depends on kinetic coupling between RNA polymerase and rho. Proc Natl Acad Sci USA 89:1453-1457.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 1453-1457
    • Jin, D.J.1    Burgess, R.R.2    Richardson, J.P.3    Gross, C.A.4
  • 27
    • 0033120034 scopus 로고    scopus 로고
    • The mechanism of intrinsic transcription termination
    • Gusarov I, Nudler E (1999) The mechanism of intrinsic transcription termination. Mol Cell 3:495-504.
    • (1999) Mol Cell , vol.3 , pp. 495-504
    • Gusarov, I.1    Nudler, E.2
  • 28
    • 0032745992 scopus 로고    scopus 로고
    • Real time in vitro analysis of transcription by RNA polymerase on immobilized DNA fibres
    • Pemberton IK, Buckle M (1999) Real time in vitro analysis of transcription by RNA polymerase on immobilized DNA fibres. J Mol Recognit 12:322-327.
    • (1999) J Mol Recognit , vol.12 , pp. 322-327
    • Pemberton, I.K.1    Buckle, M.2
  • 29
    • 0017817680 scopus 로고
    • Nonspecific interactions of Escherichia coli RNA polymerase with native and denatured DNA: Differences in the binding behavior of core and holoenzyme
    • deHaseth PL, Lohman TM, Burgess RR, Record MT, Jr (1978) Nonspecific interactions of Escherichia coli RNA polymerase with native and denatured DNA: Differences in the binding behavior of core and holoenzyme. Biochemistry 17:1612-1622.
    • (1978) Biochemistry , vol.17 , pp. 1612-1622
    • deHaseth, P.L.1    Lohman, T.M.2    Burgess, R.R.3    Record Jr, M.T.4
  • 30
    • 0025744584 scopus 로고
    • Escherichia coli sigma 70 and NusA proteins. I. Binding interactions with core RNA polymerase in solution and within the transcription complex
    • Gill SC, Weitzel SE, von Hippel PH (1991) Escherichia coli sigma 70 and NusA proteins. I. Binding interactions with core RNA polymerase in solution and within the transcription complex. J Mol Biol 220:307-324.
    • (1991) J Mol Biol , vol.220 , pp. 307-324
    • Gill, S.C.1    Weitzel, S.E.2    von Hippel, P.H.3
  • 31
    • 0014030681 scopus 로고
    • The binding of RNA polymerase to DNA
    • Richardson JP (1966) The binding of RNA polymerase to DNA. J Mol Biol 21:83-114.
    • (1966) J Mol Biol , vol.21 , pp. 83-114
    • Richardson, J.P.1
  • 32
    • 0029818631 scopus 로고    scopus 로고
    • Transcription processivity: Protein-DNA interactions holding together the elongation complex
    • Nudler E, Avetissova E, Markovtsov V, Goldfarb A (1996) Transcription processivity: protein-DNA interactions holding together the elongation complex. Science 273:211-217.
    • (1996) Science , vol.273 , pp. 211-217
    • Nudler, E.1    Avetissova, E.2    Markovtsov, V.3    Goldfarb, A.4
  • 33
    • 0031848098 scopus 로고    scopus 로고
    • Extending the range of rate constants available from BIACORE: Interpreting mass transport-influenced binding data
    • Myszka DG, He X, Dembo M, Morton TA, Goldstein B (1998) Extending the range of rate constants available from BIACORE: Interpreting mass transport-influenced binding data. Biophys J 75:583-594.
    • (1998) Biophys J , vol.75 , pp. 583-594
    • Myszka, D.G.1    He, X.2    Dembo, M.3    Morton, T.A.4    Goldstein, B.5
  • 34
    • 0029073396 scopus 로고
    • Transcription termination at intrinsic terminators: The role of the RNA hairpin
    • Wilson KS, von Hippel PH (1995) Transcription termination at intrinsic terminators: The role of the RNA hairpin. Proc Natl Acad Sci USA 92:8793-8797.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 8793-8797
    • Wilson, K.S.1    von Hippel, P.H.2
  • 35
    • 0035900642 scopus 로고    scopus 로고
    • Control of intrinsic transcription termination by N, NusA: The basic mechanisms
    • Gusarov I, Nudler E (2001) Control of intrinsic transcription termination by N, NusA: The basic mechanisms. Cell 107:437-449.
    • (2001) Cell , vol.107 , pp. 437-449
    • Gusarov, I.1    Nudler, E.2
  • 36
    • 0036385743 scopus 로고    scopus 로고
    • Active Escherichia coli transcription elongation complexes are functionally homogeneous
    • Pasman Z, von Hippel PH (2002) Active Escherichia coli transcription elongation complexes are functionally homogeneous. J Mol Biol 322:505-519.
    • (2002) J Mol Biol , vol.322 , pp. 505-519
    • Pasman, Z.1    von Hippel, P.H.2
  • 37
    • 0026544876 scopus 로고
    • Parameters affecting transcription termination by Escherichia coli RNA. II. Construction and analysis of hybrid terminators
    • Reynolds R, Chamberlin MJ (1992) Parameters affecting transcription termination by Escherichia coli RNA. II. Construction and analysis of hybrid terminators. J Mol Biol 224:53-63.
    • (1992) J Mol Biol , vol.224 , pp. 53-63
    • Reynolds, R.1    Chamberlin, M.J.2
  • 38
    • 0031585994 scopus 로고    scopus 로고
    • Multiple interactions stabilize a single paused transcription intermediate in which hairpin to 3′ end spacing distinguishes pause and termination pathways
    • Chan CL, Wang D, Landick R (1997) Multiple interactions stabilize a single paused transcription intermediate in which hairpin to 3′ end spacing distinguishes pause and termination pathways. J Mol Biol 268:54-68.
    • (1997) J Mol Biol , vol.268 , pp. 54-68
    • Chan, C.L.1    Wang, D.2    Landick, R.3


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