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Volumn 34, Issue 12, 2006, Pages 3409-3420

Lac repressor hinge flexibility and DNA looping: Single molecule kinetics by tethered particle motion

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DNA; LACI PROTEIN, BACTERIA; MICROSPHERE; REPRESSOR PROTEIN;

EID: 33746207766     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl393     Document Type: Article
Times cited : (72)

References (55)
  • 1
    • 54249116230 scopus 로고
    • Genetic regulatory mechanisms in the synthesis of proteins
    • Jacob,F. and Monod,J. (1961) Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol., 3, 318-356.
    • (1961) J. Mol. Biol. , vol.3 , pp. 318-356
    • Jacob, F.1    Monod, J.2
  • 2
    • 20444411150 scopus 로고    scopus 로고
    • The lac repressor
    • Lewis,M. (2005) The lac repressor. C. R. Biol., 328, 521-548.
    • (2005) C. R. Biol. , vol.328 , pp. 521-548
    • Lewis, M.1
  • 4
    • 0016150348 scopus 로고
    • The location of the repressor binding sites in the lac operon
    • Reznikoff,W.S., Winter,R.B. and Hurley,C.K. (1974) The location of the repressor binding sites in the lac operon. Proc. Natl Acad. Sci. USA, 71, 2314-2318.
    • (1974) Proc. Natl Acad. Sci. USA , vol.71 , pp. 2314-2318
    • Reznikoff, W.S.1    Winter, R.B.2    Hurley, C.K.3
  • 5
    • 0018800287 scopus 로고
    • 'Second' and 'third operator' of the lac operon: An investigation of their role in the regulatory mechanism
    • Pfahl,M., Gulde,V. and Bourgeois,S. (1979) 'Second' and 'third operator' of the lac operon: an investigation of their role in the regulatory mechanism. J. Mol. Biol., 127, 339-344.
    • (1979) J. Mol. Biol. , vol.127 , pp. 339-344
    • Pfahl, M.1    Gulde, V.2    Bourgeois, S.3
  • 6
    • 0033485539 scopus 로고    scopus 로고
    • Quantitative comparison of DNA looping in vitro and in vivo: Chromatin increases effective DNA flexibility at short distances
    • Ringrose,L., Chabanis,S., Angrand,P.O., Woodroofe,C. and Stewart,A.F. (1999) Quantitative comparison of DNA looping in vitro and in vivo: chromatin increases effective DNA flexibility at short distances. EMBO J., 18, 6630-6641.
    • (1999) EMBO J. , vol.18 , pp. 6630-6641
    • Ringrose, L.1    Chabanis, S.2    Angrand, P.O.3    Woodroofe, C.4    Stewart, A.F.5
  • 8
    • 0021022977 scopus 로고
    • Energetics of DNA twisting. I. Relation between twist and cyclization probability
    • Shore,D. and Baldwin,R.L. (1983) Energetics of DNA twisting. I. Relation between twist and cyclization probability. J. Mol. Biol., 170, 957-981. (Pubitemid 14249345)
    • (1983) Journal of Molecular Biology , vol.170 , Issue.4 , pp. 957-981
    • Shore, D.1    Baldwin, R.L.2
  • 11
    • 0000545475 scopus 로고
    • Ring-closure probabilities for twisted wormlike chains. Application to DNA
    • Shimada,J. and Yamakawa,H. (1984) Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules, 17, 689-698.
    • (1984) Macromolecules , vol.17 , pp. 689-698
    • Shimada, J.1    Yamakawa, H.2
  • 12
    • 0028801067 scopus 로고
    • Action at a distance: DNA-looping and initiation of transcription
    • Rippe,K., von Hippel,P.H. and Langowski,J. (1995) Action at a distance: DNA-looping and initiation of transcription. Trends Biochem. Sci., 20, 500-506.
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 500-506
    • Rippe, K.1    Von Hippel, P.H.2    Langowski, J.3
  • 13
    • 0030867320 scopus 로고    scopus 로고
    • Driving proteins off DNA using applied tension
    • Marko,J.F. and Siggia,E.D. (1997) Driving proteins off DNA using applied tension. Biophys. J., 73, 2173-2178. (Pubitemid 27425748)
    • (1997) Biophysical Journal , vol.73 , Issue.4 , pp. 2173-2178
    • Marko, J.F.1    Siggia, E.D.2
  • 14
    • 21244440748 scopus 로고    scopus 로고
    • Disruption of protein-mediated DNA looping by tension in the substrate DNA
    • DOI 10.1529/biophysj.104.054486
    • Blumberg,S., Tkachenko,A.V. and Meiners,J.C. (2005) Disruption of protein-mediated DNA looping by tension in the substrate DNA. Biophys. J., 88, 1692-1701. (Pubitemid 40976186)
    • (2005) Biophysical Journal , vol.88 , Issue.3 , pp. 1692-1701
    • Blumberg, S.1    Tkachenko, A.V.2    Meiners, J.-C.3
  • 17
    • 0022529619 scopus 로고
    • Upstream operators enhance repression of the lac promoter
    • Mossing,M.C. and Record,M.T.,Jr (1986) Upstream operators enhance repression of the lac promoter. Science, 233, 889-892. (Pubitemid 16011898)
    • (1986) Science , vol.233 , Issue.4766 , pp. 889-892
    • Mossing, M.C.1    Record Jr., M.T.2
  • 18
    • 0029975889 scopus 로고    scopus 로고
    • Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator
    • Muller,J., Oehler,S. and Muller-Hill,B. (1996) Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator. J. Mol. Biol., 257, 21-29.
    • (1996) J. Mol. Biol. , vol.257 , pp. 21-29
    • Muller, J.1    Oehler, S.2    Muller-Hill, B.3
  • 19
    • 0023665179 scopus 로고
    • Influence of sequence and distance between two operators on interaction with the lac repressor
    • Hsieh,W.T., Whitson,P.A., Matthews,K.S. and Wells,R.D. (1987) Influence of sequence and distance between two operators on interaction with the lac repressor. J. Biol. Chem., 262, 14583-14591.
    • (1987) J. Biol. Chem. , vol.262 , pp. 14583-14591
    • Hsieh, W.T.1    Whitson, P.A.2    Matthews, K.S.3    Wells, R.D.4
  • 20
    • 0028956979 scopus 로고
    • Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules
    • Finzi,L. and Gelles,J. (1995) Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules. Science, 267, 378-380.
    • (1995) Science , vol.267 , pp. 378-380
    • Finzi, L.1    Gelles, J.2
  • 21
    • 0032718889 scopus 로고    scopus 로고
    • Glycine insertion in the hinge region of lactose repressor protein alters DNA binding
    • Falcon,C.M. and Matthews,K.S. (1999) Glycine insertion in the hinge region of lactose repressor protein alters DNA binding. J. Biol. Chem., 274, 30849-30857.
    • (1999) J. Biol. Chem. , vol.274 , pp. 30849-30857
    • Falcon, C.M.1    Matthews, K.S.2
  • 22
    • 0033987659 scopus 로고    scopus 로고
    • Generation of an AraC-araBAD promoter-regulated T7 expression system
    • DOI 10.1006/abio.1999.4385
    • Wycuff,D.R. and Matthews,K.S. (2000) Generation of an AraC-araBAD promoter-regulated T7 expression system. Anal. Biochem., 277, 67-73. (Pubitemid 30041761)
    • (2000) Analytical Biochemistry , vol.277 , Issue.1 , pp. 67-73
    • Wycuff, D.R.1    Matthews, K.S.2
  • 23
    • 0026723976 scopus 로고
    • Deletion of lactose repressor carboxyl-terminal domain affects tetramer formation
    • Chen,J. and Matthews,K.S. (1992) Deletion of lactose repressor carboxyl-terminal domain affects tetramer formation. J. Biol. Chem., 267, 13843-13850.
    • (1992) J. Biol. Chem. , vol.267 , pp. 13843-13850
    • Chen, J.1    Matthews, K.S.2
  • 24
    • 0141521419 scopus 로고    scopus 로고
    • Protein synthesis by single ribosomes
    • DOI 10.1261/rna.5800303
    • Vanzi,F., Vladimirov,S., Knudsen,C.R., Goldman,Y.E. and Cooperman,B.S. (2003) Protein synthesis by single ribosomes. RNA, 9, 1174-1179. (Pubitemid 37151672)
    • (2003) RNA , vol.9 , Issue.10 , pp. 1174-1179
    • Vanzi, F.1    Vladimirov, S.2    Knudsen, C.R.3    Goldman, Y.E.4    Cooperman, B.S.5
  • 26
    • 23244442263 scopus 로고    scopus 로고
    • Three-dimensional characterization of tethered microspheres by total internal reflection fluorescence microscopy
    • DOI 10.1529/biophysj.105.061242
    • Blumberg,S., Gajraj,A., Pennington,M.W. and Meiners,J.C. (2005) Three-dimensional characterization of tethered microspheres by total internal reflection fluorescence microscopy. Biophys. J., 89, 1272-1281. (Pubitemid 41099008)
    • (2005) Biophysical Journal , vol.89 , Issue.2 , pp. 1272-1281
    • Blumberg, S.1    Gajraj, A.2    Pennington, M.W.3    Meiners, J.-C.4
  • 27
    • 0001774017 scopus 로고
    • Fitting and statistical analysis of single-channel records
    • 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
  • 28
    • 0019856889 scopus 로고
    • Fluctuations in the microsecond time range of the current through single acetylcholine receptor ion channels
    • Colquhoun,D. and Sakmann,B. (1981) Fluctuations in the microsecond time range of the current through single acetylcholine receptor ion channels. Nature, 294, 464-466. (Pubitemid 12220258)
    • (1981) Nature , vol.294 , Issue.5840 , pp. 464-466
    • Colquhoun, D.1    Sakmann, B.2
  • 29
    • 0025874018 scopus 로고
    • Stability of a Lac repressor mediated 'looped complex'
    • Brenowitz,M., Pickar,A. and Jamison,E. (1991) Stability of a Lac repressor mediated 'looped complex'. Biochemistry, 30, 5986-5998.
    • (1991) Biochemistry , vol.30 , pp. 5986-5998
    • Brenowitz, M.1    Pickar, A.2    Jamison, E.3
  • 30
    • 0030564945 scopus 로고    scopus 로고
    • Cooperative and anticooperative effects in binding of the first and second plasmid O(sym) operators to a lad tetramer: Evidence for contributions of non-operator DNA binding by wrapping and looping
    • DOI 10.1006/jmbi.1996.0431
    • Levandoski,M.M., Tsodikov,O.V., Frank,D.E., Melcher,S.E., Saecker,R.M. and Record,M.T.,Jr (1996) Cooperative and anticooperative effects in binding of the first and second plasmid Osym operators to a LacI tetramer: evidence for contributions of non-operator DNA binding by wrapping and looping. J. Mol. Biol., 260, 697-717. (Pubitemid 26270963)
    • (1996) Journal of Molecular Biology , vol.260 , Issue.5 , pp. 697-717
    • Levandoski, M.M.1    Tsodikov, O.V.2    Frank, D.E.3    Melcher, S.E.4    Saecker, R.M.5    Record Jr., M.T.6
  • 31
    • 0033580635 scopus 로고    scopus 로고
    • Thermodynamic analysis of unfolding and dissociation in lactose repressor protein
    • Barry,J.K. and Matthews,K.S. (1999) Thermodynamic analysis of unfolding and dissociation in lactose repressor protein. Biochemistry, 38, 6520-6528.
    • (1999) Biochemistry , vol.38 , pp. 6520-6528
    • Barry, J.K.1    Matthews, K.S.2
  • 32
    • 3843114319 scopus 로고
    • Intramolecular reaction in polycondensations. I. The theory of linear systems
    • Jacobson,H. and Stockmayer,W.H. (1950) Intramolecular reaction in polycondensations. I. The theory of linear systems. J. Chem. Phys., 18, 1600-1606.
    • (1950) J. Chem. Phys. , vol.18 , pp. 1600-1606
    • Jacobson, H.1    Stockmayer, W.H.2
  • 33
    • 0025867008 scopus 로고
    • Transcription by single molecules of RNA polymerase observed by light microscopy
    • Schafer,D.A., Gelles,J., Sheetz,M.P. and Landick,R. (1991) Transcription by single molecules of RNA polymerase observed by light microscopy. Nature, 352, 444-448. (Pubitemid 21896745)
    • (1991) Nature , vol.352 , Issue.6334 , pp. 444-448
    • Schafer, D.A.1    Gellest, J.2    Sheetz, M.P.3    Landick, R.4
  • 34
    • 0028143652 scopus 로고
    • Tethered particle motion method for studying transcript elongation by a single RNA polymerase molecule
    • Yin,H., Landick,R. and Gelles,J. (1994) Tethered particle motion method for studying transcript elongation by a single RNA polymerase molecule. Biophys. J., 67, 2468-2478. (Pubitemid 24369671)
    • (1994) Biophysical Journal , vol.67 , Issue.6 , pp. 2468-2478
    • Yin, H.1    Landick, R.2    Gelles, J.3
  • 35
    • 19244382579 scopus 로고    scopus 로고
    • Diversity in the Rates of Transcript Elongation by Single RNA Polymerase Molecules
    • DOI 10.1074/jbc.M310290200
    • Tolic-Norrelykke,S.F., Engh,A.M., Landick,R. and Gelles,J. (2004) Diversity in the rates of transcript elongation by single RNA polymerase molecules. J. Biol. Chem., 279, 3292-3299. (Pubitemid 38140563)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.5 , pp. 3292-3299
    • Tolic-Norrelykke, S.F.1    Engh, A.M.2    Landick, R.3    Gelles, J.4
  • 36
    • 31544452261 scopus 로고    scopus 로고
    • Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI
    • DOI 10.1093/nar/gkj432
    • van den Broek,B., Vanzi,F., Normanno,D., Pavone,F.S. and Wuite,G.J. (2006) Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI. Nucleic Acids Res., 34, 167-174. (Pubitemid 43160041)
    • (2006) Nucleic Acids Research , vol.34 , Issue.1 , pp. 167-174
    • Van Den, B.B.1    Vanzi, F.2    Normanno, D.3    Pavone, F.S.4    Wuite, G.J.L.5
  • 37
    • 0037336483 scopus 로고    scopus 로고
    • The micromechanics of DNA
    • Marko,J.F. and Cocco,S. (2003) The micromechanics of DNA. Phys. World, 16, 37-41.
    • (2003) Phys. World , vol.16 , pp. 37-41
    • Marko, J.F.1    Cocco, S.2
  • 40
    • 0030024985 scopus 로고    scopus 로고
    • Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
    • Smith,S.B., Cui,Y. and Bustamante,C. (1996) Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science, 271, 795-799.
    • (1996) Science , vol.271 , pp. 795-799
    • Smith, S.B.1    Cui, Y.2    Bustamante, C.3
  • 44
    • 0034690257 scopus 로고    scopus 로고
    • Single-molecule analysis of DNA uncoiling by a type II topoisomerase
    • DOI 10.1038/35009144
    • Strick,T.R., Croquette,V. and Bensimon,D. (2000) Single-molecule analysis of DNA uncoiling by a type II topoisomerase. Nature, 404, 901-904. (Pubitemid 30230345)
    • (2000) Nature , vol.404 , Issue.6780 , pp. 901-904
    • Strick, T.R.1    Croquette, V.2    Bensimon, D.3
  • 45
    • 0034594940 scopus 로고    scopus 로고
    • Single-molecule studies of the effect of template tension on T7 DNA polymerase activity
    • DOI 10.1038/35003614
    • Wuite,G.J., Smith,S.B., Young,M., Keller,D. and Bustamante,C. (2000) Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature, 404, 103-106. (Pubitemid 30143142)
    • (2000) Nature , vol.404 , Issue.6773 , pp. 103-106
    • Wulte, G.J.L.1    Smith, S.B.2    Young, M.3    Keller, D.4    Bustamante, C.5
  • 46
    • 0028261701 scopus 로고
    • Single myosin molecule mechanics: Piconewton forces and nanometre steps
    • DOI 10.1038/368113a0
    • Finer,J.T., Simmons,R.M. and Spudich,J.A. (1994) Single myosin molecule mechanics: piconewton forces and nanometre steps. Nature, 368, 113-119. (Pubitemid 24101520)
    • (1994) Nature , vol.368 , Issue.6467 , pp. 113-119
    • Finer, J.T.1    Simmons, R.M.2    Spudich, J.A.3
  • 47
    • 0025251665 scopus 로고
    • Force generation of organelle transport measured in vivo by an infrared laser trap
    • Ashkin,A., Schutze,K., Dziedzic,J.M., Euteneuer,U. and Schliwa,M. (1990) Force generation of organelle transport measured in vivo by an infrared laser trap. Nature, 348, 346-348. (Pubitemid 120029106)
    • (1990) Nature , vol.348 , Issue.6299 , pp. 346-348
    • Ashkin, A.1    Schutze, K.2    Dziedzic, J.M.3    Euteneuer, U.4    Schliwa, M.5
  • 48
    • 0028362896 scopus 로고
    • Force and velocity measured for single kinesin molecules
    • DOI 10.1016/0092-8674(94)90060-4
    • Svoboda,K. and Block,S.M. (1994) Force and velocity measured for single kinesin molecules. Cell, 77, 773-784. (Pubitemid 24175612)
    • (1994) Cell , vol.77 , Issue.5 , pp. 773-784
    • Svoboda, K.1    Block, S.M.2
  • 50
    • 33644676435 scopus 로고    scopus 로고
    • Volume-exclusion effects in tethered-particle experiments: Bead size matters
    • Segall,D.E., Nelson,P.C. and Phillips,R. (2006) Volume-exclusion effects in tethered-particle experiments: bead size matters. Phys. Rev. Lett., 96, 088306.
    • (2006) Phys. Rev. Lett. , vol.96 , pp. 088306
    • Segall, D.E.1    Nelson, P.C.2    Phillips, R.3
  • 52
    • 0031880930 scopus 로고    scopus 로고
    • Looping dynamics of linear DNA molecules and the effect of DNA curvature: A study by Brownian dynamics simulation
    • Merlitz,H., Rippe,K., Klenin,K.V. and Langowski,J. (1998) Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation. Biophys. J., 74, 773-779. (Pubitemid 28345272)
    • (1998) Biophysical Journal , vol.74 , Issue.2 I , pp. 773-779
    • Merlitz, H.1    Rippe, K.2    Kienin, K.V.3    Langowski, J.4
  • 53
    • 0035668536 scopus 로고    scopus 로고
    • Making contacts on a nucleic acid polymer
    • Rippe,K. (2001) Making contacts on a nucleic acid polymer. Trends Biochem. Sci., 26, 733-740.
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 733-740
    • Rippe, K.1
  • 55
    • 0037306915 scopus 로고    scopus 로고
    • Fluorescence resonance energy transfer over approximately 130 base pairs in hyperstable lac repressor-DNA loops
    • Edelman,L.M., Cheong,R. and Kahn,J.D. (2003) Fluorescence resonance energy transfer over approximately 130 base pairs in hyperstable lac repressor-DNA loops. Biophys. J., 84, 1131-1145.
    • (2003) Biophys. J. , vol.84 , pp. 1131-1145
    • Edelman, L.M.1    Cheong, R.2    Kahn, J.D.3


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