메뉴 건너뛰기




Volumn 39, Issue 22, 2011, Pages 9768-9778

Influence of ground-state structure and Mg2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; APTAMER; CYTOSINE; GUANOSINE; MAGNESIUM; RNA; URACIL;

EID: 83755205440     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr664     Document Type: Article
Times cited : (26)

References (38)
  • 3
    • 77952896659 scopus 로고    scopus 로고
    • Compact intermediates in RNA folding
    • Woodson,S.A. (2010) Compact intermediates in RNA folding. Annu. Rev. Biophys., 39, 61-77.
    • (2010) Annu. Rev. Biophys. , vol.39 , pp. 61-77
    • Woodson, S.A.1
  • 4
    • 16344371778 scopus 로고    scopus 로고
    • RNA and protein folding: Common themes and variations
    • DOI 10.1021/bi047314+
    • Thirumalai,D. and Hyeon,C. (2005) RNA and protein folding: common themes and variations. Biochemistry, 44, 4957-4970. (Pubitemid 40471212)
    • (2005) Biochemistry , vol.44 , Issue.13 , pp. 4957-4970
    • Thirumalai, D.1    Hyeon, C.2
  • 5
    • 72149126118 scopus 로고    scopus 로고
    • A switch in time: Detailing the life of a riboswitch
    • Garst,A.D. and Batey,R.T. (2009) A switch in time: detailing the life of a riboswitch. Biochim. Biophys. Acta, 1789, 584-591.
    • (2009) Biochim. Biophys. Acta , vol.1789 , pp. 584-591
    • Garst, A.D.1    Batey, R.T.2
  • 6
    • 0142075327 scopus 로고    scopus 로고
    • Genetic control by metabolite-binding riboswitches
    • DOI 10.1002/cbic.200300685
    • Winkler,W.C. and Breaker,R.R. (2003) Genetic control by metabolite-binding riboswitches. Chembiochem, 4, 1024-1032. (Pubitemid 37267591)
    • (2003) ChemBioChem , vol.4 , Issue.10 , pp. 1024-1032
    • Winkler, W.C.1    Breaker, R.R.2
  • 7
    • 34347401399 scopus 로고    scopus 로고
    • Riboswitches: small-molecule recognition by gene regulatory RNAs
    • DOI 10.1016/j.sbi.2007.05.004, PII S0959440X07000693, Nucleic acids / Sequences and topology
    • Edwards,T.E., Klein,D.J. and Ferre-D'Amaré,A.R. (2007) Riboswitches: small-molecule recognition by gene regulatory RNAs. Curr. Opin. Struct. Biol., 17, 273-279. (Pubitemid 47021358)
    • (2007) Current Opinion in Structural Biology , vol.17 , Issue.3 , pp. 273-279
    • Edwards, T.E.1    Klein, D.J.2    Ferre-D'Amare, A.R.3
  • 8
    • 34247242053 scopus 로고    scopus 로고
    • Structures of RNA switches: Insight into molecular recognition and tertiary structure
    • DOI 10.1002/anie.200604163
    • Schwalbe,H., Buck,J., Fürtig,B., Noeske,J. and Wöhnert,J. (2007) Structures of RNA switches: insight into molecular recognition and tertiary structure. Angew. Chem. Int. Ed. Engl., 46, 1212-1219. (Pubitemid 46981366)
    • (2007) Angewandte Chemie - International Edition , vol.46 , Issue.8 , pp. 1212-1219
    • Schwalbe, H.1    Buck, J.2    Furtig, B.3    Noeske, J.4    Wohnert, J.5
  • 9
    • 66549094626 scopus 로고    scopus 로고
    • The long and the short of riboswitches
    • Serganov,A. (2009) The long and the short of riboswitches. Curr. Opin. Struct. Biol., 19, 251-259.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 251-259
    • Serganov, A.1
  • 10
    • 9244225713 scopus 로고    scopus 로고
    • Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
    • DOI 10.1038/nature03037
    • Batey,R.T., Gilbert,S.D. and Montange,R.K. (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature, 432, 411-415. (Pubitemid 39551677)
    • (2004) Nature , vol.432 , Issue.7015 , pp. 411-415
    • Batey, R.T.1    Gilbert, S.D.2    Montange, R.K.3
  • 12
    • 77955081034 scopus 로고    scopus 로고
    • Dissecting the influence of Mg2+ on 3D architecture and ligand-binding of the guanine-sensing riboswitch aptamer domain
    • Buck,J., Noeske,J., Wöhnert,J. and Schwalbe,H. (2010) Dissecting the influence of Mg2+ on 3D architecture and ligand-binding of the guanine-sensing riboswitch aptamer domain. Nucleic Acids Res., 38, 4143-4153.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 4143-4153
    • Buck, J.1    Noeske, J.2    Wöhnert, J.3    Schwalbe, H.4
  • 13
    • 73449116019 scopus 로고    scopus 로고
    • Design and antimicrobial action of purine analogues that bind guanine riboswitches
    • Kim,J.N., Blount,K.F., Puskarz,I., Lim,J., Link,K.H. and Breaker,R.R. (2009) Design and antimicrobial action of purine analogues that bind guanine riboswitches. ACS Chem. Biol., 4, 915-927.
    • (2009) ACS Chem. Biol. , vol.4 , pp. 915-927
    • Kim, J.N.1    Blount, K.F.2    Puskarz, I.3    Lim, J.4    Link, K.H.5    Breaker, R.R.6
  • 14
    • 76449099287 scopus 로고    scopus 로고
    • XDS
    • Kabsch,W. (2010) XDS. Acta Cryst., D66, 125-132.
    • (2010) Acta Cryst. , vol.D66 , pp. 125-132
    • Kabsch, W.1
  • 17
    • 0031059039 scopus 로고    scopus 로고
    • Detecting and overcoming crystal twinning
    • DOI 10.1016/S0076-6879(97)76068-3
    • Yeates,T.O. (1997) Detecting and overcoming crystal twinning. Methods Enzymol., 276, 344-358. (Pubitemid 27085613)
    • (1997) Methods in Enzymology , vol.276 , pp. 344-358
    • Yeates, T.O.1
  • 18
    • 37049014272 scopus 로고    scopus 로고
    • Version 1.2 of the crystallography and NMR system
    • Brunger,A.T. (2007) Version 1.2 of the crystallography and NMR system. Nat. Protocols, 2, 2728-2733.
    • (2007) Nat. Protocols , vol.2 , pp. 2728-2733
    • Brunger, A.T.1
  • 20
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • DOI 10.1093/nar/gkg680
    • Lu,X.J. and Olson,W.K. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of threeimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121. (Pubitemid 37441878)
    • (2003) Nucleic Acids Research , vol.31 , Issue.17 , pp. 5108-5121
    • Lu, X.-J.1    Olson, W.K.2
  • 21
    • 0142095013 scopus 로고    scopus 로고
    • Rapid sample-mixing technique for transient NMR and photo-CIDNP spectroscopy: Applications to real-time protein folding
    • DOI 10.1021/ja036357v
    • Mok,K.H., Nagashima,T., Day,I.J., Jones,J.A., Jones,C.J., Dobson,C.M. and Hore,P.J. (2003) Rapid sample-mixing technique for transient NMR and photo-CIDNP spectroscopy: applications to real-time protein folding. J. Am. Chem. Soc., 125, 12484-12492. (Pubitemid 37264932)
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.41 , pp. 12484-12492
    • Mok, K.H.1    Nagashima, T.2    Day, I.J.3    Jones, J.A.4    Jones, C.J.V.5    Dobson, C.M.6    Hore, P.J.7
  • 23
    • 77951688391 scopus 로고    scopus 로고
    • Heterogeneity and dynamics of the ligand recognition mode in purine-sensing riboswitches
    • Jain,N., Zhao,L., Liu,J.D. and Xia,T. (2010) Heterogeneity and dynamics of the ligand recognition mode in purine-sensing riboswitches. Biochemistry, 49, 3703-3714.
    • (2010) Biochemistry , vol.49 , pp. 3703-3714
    • Jain, N.1    Zhao, L.2    Liu, J.D.3    Xia, T.4
  • 24
    • 66349133602 scopus 로고    scopus 로고
    • Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs
    • Gilbert,S.D., Reyes,F.E., Edwards,A.L. and Batey,R.T. (2009) Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. Structure, 17, 857-868.
    • (2009) Structure , vol.17 , pp. 857-868
    • Gilbert, S.D.1    Reyes, F.E.2    Edwards, A.L.3    Batey, R.T.4
  • 25
    • 58149138753 scopus 로고    scopus 로고
    • A structural basis for the recognition of 20-deoxyguanosine by the purine riboswitch
    • Edwards,A.L. and Batey,R.T. (2009) A structural basis for the recognition of 20-deoxyguanosine by the purine riboswitch. J. Mol. Biol., 385, 938-948.
    • (2009) J. Mol. Biol. , vol.385 , pp. 938-948
    • Edwards, A.L.1    Batey, R.T.2
  • 26
    • 38849103659 scopus 로고    scopus 로고
    • Purine sensing by riboswitches
    • DOI 10.1042/BC20070088
    • Kim,J.N. and Breaker,R.R. (2008) Purine sensing by riboswitches. Biol. Cell, 100, 1-11. (Pubitemid 351201429)
    • (2008) Biology of the Cell , vol.100 , Issue.1 , pp. 1-11
    • Kim, J.N.1    Breaker, R.R.2
  • 27
    • 80052968050 scopus 로고    scopus 로고
    • Structure and dynamics of the deoxyguanosine-sensing riboswitch studied by NMR-spectroscopy
    • Epub ahead of print May 16, 2011
    • Wacker,A., Buck,J., Mathieu,D., Richter,C., Wohnert,J. and Schwalbe,H. (2011) Structure and dynamics of the deoxyguanosine-sensing riboswitch studied by NMR-spectroscopy. Nucleic Acids Res., Epub ahead of print May 16, 2011.
    • (2011) Nucleic Acids Res.
    • Wacker, A.1    Buck, J.2    Mathieu, D.3    Richter, C.4    Wohnert, J.5    Schwalbe, H.6
  • 28
    • 33846898497 scopus 로고    scopus 로고
    • Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch
    • DOI 10.1093/nar/gkl1094
    • Noeske,J., Buck,J., Fürtig,B., Nasiri,H.R., Schwalbe,H. and Wöhnert,J. (2007) Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch. Nucleic Acids Res., 35, 572-583. (Pubitemid 46232073)
    • (2007) Nucleic Acids Research , vol.35 , Issue.2 , pp. 572-583
    • Noeske, J.1    Buck, J.2    Furtig, B.3    Nasiri, H.R.4    Schwalbe, H.5    Wohnert, J.6
  • 30
    • 34548761368 scopus 로고    scopus 로고
    • Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach
    • DOI 10.1093/nar/gkm580
    • Lang,K., Rieder,R. and Micura,R. (2007) Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach. Nucleic Acids Res., 35, 5370-5378. (Pubitemid 47423911)
    • (2007) Nucleic Acids Research , vol.35 , Issue.16 , pp. 5370-5378
    • Lang, K.1    Rieder, R.2    Micura, R.3
  • 31
    • 38649085954 scopus 로고    scopus 로고
    • Tertiary interactions determine the accuracy of RNA folding
    • DOI 10.1021/ja076166i
    • Chauhan,S. and Woodson,S.A. (2008) Tertiary interactions determine the accuracy of RNA folding. J. Am. Chem. Soc., 130, 1296-1303. (Pubitemid 351171008)
    • (2008) Journal of the American Chemical Society , vol.130 , Issue.4 , pp. 1296-1303
    • Chauhan, S.1    Woodson, S.A.2
  • 32
    • 0033544723 scopus 로고    scopus 로고
    • The effect of long-range loop-loop interactions on folding of the Tetrahymena self-splicing RNA
    • DOI 10.1006/jmbi.1999.3298
    • Pan,J. and Woodson,S.A. (1999) The effect of long-range loop-loop interactions on folding of the Tetrahymena self-splicing RNA. J. Mol. Biol., 294, 955-965. (Pubitemid 30000387)
    • (1999) Journal of Molecular Biology , vol.294 , Issue.4 , pp. 955-965
    • Pan, J.1    Woodson, S.A.2
  • 37
    • 6344242969 scopus 로고    scopus 로고
    • Principles of RNA compaction: Insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations
    • DOI 10.1016/j.jmb.2004.08.080, PII S0022283604010800
    • Takamoto,K., Das,R., He,Q., Doniach,S., Brenowitz,M., Herschlag,D. and Chance,M.R. (2004) Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations. J. Mol. Biol., 343, 1195-1206. (Pubitemid 39387820)
    • (2004) Journal of Molecular Biology , vol.343 , Issue.5 , pp. 1195-1206
    • Takamoto, K.1    Das, R.2    He, Q.3    Doniach, S.4    Brenowitz, M.5    Herschlag, D.6    Chance, M.R.7
  • 38
    • 79960466968 scopus 로고    scopus 로고
    • RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways
    • Mitra,S., Laederach,A., Golden,B.L., Altman,R.B. and Brenowitz,M. (2011) RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. RNA, 17, 1589-1603.
    • (2011) RNA , vol.17 , pp. 1589-1603
    • Mitra, S.1    Laederach, A.2    Golden, B.L.3    Altman, R.B.4    Brenowitz, M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.