메뉴 건너뛰기




Volumn 110, Issue 11, 2013, Pages 4188-4193

Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution

Author keywords

Allosteric effect; Ergodicity; RNA; Site specific labeling; Structural preorganization

Indexed keywords

APTAMER; COCARBOXYLASE; MAGNESIUM;

EID: 84875043544     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1218062110     Document Type: Article
Times cited : (104)

References (48)
  • 1
    • 80052973462 scopus 로고    scopus 로고
    • Prospects for riboswitch discovery and analysis
    • Breaker RR (2011) Prospects for riboswitch discovery and analysis. Mol Cell 43(6): 867-879.
    • (2011) Mol Cell , vol.43 , Issue.6 , pp. 867-879
    • Breaker, R.R.1
  • 2
    • 84863878432 scopus 로고    scopus 로고
    • Riboswitches: Structures and mechanisms
    • pii: a003533, 10.1101/cshperspect.a003533
    • Garst AD, Edwards AL, Batey RT (2011) Riboswitches: Structures and mechanisms. Cold Spring Harb Perspect Biol 3(6):pii: a003533, 10.1101/cshperspect.a003533.
    • (2011) Cold Spring Harb Perspect Biol , vol.3 , Issue.6
    • Garst, A.D.1    Edwards, A.L.2    Batey, R.T.3
  • 3
    • 80053041142 scopus 로고    scopus 로고
    • Riboswitches: Discovery of drugs that target bacterial gene-regulatory RNAs
    • Deigan KE, Ferré-D'Amaré AR (2011) Riboswitches: Discovery of drugs that target bacterial gene-regulatory RNAs. Acc Chem Res 44(12):1329-1338.
    • (2011) Acc Chem Res , vol.44 , Issue.12 , pp. 1329-1338
    • Deigan, K.E.1    Ferré-D'Amaré, A.R.2
  • 4
    • 84862591360 scopus 로고    scopus 로고
    • Molecular recognition and function of riboswitches
    • Serganov A, Patel DJ (2012) Molecular recognition and function of riboswitches. Curr Opin Struct Biol 22(3):279-286.
    • (2012) Curr Opin Struct Biol , vol.22 , Issue.3 , pp. 279-286
    • Serganov, A.1    Patel, D.J.2
  • 6
    • 0346687595 scopus 로고    scopus 로고
    • The riboswitch control of bacterial metabolism
    • Nudler E, Mironov AS (2004) The riboswitch control of bacterial metabolism. Trends Biochem Sci 29(1):11-17.
    • (2004) Trends Biochem Sci , vol.29 , Issue.1 , pp. 11-17
    • Nudler, E.1    Mironov, A.S.2
  • 7
    • 34247242053 scopus 로고    scopus 로고
    • Structures of RNA switches: Insight into molecular recognition and tertiary structure
    • Schwalbe H, Buck J, Fürtig B, Noeske J, Wöhnert J (2007) Structures of RNA switches: Insight into molecular recognition and tertiary structure. Angew Chem Int Ed Engl 46(8):1212-1219.
    • (2007) Angew Chem Int Ed Engl , vol.46 , Issue.8 , pp. 1212-1219
    • Schwalbe, H.1    Buck, J.2    Fürtig, B.3    Noeske, J.4    Wöhnert, J.5
  • 8
    • 74549174202 scopus 로고    scopus 로고
    • Determination of riboswitch structures: Light at the end of the tunnel?
    • Serganov A (2010) Determination of riboswitch structures: Light at the end of the tunnel? RNA Biol 7(1):98-103.
    • (2010) RNA Biol , vol.7 , Issue.1 , pp. 98-103
    • Serganov, A.1
  • 9
    • 80052982281 scopus 로고    scopus 로고
    • The dynamic nature of RNA as key to understanding riboswitch mechanisms
    • Haller A, Soulière MF, Micura R (2011) The dynamic nature of RNA as key to understanding riboswitch mechanisms. Acc Chem Res 44(12):1339-1348.
    • (2011) Acc Chem Res , vol.44 , Issue.12 , pp. 1339-1348
    • Haller, A.1    Soulière, M.F.2    Micura, R.3
  • 10
    • 0037206833 scopus 로고    scopus 로고
    • Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
    • Winkler W, Nahvi A, Breaker RR (2002) Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419(6910):952-956.
    • (2002) Nature , vol.419 , Issue.6910 , pp. 952-956
    • Winkler, W.1    Nahvi, A.2    Breaker, R.R.3
  • 11
    • 0038136962 scopus 로고    scopus 로고
    • Metabolite-binding RNA domains are present in the genes of eukaryotes
    • Sudarsan N, Barrick JE, Breaker RR (2003) Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9(6):644-647.
    • (2003) RNA , vol.9 , Issue.6 , pp. 644-647
    • Sudarsan, N.1    Barrick, J.E.2    Breaker, R.R.3
  • 12
    • 34249278470 scopus 로고    scopus 로고
    • Control of alternative RNA splicing and gene expression by eukaryotic riboswitches
    • Cheah MT, Wachter A, Sudarsan N, Breaker RR (2007) Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447(7143):497-500.
    • (2007) Nature , vol.447 , Issue.7143 , pp. 497-500
    • Cheah, M.T.1    Wachter, A.2    Sudarsan, N.3    Breaker, R.R.4
  • 13
    • 33749986680 scopus 로고    scopus 로고
    • Tandem riboswitch architectures exhibit complex gene control functions
    • Sudarsan N, et al. (2006) Tandem riboswitch architectures exhibit complex gene control functions. Science 314(5797):300-304.
    • (2006) Science , vol.314 , Issue.5797 , pp. 300-304
    • Sudarsan, N.1
  • 14
    • 33947714417 scopus 로고    scopus 로고
    • Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis
    • Welz R, Breaker RR (2007) Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. RNA 13(4):573-582.
    • (2007) RNA , vol.13 , Issue.4 , pp. 573-582
    • Welz, R.1    Breaker, R.R.2
  • 15
    • 33745635350 scopus 로고    scopus 로고
    • Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
    • Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ (2006) Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441(7097): 1167-1171.
    • (2006) Nature , vol.441 , Issue.7097 , pp. 1167-1171
    • Serganov, A.1    Polonskaia, A.2    Phan, A.T.3    Breaker, R.R.4    Patel, D.J.5
  • 16
    • 33744469562 scopus 로고    scopus 로고
    • Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand
    • Thore S, Leibundgut M, Ban N (2006) Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312(5777):1208-1211.
    • (2006) Science , vol.312 , Issue.5777 , pp. 1208-1211
    • Thore, S.1    Leibundgut, M.2    Ban, N.3
  • 17
    • 33748300801 scopus 로고    scopus 로고
    • Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition
    • Edwards TE, Ferré-D'Amaré AR (2006) Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14(9):1459-1468.
    • (2006) Structure , vol.14 , Issue.9 , pp. 1459-1468
    • Edwards, T.E.1    Ferré-D'Amaré, A.R.2
  • 18
    • 84865243362 scopus 로고    scopus 로고
    • Riboswitch structure in the ligand-free state
    • Liberman JA, Wedekind JE (2012) Riboswitch structure in the ligand-free state. Wiley Interdiscip Rev RNA 3(3):369-384.
    • (2012) Wiley Interdiscip Rev RNA , vol.3 , Issue.3 , pp. 369-384
    • Liberman, J.A.1    Wedekind, J.E.2
  • 19
    • 84857771826 scopus 로고    scopus 로고
    • Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch
    • Perdrizet GA, II, Artsimovitch I, Furman R, Sosnick TR, Pan T (2012) Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch. Proc Natl Acad Sci USA 109(9):3323-3328.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.9 , pp. 3323-3328
    • Perdrizet, I.I.G.A.1    Artsimovitch, I.2    Furman, R.3    Sosnick, T.R.4    Pan, T.5
  • 20
    • 77954649456 scopus 로고    scopus 로고
    • RNA folding during transcription: Protocols and studies
    • Wong TN, Pan T (2009) RNA folding during transcription: Protocols and studies. Methods Enzymol 468:167-193.
    • (2009) Methods Enzymol , vol.468 , pp. 167-193
    • Wong, T.N.1    Pan, T.2
  • 22
    • 34548761368 scopus 로고    scopus 로고
    • Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach
    • Lang K, Rieder R, Micura R (2007) Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach. Nucleic Acids Res 35(16):5370-5378.
    • (2007) Nucleic Acids Res , vol.35 , Issue.16 , pp. 5370-5378
    • Lang, K.1    Rieder, R.2    Micura, R.3
  • 23
    • 74649084566 scopus 로고    scopus 로고
    • The ligand-free state of the TPP riboswitch: A partially folded RNA structure
    • Ali M, Lipfert J, Seifert S, Herschlag D, Doniach SJ (2010) The ligand-free state of the TPP riboswitch: A partially folded RNA structure. J Mol Biol 396(1):153-165.
    • (2010) J Mol Biol , vol.396 , Issue.1 , pp. 153-165
    • Ali, M.1    Lipfert, J.2    Seifert, S.3    Herschlag, D.4    Doniach, S.J.5
  • 24
    • 77955500520 scopus 로고    scopus 로고
    • Riboswitch function: Flipping the switch or tuning the dimmer?
    • Baird NJ, Kulshina N, Ferré-D'Amaré AR (2010) Riboswitch function: Flipping the switch or tuning the dimmer? RNA Biol 7(3):328-332.
    • (2010) RNA Biol , vol.7 , Issue.3 , pp. 328-332
    • Baird, N.J.1    Kulshina, N.2    Ferré-D'Amaré, A.R.3
  • 25
    • 77149165421 scopus 로고    scopus 로고
    • Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis
    • Baird NJ, Ferré-D'Amaré AR (2010) Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis. RNA 16(3):598-609.
    • (2010) RNA , vol.16 , Issue.3 , pp. 598-609
    • Baird, N.J.1    Ferré-D'Amaré, A.R.2
  • 26
    • 77955834766 scopus 로고    scopus 로고
    • Selective 2′-hydroxyl acylation analyzed by protection from exoribonuclease
    • Steen K-A, Malhotra A, Weeks KM (2010) Selective 2′-hydroxyl acylation analyzed by protection from exoribonuclease. J Am Chem Soc 132(29):9940-9943.
    • (2010) J Am Chem Soc , vol.132 , Issue.29 , pp. 9940-9943
    • Steen, K.-A.1    Malhotra, A.2    Weeks, K.M.3
  • 27
    • 84865133584 scopus 로고    scopus 로고
    • Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity
    • Steen K-A, Rice GM, Weeks KM (2012) Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity. J Am Chem Soc 134(32):13160-13163.
    • (2012) J Am Chem Soc , vol.134 , Issue.32 , pp. 13160-13163
    • Steen, K.-A.1    Rice, G.M.2    Weeks, K.M.3
  • 28
    • 75649088957 scopus 로고    scopus 로고
    • Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch
    • Kulshina N, Edwards TE, Ferré-D'Amaré AR (2010) Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch. RNA 16(1):186-196.
    • (2010) RNA , vol.16 , Issue.1 , pp. 186-196
    • Kulshina, N.1    Edwards, T.E.2    Ferré-D'Amaré, A.R.3
  • 29
    • 84855698066 scopus 로고    scopus 로고
    • KinITC: A new method for obtaining joint thermodynamic and kinetic data by isothermal titration calorimetry
    • Burnouf D, et al. (2012) kinITC: A new method for obtaining joint thermodynamic and kinetic data by isothermal titration calorimetry. J Am Chem Soc 134(1):559-565.
    • (2012) J Am Chem Soc , vol.134 , Issue.1 , pp. 559-565
    • Burnouf, D.1
  • 30
    • 84857133512 scopus 로고    scopus 로고
    • Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer
    • Anthony PC, Perez CF, García-García C, Block SM (2012) Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer. Proc Natl Acad Sci USA 109(5): 1485-1489.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.5 , pp. 1485-1489
    • Anthony, P.C.1    Perez, C.F.2    García-García, C.3    Block, S.M.4
  • 31
    • 44449134820 scopus 로고    scopus 로고
    • A practical guide to single-molecule FRET
    • Roy R, Hohng S, Ha T (2008) A practical guide to single-molecule FRET. Nat Methods 5(6):507-516.
    • (2008) Nat Methods , vol.5 , Issue.6 , pp. 507-516
    • Roy, R.1    Hohng, S.2    Ha, T.3
  • 33
    • 84862109207 scopus 로고    scopus 로고
    • Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding
    • Wood S, Ferré-D'Amaré AR, Rueda D (2012) Allosteric tertiary interactions preorganize the c-di-GMP riboswitch and accelerate ligand binding. ACS Chem Biol 7(5): 920-927.
    • (2012) ACS Chem Biol , vol.7 , Issue.5 , pp. 920-927
    • Wood, S.1    Ferré-D'Amaré, A.R.2    Rueda, D.3
  • 34
    • 51649088750 scopus 로고    scopus 로고
    • The preparation of site-specifically modified riboswitch domains as an example for enzymatic ligation of chemically synthesized RNA fragments
    • Lang K, Micura R (2008) The preparation of site-specifically modified riboswitch domains as an example for enzymatic ligation of chemically synthesized RNA fragments. Nat Protoc 3(9):1457-1466.
    • (2008) Nat Protoc , vol.3 , Issue.9 , pp. 1457-1466
    • Lang, K.1    Micura, R.2
  • 35
    • 33847051154 scopus 로고    scopus 로고
    • Identification of two distinct hybrid state intermediates on the ribosome
    • Munro JB, Altman RB, O'Connor N, Blanchard SC (2007) Identification of two distinct hybrid state intermediates on the ribosome. Mol Cell 25(4):505-517.
    • (2007) Mol Cell , vol.25 , Issue.4 , pp. 505-517
    • Munro, J.B.1    Altman, R.B.2    O'Connor, N.3    Blanchard, S.C.4
  • 36
    • 66149152243 scopus 로고    scopus 로고
    • Mitigating unwanted photophysical processes for improved single-molecule fluorescence imaging
    • Dave R, Terry DS, Munro JB, Blanchard SC (2009) Mitigating unwanted photophysical processes for improved single-molecule fluorescence imaging. Biophys J 96(6): 2371-2381.
    • (2009) Biophys J , vol.96 , Issue.6 , pp. 2371-2381
    • Dave, R.1    Terry, D.S.2    Munro, J.B.3    Blanchard, S.C.4
  • 38
    • 0021982448 scopus 로고
    • Actin and tubulin polymerization: The use of kinetic methods to determine mechanism
    • Frieden C (1985) Actin and tubulin polymerization: The use of kinetic methods to determine mechanism. Annu Rev Biophys Biophys Chem 14:189-210.
    • (1985) Annu Rev Biophys Biophys Chem , vol.14 , pp. 189-210
    • Frieden, C.1
  • 39
    • 0034674420 scopus 로고    scopus 로고
    • A single-molecule study of RNA catalysis and folding
    • Zhuang X, et al. (2000) A single-molecule study of RNA catalysis and folding. Science 288(5473):2048-2051.
    • (2000) Science , vol.288 , Issue.5473 , pp. 2048-2051
    • Zhuang, X.1
  • 40
    • 76249126156 scopus 로고    scopus 로고
    • Multiple native states reveal persistent ruggedness of an RNA folding landscape
    • Solomatin SV, Greenfeld M, Chu S, Herschlag D (2010) Multiple native states reveal persistent ruggedness of an RNA folding landscape. Nature 463(7281):681-684.
    • (2010) Nature , vol.463 , Issue.7281 , pp. 681-684
    • Solomatin, S.V.1    Greenfeld, M.2    Chu, S.3    Herschlag, D.4
  • 41
    • 15944382675 scopus 로고    scopus 로고
    • The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch
    • Wickiser JK, Winkler WC, Breaker RR, Crothers DM (2005) The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell 18(1): 49-60.
    • (2005) Mol Cell , vol.18 , Issue.1 , pp. 49-60
    • Wickiser, J.K.1    Winkler, W.C.2    Breaker, R.R.3    Crothers, D.M.4
  • 42
    • 72149126118 scopus 로고    scopus 로고
    • A switch in time: Detailing the life of a riboswitch
    • Garst AD, Batey RT (2009) A switch in time: Detailing the life of a riboswitch. Biochim Biophys Acta 1789(9-10):584-591.
    • (2009) Biochim Biophys Acta , vol.1789 , Issue.9-10 , pp. 584-591
    • Garst, A.D.1    Batey, R.T.2
  • 43
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr DD, Nussinov R, Wright PE (2009) The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 5(11):789-796.
    • (2009) Nat Chem Biol , vol.5 , Issue.11 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 44
    • 0035838382 scopus 로고    scopus 로고
    • Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture
    • Leulliot N, Varani G (2001) Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture. Biochemistry 40(27):7947-7956.
    • (2001) Biochemistry , vol.40 , Issue.27 , pp. 7947-7956
    • Leulliot, N.1    Varani, G.2
  • 45
    • 0034603154 scopus 로고    scopus 로고
    • Adaptive recognition by nucleic acid aptamers
    • Hermann T, Patel DJ (2000) Adaptive recognition by nucleic acid aptamers. Science 287(5454):820-825.
    • (2000) Science , vol.287 , Issue.5454 , pp. 820-825
    • Hermann, T.1    Patel, D.J.2
  • 46
    • 77956026739 scopus 로고    scopus 로고
    • Highly modular structure and ligand binding by conformational capture in a minimalistic riboswitch
    • Duchardt-Ferner E, et al. (2010) Highly modular structure and ligand binding by conformational capture in a minimalistic riboswitch. Angew Chem Int Ed Engl 49(35): 6216-6219.
    • (2010) Angew Chem Int Ed Engl , vol.49 , Issue.35 , pp. 6216-6219
    • Duchardt-Ferner, E.1
  • 47
    • 77749304812 scopus 로고    scopus 로고
    • Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine
    • Brenner MD, Scanlan MS, Nahas MK, Ha T, Silverman SK (2010) Multivector fluorescence analysis of the xpt guanine riboswitch aptamer domain and the conformational role of guanine. Biochemistry 49(8):1596-1605.
    • (2010) Biochemistry , vol.49 , Issue.8 , pp. 1596-1605
    • Brenner, M.D.1    Scanlan, M.S.2    Nahas, M.K.3    Ha, T.4    Silverman, S.K.5
  • 48
    • 4444324112 scopus 로고    scopus 로고
    • Model-based fitting of single-channel dwell-time distributions
    • Qin F, Li L (2004) Model-based fitting of single-channel dwell-time distributions. Biophys J 87(3):1657-1671.
    • (2004) Biophys J , vol.87 , Issue.3 , pp. 1657-1671
    • Qin, F.1    Li, L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.