메뉴 건너뛰기




Volumn 13, Issue 3, 2007, Pages 339-350

Core requirements of the adenine riboswitch aptamer for ligand binding

Author keywords

Aptamer; Fluorescence spectroscopy; Molecular recognition; Riboswitch; RNA folding; RNA structure

Indexed keywords

2 AMINOPURINE; ADENINE;

EID: 33847308180     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.142007     Document Type: Article
Times cited : (59)

References (51)
  • 2
    • 9244225713 scopus 로고    scopus 로고
    • Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
    • 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.
    • (2004) Nature , vol.432 , pp. 411-415
    • Batey, R.T.1    Gilbert, S.D.2    Montange, R.K.3
  • 3
    • 3242881589 scopus 로고    scopus 로고
    • Riboswitch finder - A tool for identification of riboswitch RNAs
    • Bengert, P. and Dandekar, T. 2004. Riboswitch finder - A tool for identification of riboswitch RNAs. Nucleic Acids Res. 32: W154-W159.
    • (2004) Nucleic Acids Res , vol.32
    • Bengert, P.1    Dandekar, T.2
  • 4
    • 11144330098 scopus 로고    scopus 로고
    • Natural and engineered nucleic acids as tools to explore biology
    • Breaker, R.R. 2004. Natural and engineered nucleic acids as tools to explore biology. Nature 432: 838-845.
    • (2004) Nature , vol.432 , pp. 838-845
    • Breaker, R.R.1
  • 6
    • 33748300801 scopus 로고    scopus 로고
    • Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition
    • Edwards, T.E. and Ferre-D'Amare, A.R. 2006. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14: 1459-1468.
    • (2006) Structure , vol.14 , pp. 1459-1468
    • Edwards, T.E.1    Ferre-D'Amare, A.R.2
  • 7
    • 0038476616 scopus 로고    scopus 로고
    • The riboswitch-mediated control of sulfur metabolism in bacteria
    • Epshtein, V., Mironov, A.S., and Nudler, E. 2003. The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl. Acad. Sci. 100: 5052-5056.
    • (2003) Proc. Natl. Acad. Sci , vol.100 , pp. 5052-5056
    • Epshtein, V.1    Mironov, A.S.2    Nudler, E.3
  • 9
    • 33646768226 scopus 로고    scopus 로고
    • Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain
    • Gilbert, S.D., Stoddard, C.D., Wise, S.J., and Batey, R.T. 2006. Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J. Mol. Biol. 359: 754-768.
    • (2006) J. Mol. Biol , vol.359 , pp. 754-768
    • Gilbert, S.D.1    Stoddard, C.D.2    Wise, S.J.3    Batey, R.T.4
  • 10
    • 0142123125 scopus 로고    scopus 로고
    • The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes
    • Grundy, F.J., Lehman, S.C., and Henkin, T.M. 2003. The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc. Natl. Acad. Sci. 100: 12057-12062.
    • (2003) Proc. Natl. Acad. Sci , vol.100 , pp. 12057-12062
    • Grundy, F.J.1    Lehman, S.C.2    Henkin, T.M.3
  • 11
    • 0042890402 scopus 로고    scopus 로고
    • Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL)
    • Johansen, L.E., Nygaard, P., Lassen, C., Agerso, Y., and Saxild, H.H. 2003. Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL). J. Bacteriol. 185: 5200-5209.
    • (2003) J. Bacteriol , vol.185 , pp. 5200-5209
    • Johansen, L.E.1    Nygaard, P.2    Lassen, C.3    Agerso, Y.4    Saxild, H.H.5
  • 12
    • 33748325570 scopus 로고    scopus 로고
    • Structural basis of glmS ribozyme activation by glucosamine-6-phosphate
    • Klein, D.J. and Ferre-D'Amare, A.R. 2006. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313: 1752-1756.
    • (2006) Science , vol.313 , pp. 1752-1756
    • Klein, D.J.1    Ferre-D'Amare, A.R.2
  • 13
    • 0346366823 scopus 로고    scopus 로고
    • Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR
    • Kubodera, T., Watanabe, M., Yoshiuchi, K., Yamashita, N., Nishimura, A., Nakai, S., Gomi, K., and Hanamoto, H. 2003. Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR. FEBS Lett. 555: 516-520.
    • (2003) FEBS Lett , vol.555 , pp. 516-520
    • Kubodera, T.1    Watanabe, M.2    Yoshiuchi, K.3    Yamashita, N.4    Nishimura, A.5    Nakai, S.6    Gomi, K.7    Hanamoto, H.8
  • 15
    • 12344273534 scopus 로고    scopus 로고
    • Riboswitch structures: Purine ligands replace tertiary contacts
    • Lescoute, A. and Westhof, E. 2005. Riboswitch structures: Purine ligands replace tertiary contacts. Chem. Biol. 12: 10-13.
    • (2005) Chem. Biol , vol.12 , pp. 10-13
    • Lescoute, A.1    Westhof, E.2
  • 16
    • 0032439514 scopus 로고    scopus 로고
    • Folding of branched RNA species
    • Lilley, D.M. 1998. Folding of branched RNA species. Biopolymers 48: 101-112.
    • (1998) Biopolymers , vol.48 , pp. 101-112
    • Lilley, D.M.1
  • 17
    • 0842334528 scopus 로고    scopus 로고
    • Adenine riboswitches and gene activation by disruption of a transcription terminator
    • Mandal, M. and Breaker, R.R. 2004a. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat. Struct. Mol. Biol. 11: 29-35.
    • (2004) Nat. Struct. Mol. Biol , vol.11 , pp. 29-35
    • Mandal, M.1    Breaker, R.R.2
  • 19
    • 0038210214 scopus 로고    scopus 로고
    • Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
    • Mandal, M., Boese, B., Barrick, J.E., Winkler, W.C., and Breaker, R.R. 2003. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113: 577-586.
    • (2003) Cell , vol.113 , pp. 577-586
    • Mandal, M.1    Boese, B.2    Barrick, J.E.3    Winkler, W.C.4    Breaker, R.R.5
  • 20
    • 5044234799 scopus 로고    scopus 로고
    • A glycine-dependent riboswitch that uses cooperative binding to control gene expression
    • Mandal, M., Lee, M., Barrick, J.E., Weinberg, Z., Emilsson, G.M., Ruzzo, W.L., and Breaker, R.R. 2004. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306: 275-279.
    • (2004) Science , vol.306 , pp. 275-279
    • Mandal, M.1    Lee, M.2    Barrick, J.E.3    Weinberg, Z.4    Emilsson, G.M.5    Ruzzo, W.L.6    Breaker, R.R.7
  • 21
    • 0037453069 scopus 로고    scopus 로고
    • Transcription termination control of the S box system: Direct measurement of S-adenosylmethionine by the leader RNA
    • McDaniel, B.A., Grundy, F.J., Artsimovitch, I., and Henkin, T.M. 2003. Transcription termination control of the S box system: Direct measurement of S-adenosylmethionine by the leader RNA. Proc. Natl. Acad. Sci. 100: 3083-3088.
    • (2003) Proc. Natl. Acad. Sci , vol.100 , pp. 3083-3088
    • McDaniel, B.A.1    Grundy, F.J.2    Artsimovitch, I.3    Henkin, T.M.4
  • 22
    • 0023651444 scopus 로고
    • Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
    • Milligan, J.F., Groebe, D.R., Witherell, G.W., and Uhlenbeck, O.C. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15: 8783-8798.
    • (1987) Nucleic Acids Res , vol.15 , pp. 8783-8798
    • Milligan, J.F.1    Groebe, D.R.2    Witherell, G.W.3    Uhlenbeck, O.C.4
  • 24
    • 33745628336 scopus 로고    scopus 로고
    • Structure of the S-adenosyl-methionine riboswitch regulatory mRNA element
    • Montange, R.K. and Batey, R.T. 2006. Structure of the S-adenosyl-methionine riboswitch regulatory mRNA element. Nature 441: 1172-1175.
    • (2006) Nature , vol.441 , pp. 1172-1175
    • Montange, R.K.1    Batey, R.T.2
  • 26
    • 1242320304 scopus 로고    scopus 로고
    • Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes
    • Nahvi, A., Barrick, J.E., and Breaker, R.R. 2004. Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res. 32: 143-150.
    • (2004) Nucleic Acids Res , vol.32 , pp. 143-150
    • Nahvi, A.1    Barrick, J.E.2    Breaker, R.R.3
  • 27
    • 0346687595 scopus 로고    scopus 로고
    • The riboswitch control of bacterial metabolism
    • Nudler, E. and Mironov, A.S. 2004. The riboswitch control of bacterial metabolism. Trends Biochem. Sci. 29: 11-17.
    • (2004) Trends Biochem. Sci , vol.29 , pp. 11-17
    • Nudler, E.1    Mironov, A.S.2
  • 28
    • 11844290117 scopus 로고    scopus 로고
    • The purine efflux pump PbuE in Bacillus subtilis modulates expression of the PurR and G-box (XptR) regulons by adjusting the purine base pool size
    • Nygaard, P. and Saxild, H.H. 2005. The purine efflux pump PbuE in Bacillus subtilis modulates expression of the PurR and G-box (XptR) regulons by adjusting the purine base pool size. J. Bacteriol. 187: 791-794.
    • (2005) J. Bacteriol , vol.187 , pp. 791-794
    • Nygaard, P.1    Saxild, H.H.2
  • 29
    • 0033215448 scopus 로고    scopus 로고
    • Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme
    • Perrotta, A.T., Shih, I., and Been, M.D. 1999. Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme. Science 286: 123-126.
    • (1999) Science , vol.286 , pp. 123-126
    • Perrotta, A.T.1    Shih, I.2    Been, M.D.3
  • 30
    • 0031686310 scopus 로고    scopus 로고
    • T7 RNA polymerase produces 59 end heterogeneity during in vitro transcription from certain templates
    • Pleiss, J.A., Derrick, M.L., and Uhlenbeck, O.C. 1998. T7 RNA polymerase produces 59 end heterogeneity during in vitro transcription from certain templates. RNA 4: 1313-1317.
    • (1998) RNA , vol.4 , pp. 1313-1317
    • Pleiss, J.A.1    Derrick, M.L.2    Uhlenbeck, O.C.3
  • 31
    • 0035368861 scopus 로고    scopus 로고
    • Association of an RNA kissing complex analyzed using 2-aminopurine fluorescence
    • Rist, M. and Marino, J. 2001. Association of an RNA kissing complex analyzed using 2-aminopurine fluorescence. Nucleic Acids Res. 29: 2401-2408.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2401-2408
    • Rist, M.1    Marino, J.2
  • 32
    • 33745635350 scopus 로고    scopus 로고
    • Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
    • Serganov, A., Polonskaia, A., Phan, A.T., Breaker, R.R., and Patel, D.J. 2006. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441: 1167-1171.
    • (2006) Nature , vol.441 , pp. 1167-1171
    • Serganov, A.1    Polonskaia, A.2    Phan, A.T.3    Breaker, R.R.4    Patel, D.J.5
  • 34
    • 0033529336 scopus 로고    scopus 로고
    • Energetics and cooperativity of tertiary hydrogen bonds in RNA structure
    • Silverman, S.K. and Cech, T.R. 1999. Energetics and cooperativity of tertiary hydrogen bonds in RNA structure. Biochemistry 38: 8691-8702.
    • (1999) Biochemistry , vol.38 , pp. 8691-8702
    • Silverman, S.K.1    Cech, T.R.2
  • 35
    • 0032763658 scopus 로고    scopus 로고
    • Quantifying the energetic interplay of RNA tertiary and secondary structure interactions
    • Silverman, S.K., Zheng, M., Wu, M., Tinoco Jr., I., and Cech, T.R. 1999. Quantifying the energetic interplay of RNA tertiary and secondary structure interactions. RNA 5: 1665-1674.
    • (1999) RNA , vol.5 , pp. 1665-1674
    • Silverman, S.K.1    Zheng, M.2    Wu, M.3    Tinoco Jr., I.4    Cech, T.R.5
  • 36
    • 0032831634 scopus 로고    scopus 로고
    • Relationship between internucleotide linkage geometry and the stability of RNA
    • Soukup, G.A. and Breaker, R.R. 1999. Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5: 1308-1325.
    • (1999) RNA , vol.5 , pp. 1308-1325
    • Soukup, G.A.1    Breaker, R.R.2
  • 37
    • 2942549198 scopus 로고    scopus 로고
    • Riboswitches exert genetic control through metabolite-induced conformational change
    • Soukup, J.K. and Soukup, G.A. 2004. Riboswitches exert genetic control through metabolite-induced conformational change. Curr. Opin. Struct. Biol. 14: 344-349.
    • (2004) Curr. Opin. Struct. Biol , vol.14 , pp. 344-349
    • Soukup, J.K.1    Soukup, G.A.2
  • 38
    • 0038136962 scopus 로고    scopus 로고
    • Metabolite-binding RNA domains are present in the genes of eukaryotes
    • Sudarsan, N., Barrick, J.E., and Breaker, R.R. 2003a. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9: 644-647.
    • (2003) RNA , vol.9 , pp. 644-647
    • Sudarsan, N.1    Barrick, J.E.2    Breaker, R.R.3
  • 39
    • 0242298623 scopus 로고    scopus 로고
    • An mRNA structure in bacteria that controls gene expression by binding lysine
    • Sudarsan, N., Wickiser, J.K., Nakamura, S., Ebert, M.S., and Breaker, R.R. 2003b. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes & Dev. 17: 2688-2697.
    • (2003) Genes & Dev , vol.17 , pp. 2688-2697
    • Sudarsan, N.1    Wickiser, J.K.2    Nakamura, S.3    Ebert, M.S.4    Breaker, R.R.5
  • 40
    • 28844492215 scopus 로고    scopus 로고
    • Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine
    • Sudarsan, N., Cohen-Chalamish, S., Nakamura, S., Emilsson, G.M., and Breaker, R.R. 2005. Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chem. Biol. 12: 1325-1335.
    • (2005) Chem. Biol , vol.12 , pp. 1325-1335
    • Sudarsan, N.1    Cohen-Chalamish, S.2    Nakamura, S.3    Emilsson, G.M.4    Breaker, R.R.5
  • 41
    • 33744469562 scopus 로고    scopus 로고
    • Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand
    • Thore, S., Leibundgut, M., and Ban, N. 2006. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312: 1208-1211.
    • (2006) Science , vol.312 , pp. 1208-1211
    • Thore, S.1    Leibundgut, M.2    Ban, N.3
  • 42
    • 20444478991 scopus 로고    scopus 로고
    • Riboswitches as versatile gene control elements
    • Tucker, B.J. and Breaker, R.R. 2005. Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol. 15: 342-348.
    • (2005) Curr. Opin. Struct. Biol , vol.15 , pp. 342-348
    • Tucker, B.J.1    Breaker, R.R.2
  • 43
    • 26444620938 scopus 로고    scopus 로고
    • The kinetics of ligand binding by an adenine-sensing riboswitch
    • Wickiser, J.K., Cheah, M.T., Breaker, R.R., and Crothers, D.M. 2005. The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 44: 13404-13414.
    • (2005) Biochemistry , vol.44 , pp. 13404-13414
    • Wickiser, J.K.1    Cheah, M.T.2    Breaker, R.R.3    Crothers, D.M.4
  • 44
    • 27744519876 scopus 로고    scopus 로고
    • Riboswitches and the role of noncoding RNAs in bacterial metabolic control
    • Winkler, W.C. 2005. Riboswitches and the role of noncoding RNAs in bacterial metabolic control. Curr. Opin. Chem. Biol. 9: 594-602.
    • (2005) Curr. Opin. Chem. Biol , vol.9 , pp. 594-602
    • Winkler, W.C.1
  • 45
    • 0037206833 scopus 로고    scopus 로고
    • Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
    • Winkler, W., Nahvi, A., and Breaker, R.R. 2002a. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419: 952-956.
    • (2002) Nature , vol.419 , pp. 952-956
    • Winkler, W.1    Nahvi, A.2    Breaker, R.R.3
  • 46
    • 0037058920 scopus 로고    scopus 로고
    • An mRNA structure that controls gene expression by binding FMN
    • Winkler, W.C., Cohen-Chalamish, S., and Breaker, R.R. 2002b. An mRNA structure that controls gene expression by binding FMN. Proc. Natl. Acad. Sci. 99: 15908-15913.
    • (2002) Proc. Natl. Acad. Sci , vol.99 , pp. 15908-15913
    • Winkler, W.C.1    Cohen-Chalamish, S.2    Breaker, R.R.3
  • 47
    • 0142075327 scopus 로고    scopus 로고
    • Genetic control by metabolite-binding riboswitches
    • Winkler, W.C. and Breaker, R.R. 2003. Genetic control by metabolite-binding riboswitches. ChemBioChem 4: 1024-1032.
    • (2003) ChemBioChem , vol.4 , pp. 1024-1032
    • Winkler, W.C.1    Breaker, R.R.2
  • 48
    • 27144527479 scopus 로고    scopus 로고
    • Regulation of bacterial gene expression by riboswitches
    • Winkler, W.C. and Breaker, R.R. 2005. Regulation of bacterial gene expression by riboswitches. Annu. Rev. Microbiol. 59: 487-517.
    • (2005) Annu. Rev. Microbiol , vol.59 , pp. 487-517
    • Winkler, W.C.1    Breaker, R.R.2
  • 49
    • 0042320361 scopus 로고    scopus 로고
    • An mRNA structure that controls gene expression by binding S-adenosylmethionine
    • Winkler, W.C., Nahvi, A., Sudarsan, N., Barrick, J.E., and Breaker, R.R. 2003. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat. Struct. Biol. 10: 701-707.
    • (2003) Nat. Struct. Biol , vol.10 , pp. 701-707
    • Winkler, W.C.1    Nahvi, A.2    Sudarsan, N.3    Barrick, J.E.4    Breaker, R.R.5
  • 50
    • 1642586299 scopus 로고    scopus 로고
    • Control of gene expression by a natural metabolite-responsive ribozyme
    • Winkler, W.C., Nahvi, A., Roth, A., Collins, J.A., and Breaker, R.R. 2004. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428: 281-286.
    • (2004) Nature , vol.428 , pp. 281-286
    • Winkler, W.C.1    Nahvi, A.2    Roth, A.3    Collins, J.A.4    Breaker, R.R.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.