메뉴 건너뛰기




Volumn 272, Issue 5, 1997, Pages 645-664

Structure, recognition and adaptive binding in RNA aptamer complexes

Author keywords

Amino acid and aminoglycoside antibiotic ligands; Cofactor; NMR based solution structures; RNA aptamer complexes; Sequence specific recognition and discrimination

Indexed keywords

ADENOSINE PHOSPHATE; AMINO ACID; AMINOGLYCOSIDE ANTIBIOTIC AGENT; ARGININE; CITRULLINE; FLAVINE MONONUCLEOTIDE; OLIGORIBONUCLEOTIDE; PEPTIDE; TOBRAMYCIN;

EID: 0031563817     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1281     Document Type: Review
Times cited : (252)

References (81)
  • 1
    • 0029082529 scopus 로고
    • Structure of the P1 helix from group I self-splicing introns
    • Allain F. H. T., Varani G. Structure of the P1 helix from group I self-splicing introns. J. Mol. Biol. 250:1995;333-353.
    • (1995) J. Mol. Biol. , vol.250 , pp. 333-353
    • Allain, F.H.T.1    Varani, G.2
  • 2
    • 0029920331 scopus 로고    scopus 로고
    • Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation
    • Allain F. H. T., Gubser C. C., Howe P. W. A., Nagai K., Neuhaus D., Varani G. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation. Nature. 380:1996;646-650.
    • (1996) Nature , vol.380 , pp. 646-650
    • Allain, F.H.T.1    Gubser, C.C.2    Howe, P.W.A.3    Nagai, K.4    Neuhaus, D.5    Varani, G.6
  • 3
    • 0026744912 scopus 로고
    • Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA
    • Batey R. T., Inada M., Kujawinski E., Puglisi J., Williamson J. R. Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA. Nucl. Acids Res. 20:1992;4515-4523.
    • (1992) Nucl. Acids Res. , vol.20 , pp. 4515-4523
    • Batey, R.T.1    Inada, M.2    Kujawinski, E.3    Puglisi, J.4    Williamson, J.R.5
  • 6
    • 0027995790 scopus 로고
    • Isolation of RNA aptamers for biological cofactors byin vitro
    • Burgstaller A. T., Famulok M. Isolation of RNA aptamers for biological cofactors byin vitro. Angew. Chem. Intl. Edn. Eng. 33:1994;1084-1087.
    • (1994) Angew. Chem. Intl. Edn. Eng. , vol.33 , pp. 1084-1087
    • Burgstaller, A.T.1    Famulok, M.2
  • 7
    • 0028874701 scopus 로고
    • Structural probing and damage selection of citrulline- and arginine-specific RNA aptamers identify base positions required for binding
    • Burgstaller P., Kochoyan M., Famulok M. Structural probing and damage selection of citrulline- and arginine-specific RNA aptamers identify base positions required for binding. Nucl. Acids Res. 23:1995;4769-4776.
    • (1995) Nucl. Acids Res. , vol.23 , pp. 4769-4776
    • Burgstaller, P.1    Kochoyan, M.2    Famulok, M.3
  • 8
    • 0026737313 scopus 로고
    • Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures
    • Cheong C., Moore P. B. Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures. Biochemistry. 31:1992;8406-8414.
    • (1992) Biochemistry , vol.31 , pp. 8406-8414
    • Cheong, C.1    Moore, P.B.2
  • 9
    • 0029113144 scopus 로고
    • Neomycin inhibition of the hammerhead ribozyme involves ionic interactions
    • Clouet-d'Orval B., Stage T. K., Uhlenbeck O. C. Neomycin inhibition of the hammerhead ribozyme involves ionic interactions. Biochemistry. 34:1995;11186-11190.
    • (1995) Biochemistry , vol.34 , pp. 11186-11190
    • Clouet-d'Orval, B.1    Stage, T.K.2    Uhlenbeck, O.C.3
  • 10
    • 0008451711 scopus 로고    scopus 로고
    • Porphyrin metalation catalyzed by a small RNA molecule
    • Conn M. M., Prudent J. R., Schultz P. G. Porphyrin metalation catalyzed by a small RNA molecule. J. Am. Chem. Soc. 118:1996;7012-7013.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 7012-7013
    • Conn, M.M.1    Prudent, J.R.2    Schultz, P.G.3
  • 11
    • 0028032235 scopus 로고
    • Heteronuclear techniques in NMR studies of RNA and DNA
    • Dieckmann T., Feigon J. Heteronuclear techniques in NMR studies of RNA and DNA. Curr. Opin. Struct. Biol. 4:1994;745-749.
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 745-749
    • Dieckmann, T.1    Feigon, J.2
  • 12
    • 0029904020 scopus 로고    scopus 로고
    • Solution structure of an ATP-binding RNA aptamer reveals a novel fold
    • Dieckmann T., Suzuki E., Nakamura G. K., Feigon J. Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA. 2:1996;628-640.
    • (1996) RNA , vol.2 , pp. 628-640
    • Dieckmann, T.1    Suzuki, E.2    Nakamura, G.K.3    Feigon, J.4
  • 14
    • 0028011717 scopus 로고
    • Molecular recognition of amino acids by RNA aptamers: AnLL
    • Famulok M. Molecular recognition of amino acids by RNA aptamers: anLL. J. Am. Chem. Soc. 116:1994;1698-1706.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 1698-1706
    • Famulok, M.1
  • 15
    • 0029864853 scopus 로고    scopus 로고
    • Molecular recognition in the FMN-RNA aptamer complex
    • Fan P., Suri A. K., Fiala R., Live D., Patel D. J. Molecular recognition in the FMN-RNA aptamer complex. J. Mol. Biol. 258:1996;480-500.
    • (1996) J. Mol. Biol. , vol.258 , pp. 480-500
    • Fan, P.1    Suri, A.K.2    Fiala, R.3    Live, D.4    Patel, D.J.5
  • 18
    • 0029954443 scopus 로고    scopus 로고
    • Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA
    • Fountain M. A., Serra M. J., Krugh T. R., Turner D. Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA. Biochemistry. 35:1996;6539-6548.
    • (1996) Biochemistry , vol.35 , pp. 6539-6548
    • Fountain, M.A.1    Serra, M.J.2    Krugh, T.R.3    Turner, D.4
  • 20
    • 0003604405 scopus 로고
    • Cold Spring Harbor: Cold Spring Harbor Laboratory Press
    • Gesteland R. F., Atkins J. F. The RNA World. 1993;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
    • (1993) The RNA World
    • Gesteland, R.F.1    Atkins, J.F.2
  • 23
    • 0028864424 scopus 로고
    • Studies of base-pair kinetics by NMR measurement of proton exchange
    • Gueron M., Leroy J. L. Studies of base-pair kinetics by NMR measurement of proton exchange. Methods Enzymol. 261:1995;383-413.
    • (1995) Methods Enzymol. , vol.261 , pp. 383-413
    • Gueron, M.1    Leroy, J.L.2
  • 24
    • 0026423027 scopus 로고
    • Structural features that give rise to unusual stability of RNA hairpins containing GNRA loops
    • Heus H. A., Pardi A. Structural features that give rise to unusual stability of RNA hairpins containing GNRA loops. Science. 253:1991;191-194.
    • (1991) Science , vol.253 , pp. 191-194
    • Heus, H.A.1    Pardi, A.2
  • 25
    • 0029998660 scopus 로고    scopus 로고
    • Structure of a hexanucleotide RNA hairpin loop conserved in ribosomal RNAs
    • Huang S., Wang Y. X., Draper D. E. Structure of a hexanucleotide RNA hairpin loop conserved in ribosomal RNAs. J. Mol. Biol. 258:1996;308-321.
    • (1996) J. Mol. Biol. , vol.258 , pp. 308-321
    • Huang, S.1    Wang, Y.X.2    Draper, D.E.3
  • 26
    • 0028294458 scopus 로고
    • Involvement of a GNRA tetraloop in long-range RNA tertiary interactions
    • Jaeger L., Michel F., Westhof E. Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J. Mol. Biol. 236:1994;1271-1276.
    • (1994) J. Mol. Biol. , vol.236 , pp. 1271-1276
    • Jaeger, L.1    Michel, F.2    Westhof, E.3
  • 27
    • 0028224199 scopus 로고
    • High resolution molecular discrimination by RNA
    • Jenison R. D., Gill S. C., Pardi A., Polisky B. High resolution molecular discrimination by RNA. Science. 263:1994;1425-1429.
    • (1994) Science , vol.263 , pp. 1425-1429
    • Jenison, R.D.1    Gill, S.C.2    Pardi, A.3    Polisky, B.4
  • 29
    • 0029946537 scopus 로고    scopus 로고
    • Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex
    • Jiang F., Kumar R. A., Jones R. A., Patel D. J. Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature. 382:1996a;183-186.
    • (1996) Nature , vol.382 , pp. 183-186
    • Jiang, F.1    Kumar, R.A.2    Jones, R.A.3    Patel, D.J.4
  • 30
    • 0029847611 scopus 로고    scopus 로고
    • RNA folding topology and intermolecular contacts in the AMP-RNA aptamer complex
    • Jiang F., Fiala R., Live D., Kumar R. A., Patel D. J. RNA folding topology and intermolecular contacts in the AMP-RNA aptamer complex. Biochemistry. 35:1996b;13250-13256.
    • (1996) Biochemistry , vol.35 , pp. 13250-13256
    • Jiang, F.1    Fiala, R.2    Live, D.3    Kumar, R.A.4    Patel, D.J.5
  • 31
    • 0030641357 scopus 로고    scopus 로고
    • Specific labeling approaches to guanine and adenine imino and amino proton assignments in the AMP-RNA aptamer complex
    • Jiang F., Patel D. J., Zhang X., Zhao H., Jones R. A. Specific labeling approaches to guanine and adenine imino and amino proton assignments in the AMP-RNA aptamer complex. J. Biomol. NMR. 9:1997a;55-62.
    • (1997) J. Biomol. NMR. , vol.9 , pp. 55-62
    • Jiang, F.1    Patel, D.J.2    Zhang, X.3    Zhao, H.4    Jones, R.A.5
  • 32
    • 0030887815 scopus 로고    scopus 로고
    • Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex
    • Jiang L., Suri A. K., Fiala R., Patel D. J. Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex. Chem. Biol. 4:1997b;35-50.
    • (1997) Chem. Biol. , vol.4 , pp. 35-50
    • Jiang, L.1    Suri, A.K.2    Fiala, R.3    Patel, D.J.4
  • 36
    • 0028136665 scopus 로고
    • The application of a modified nucleotide in apta mer selection: Novel thrombin aptamers containing 5-(1-pentenyl)-2′-deoxyuridine
    • Latham J. A., Johnson R., Toole J. J. The application of a modified nucleotide in apta mer selection: novel thrombin aptamers containing 5-(1-pentenyl)-2′-deoxyuridine. Nucl. Acids Res. 22:1994;2817-2822.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 2817-2822
    • Latham, J.A.1    Johnson, R.2    Toole, J.J.3
  • 38
    • 0029138009 scopus 로고
    • RNA aptamers that bind flavin and nicotinamide factors
    • Lauhon C. T., Szostak J. W. RNA aptamers that bind flavin and nicotinamide factors. J. Am. Chem. Soc. 117:1995;1246-1257.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 1246-1257
    • Lauhon, C.T.1    Szostak, J.W.2
  • 39
    • 0026053768 scopus 로고
    • NMR and molecular evidence for a G·A mismatch base-pair in a purine-rich DNA duplex
    • Li Y., Zon G., Wilson W. D. NMR and molecular evidence for a G·A mismatch base-pair in a purine-rich DNA duplex. Proc. Natl Acad. Sci. USA. 88:1991;26-30.
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 26-30
    • Li, Y.1    Zon, G.2    Wilson, W.D.3
  • 40
    • 0009683628 scopus 로고    scopus 로고
    • Encapsulating an amino acid in a DNA fold
    • Lin C. H., Patel D. J. Encapsulating an amino acid in a DNA fold. Nature Struct. Biol. 3:1996;1046-1050.
    • (1996) Nature Struct. Biol. , vol.3 , pp. 1046-1050
    • Lin, C.H.1    Patel, D.J.2
  • 44
    • 0030072640 scopus 로고    scopus 로고
    • Chance and necessity in the selection of nucleic acid catalysts
    • Lorsch J. R., Szostak J. W. Chance and necessity in the selection of nucleic acid catalysts. Acc. Chem. Res. 29:1996;103-110.
    • (1996) Acc. Chem. Res. , vol.29 , pp. 103-110
    • Lorsch, J.R.1    Szostak, J.W.2
  • 45
    • 0023238983 scopus 로고
    • Interaction of antibiotics with functional sites in 16 S ribosomal RNA
    • Moazed D., Noller H. F. Interaction of antibiotics with functional sites in 16 S ribosomal RNA. Nature. 327:1987;389-394.
    • (1987) Nature , vol.327 , pp. 389-394
    • Moazed, D.1    Noller, H.F.2
  • 46
    • 0000392662 scopus 로고
    • Determination of RNA conformation by nuclear magnetic resonance
    • Moore P. B. Determination of RNA conformation by nuclear magnetic resonance. Acc. Chem. Res. 28:1995;251-256.
    • (1995) Acc. Chem. Res. , vol.28 , pp. 251-256
    • Moore, P.B.1
  • 49
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls A., Sharp K. A., Honig B. H. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11:1991;281-296.
    • (1991) Proteins: Struct. Funct. Genet. , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.H.3
  • 52
    • 0031547976 scopus 로고    scopus 로고
    • Imino proton exchange and base-pair kinetics in the AMP-RNA aptamer complex
    • Nonin S., Jiang F., Patel D. J. Imino proton exchange and base-pair kinetics in the AMP-RNA aptamer complex. J. Mol. Biol. 268:1997;359-379.
    • (1997) J. Mol. Biol. , vol.268 , pp. 359-379
    • Nonin, S.1    Jiang, F.2    Patel, D.J.3
  • 54
    • 0028885514 scopus 로고
    • Multidimensional heteronuclear NMR experiments for structure determination of isotopically labeled RNA
    • Pardi A. Multidimensional heteronuclear NMR experiments for structure determination of isotopically labeled RNA. Methods Enzymol. 261:1995;350-380.
    • (1995) Methods Enzymol. , vol.261 , pp. 350-380
    • Pardi, A.1
  • 55
    • 0011120533 scopus 로고    scopus 로고
    • Structure, recognition and adaptive binding in regulatory immunodeficiency viral peptide-RNA complexes
    • Patel D. J., Ye X., Kumar R. A., Gorin A. Structure, recognition and adaptive binding in regulatory immunodeficiency viral peptide-RNA complexes. J. Mol. Biol. 1998.
    • (1998) J. Mol. Biol.
    • Patel, D.J.1    Ye, X.2    Kumar, R.A.3    Gorin, A.4
  • 56
    • 0028063567 scopus 로고
    • Three dimensional structure of a hammerhead ribozyme
    • Pley H. W., Flahorty K. M., McKay D. B. Three dimensional structure of a hammerhead ribozyme. Nature. 372:1994;111-113.
    • (1994) Nature , vol.372 , pp. 111-113
    • Pley, H.W.1    Flahorty, K.M.2    McKay, D.B.3
  • 57
    • 0028030688 scopus 로고
    • Expanding the scope of RNA catalysis
    • Prudent J. R., Uno T., Schultz P. G. Expanding the scope of RNA catalysis. Science. 264:1994;1924-1927.
    • (1994) Science , vol.264 , pp. 1924-1927
    • Prudent, J.R.1    Uno, T.2    Schultz, P.G.3
  • 59
    • 0028858599 scopus 로고
    • Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex
    • Puglisi J. D., Chen L., Blanchard S., Frankel A. D. Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex. Science. 270:1995;1200-1203.
    • (1995) Science , vol.270 , pp. 1200-1203
    • Puglisi, J.D.1    Chen, L.2    Blanchard, S.3    Frankel, A.D.4
  • 60
    • 1842388479 scopus 로고    scopus 로고
    • RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide
    • Recht M. I., Fourmy D., Blanchard S. C., Dahlquist K. D., Puglisi J. D. RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide. J. Mol. Biol. 262:1996;421-436.
    • (1996) J. Mol. Biol. , vol.262 , pp. 421-436
    • Recht, M.I.1    Fourmy, D.2    Blanchard, S.C.3    Dahlquist, K.D.4    Puglisi, J.D.5
  • 62
    • 0025332385 scopus 로고
    • Selectionin vitro
    • Robertson D. L., Joyce G. F. Selectionin vitro. Nature. 344:1990;467-468.
    • (1990) Nature , vol.344 , pp. 467-468
    • Robertson, D.L.1    Joyce, G.F.2
  • 64
    • 0027180473 scopus 로고
    • An RNA motif that binds ATP
    • Sassanfar M., Szostak J. W. An RNA motif that binds ATP. Nature. 364:1993;550-553.
    • (1993) Nature , vol.364 , pp. 550-553
    • Sassanfar, M.1    Szostak, J.W.2
  • 68
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 249:1990;505-510.
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 69
    • 0026651981 scopus 로고
    • RNA pseudoknots that inhibit human immunodeficiency virus type I reverse transcriptase
    • Tuerk C., MacDougal S., Gold L. RNA pseudoknots that inhibit human immunodeficiency virus type I reverse transcriptase. Proc. Natl Acad. Sci. USA. 89:1992;6988-6992.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 6988-6992
    • Tuerk, C.1    MacDougal, S.2    Gold, L.3
  • 71
    • 0025873818 scopus 로고
    • Antibiotic inhibition of group I ribozyme function
    • von Ahsen U., Davies J., Schroeder R. Antibiotic inhibition of group I ribozyme function. Nature. 353:1991;368-370.
    • (1991) Nature , vol.353 , pp. 368-370
    • Von Ahsen, U.1    Davies, J.2    Schroeder, R.3
  • 73
    • 0029294539 scopus 로고
    • Specific binding of aminoglycoside antibiotics to RNA
    • Wang Y., Rando R. R. Specific binding of aminoglycoside antibiotics to RNA. Chem. Biol. 2:1995;281-290.
    • (1995) Chem. Biol. , vol.2 , pp. 281-290
    • Wang, Y.1    Rando, R.R.2
  • 74
    • 0027370486 scopus 로고
    • Major groove accessibility of RNA
    • Weeks K. M., Crothers D. M. Major groove accessibility of RNA. Science. 261:1993;1574-1577.
    • (1993) Science , vol.261 , pp. 1574-1577
    • Weeks, K.M.1    Crothers, D.M.2
  • 76
    • 0027439912 scopus 로고
    • The conformation of loop E of eukaryotic 5 S ribosomal RNA
    • Wimberly B., Varani G., Tinoco I. Jr. The conformation of loop E of eukaryotic 5 S ribosomal RNA. Biochemistry. 32:1993;1078-1087.
    • (1993) Biochemistry , vol.32 , pp. 1078-1087
    • Wimberly, B.1    Varani, G.2    Tinoco I., Jr.3
  • 77
    • 0025047647 scopus 로고
    • Architecture of ribosomal RNA: Constraints on the sequences of "tetra-loops"
    • Woese C. R., Winker S., Guttell R. R. Architecture of ribosomal RNA: constraints on the sequences of "tetra-loops" Proc. Natl Acad. Sci. USA. 87:1990;8467-8471.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 8467-8471
    • Woese, C.R.1    Winker, S.2    Guttell, R.R.3
  • 78
    • 0029972909 scopus 로고    scopus 로고
    • Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy
    • Yang Y., Kochoyan M., Burgstaller P., Westhof E., Famulok M. Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science. 272:1996;1343-1347.
    • (1996) Science , vol.272 , pp. 1343-1347
    • Yang, Y.1    Kochoyan, M.2    Burgstaller, P.3    Westhof, E.4    Famulok, M.5
  • 79
    • 0029613238 scopus 로고
    • Molecular recognition of the bovine immunodeficiency virus Tat peptide-TAR RNA complex
    • Ye X., Kumar R. A., Patel D. J. Molecular recognition of the bovine immunodeficiency virus Tat peptide-TAR RNA complex. Chem. Biol. 2:1995;827-840.
    • (1995) Chem. Biol. , vol.2 , pp. 827-840
    • Ye, X.1    Kumar, R.A.2    Patel, D.J.3
  • 80
    • 0030475417 scopus 로고    scopus 로고
    • Deep penetration of an α-helix into a widened RNA major groove in the HIV-1 Rev peptide-RNA aptamer complex
    • Ye X., Gorin A., Ellington A. D., Patel D. J. Deep penetration of an α-helix into a widened RNA major groove in the HIV-1 Rev peptide-RNA aptamer complex. Nature Struct. Biol. 3:1996;1026-1033.
    • (1996) Nature Struct. Biol. , vol.3 , pp. 1026-1033
    • Ye, X.1    Gorin, A.2    Ellington, A.D.3    Patel, D.J.4
  • 81
    • 0027370433 scopus 로고
    • Small molecules that selectively block RNA binding of HIV-1 Rev protein inhibit Rev function and viral production
    • Zapp M. L., Stern S., Green M. R. Small molecules that selectively block RNA binding of HIV-1 Rev protein inhibit Rev function and viral production. Cell. 74:1993;969-978.
    • (1993) Cell , vol.74 , pp. 969-978
    • Zapp, M.L.1    Stern, S.2    Green, M.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.