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Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
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0028869690
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A historic account of oligonucleotide in vitro selections
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Gold L, Polisky B, Uhlenbeck O, Yarus M: Diversity of oligonucleotide functions. Annu Rev Biochem 1995, 64:763-797. A historic account of oligonucleotide in vitro selections.
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Gold, L.1
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Uphoff, KW, Bell SD, Ellington AD: In vitro selection of aptamers: the dearth of pure reason. Curr Biol 1996, 6:281-287. A recent review of aptamers and their use both as therapeutics and as tools for molecular recognition.
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Uphoff, K.W.1
Bell, S.D.2
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Gold L: Oligonucleotides as research, diagnostic, and therapeutic agents. J Biol Chem 1995, 270:13581-13584. A concise review that contrasts Oligonucleotides to other combinatorial libraries and describes their potential uses.
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Gold, L.1
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0030072640
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Chance and necessity in the selection of nucleic acid catalysts
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Lorsch JR, Szostak JW: Chance and necessity in the selection of nucleic acid catalysts. Accounts Chem Res 1996, 29:103-110. An excellent review of the state of nucleic acid catalysts discovered by in vitro selection.
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Accounts Chem Res
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Lorsch, J.R.1
Szostak, J.W.2
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Artificial evolution and natural ribozymes
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Ribozyme-catalysed amino-acid transfer reactions
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Lohse PA, Szostak JW: Ribozyme-catalysed amino-acid transfer reactions. Nature 1996, 381:442-444. This paper describes the first amide bond formation catalyzed by RNA and demonstrates how powerful substrate alignment by duplex formation with the selected catalytic nucleic acid can be.
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Nature
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Lohse, P.A.1
Szostak, J.W.2
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0028969534
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Aminoacyl-RNA synthesis catalyzed by an RNA
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Illangasekare M, Sanchez G, Nickles T, Yarus M: Aminoacyl-RNA synthesis catalyzed by an RNA. Science 1995, 267:643-647. The first example of ester bond formation is described as well as HPLC partitioning of RNA catalysts.
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Science
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Illangasekare, M.1
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Specialization of the DNA-cleaving activity of a Group I ribozyme through in vitro evolution
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Tsang J, Joyce GF: Specialization of the DNA-cleaving activity of a Group I ribozyme through in vitro evolution. J Mol Biol 1996, 262:31-42. A powerful example of how in vitro evolution can be used to identify specialized ribozymes, which are perhaps superior to those found naturally.
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J Mol Biol
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Tsang, J.1
Joyce, G.F.2
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0028911845
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In vitro evolution of a self-alkylating ribozyme
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Wilson C, Szostak JW: In vitro evolution of a self-alkylating ribozyme. Nature 1995, 374:777-782.
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Nature
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Wilson, C.1
Szostak, J.W.2
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0029903899
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In vitro selection of a novel catalytic RNA: Characterization of a sulfur alkylation reaction and interaction with a small peptide
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Wecker M, Smith D, Gold L: In vitro selection of a novel catalytic RNA: characterization of a sulfur alkylation reaction and interaction with a small peptide. RNA 1996, 2:982-994.
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RNA
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Wecker, M.1
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0029147392
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Structurally complex and highly active RNA ligases derived from random RNA sequences
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Ekland EH, Szostak JW, Bartel DP: Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 1995, 269:364-370. This paper demonstrates how nucleic acid selection can identify nucleic acids catalysts that rival proteins for related chemical transformations.
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Science
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Ekland, E.H.1
Szostak, J.W.2
Bartel, D.P.3
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0029037713
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A DNA metalloenzyme with DNA ligase activity
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Cuenoud B, Szostak JW: A DNA metalloenzyme with DNA ligase activity. Nature 1995, 375:611-614.
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Nature
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Cuenoud, B.1
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Burgstaller P, Famulok M: Synthetic ribozymes and the first deoxyribozyme. Angew Chem Int Ed 1995, 34:1189-1192.
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Angew Chem Int Ed
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Porphyrin metalation catalyzed by a small RNa molecule
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Conn MM, Prudent JR, Schultz PG: Porphyrin metalation catalyzed by a small RNA molecule. J Am Chem Soc 1996, 118:7012-7013. An excellent example of how the transition-state analog approach, used so successfully in the catalytic antibody field, can be employed for the selection of RNA catalysts.
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J Am Chem Soc
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Conn, M.M.1
Prudent, J.R.2
Schultz, P.G.3
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Kinetic and mechanistic analysis of nonenzymatic, template-directed oligonucleotide ligation
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Rohatgi R, Bartel DP, Szostak JW: Kinetic and mechanistic analysis of nonenzymatic, template-directed oligonucleotide ligation. J Am Chem Soc 1996, 118:3332-3339.
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J am Chem Soc
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Rohatgi, R.1
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Szostak, J.W.3
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RNA-catalyzed RNA polymerization using nucleoside triphosphates
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Ekland EH, Bartel DP: RNA-catalyzed RNA polymerization using nucleoside triphosphates. Nature 1996, 382:373-376.
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Ekland, E.H.1
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Nonenzymatic, template-directed ligation of oligonucleotides is a highly regioselective for the formation of 3′→5′ phosphosphodiester bonds
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Rohatgi R, Bartel DP, Szostak JW: Nonenzymatic, template-directed ligation of oligonucleotides is a highly regioselective for the formation of 3′→5′ phosphosphodiester bonds. J Am Chem Soc 1996, 118:3340-3344.
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J Am Chem Soc
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0029766901
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RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities
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Wang Y, Killian J, Hamasaki K, Rando R: RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities. Biochemistry 1996, 35:12338-12346. This paper describes the use of fluorescence depolarization to map aminoglycoside binding to selected aptamers.
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Wang, Y.1
Killian, J.2
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A novel RNA motif for neomycin recognition
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Wallis MG, von Ahsen U, Schroeder R, Famulok M: A novel RNA motif for neomycin recognition. Chem Biol 1995, 2:543-552. Comprehensive characterization of aminoglycoside binding aptamers demonstrating how exquisite aptamer recognition can be for small molecules.
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Chem Biol
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Wallis, M.G.1
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24
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Specific binding of aminoglycoside antibiotics to RNA
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Wang Y, Rando RR: Specific binding of aminoglycoside antibiotics to RNA. Chem Biol 1995, 2:281-290.
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Chem Biol
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Wang, Y.1
Rando, R.R.2
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25
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0028874701
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Structural probing and damage selection of citrulline- And arginine-specific RNA aptamers identify base positions required for binding
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Burgstaller P, Kochoyan M, Famulok M: Structural probing and damage selection of citrulline- and arginine-specific RNA aptamers identify base positions required for binding. Nucleic Acids Res 1995, 23:4769-4776.
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Burgstaller, P.1
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0028965943
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A DNA aptamer that binds adenosine and ATP
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Huizenga DE, Szostak JW: A DNA aptamer that binds adenosine and ATP. Biochemistry 1995, 34:656-665.
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Biochemistry
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De Huizenga1
Szostak, J.W.2
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0029138009
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RNA aptamers that bind flavin and nicotinamide redox cofactors
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Lauhon CT, Szostak JW: RNA aptamers that bind flavin and nicotinamide redox cofactors. J Am Chem Soc 1995, 117:1246-1257. A remarkable demonstration of how specific aptamers to small molecules can be. NAD can be distinguished from NADH by the selected aptamers.
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J am Chem Soc
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Lauhon, C.T.1
Szostak, J.W.2
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Arginine-binding RNAs resembling TAR identified by in vitro selection
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Tao J, Frankel AD: Arginine-binding RNAs resembling TAR identified by in vitro selection. Biochemistry 1996, 35:2229-2238.
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Biochemistry
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Tao, J.1
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0029361759
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Conrad RC, Baskerville S, Ellington AD: In vitro selection methodologies to probe RNA function and structure. Mol Divers 1995, 1:69-78.
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Mol Divers
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Conrad, R.C.1
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Ellington, A.D.3
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0029295966
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Dissecting protein:protein interactions between transcription factors with an RNA aptamer
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Tian Y, Adya N, Wagner S, Giam C, Green M, Ellington AD: Dissecting protein:protein interactions between transcription factors with an RNA aptamer. RNA 1995, 1:317-326. This paper provides an illustration of how aptamers can be used as molecular tools to investigate complex biological interactions.
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RNA
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Tian, Y.1
Adya, N.2
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In vitro selection of RNA ligands for the ribosomal L22 protein associated with Epstein-Barr Virus expressed RNA by using randomized and cDNA-derived RNA libraries
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Dobbelstein M, Shenk T: In vitro selection of RNA ligands for the ribosomal L22 protein associated with Epstein-Barr Virus expressed RNA by using randomized and cDNA-derived RNA libraries. J Virol 1995, 69:8027-8034.
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O'Connell D, Koenig A, Jennings S, Hicke B, Han H, Fitzwater T, Chang Y, Varki N, Parma D, Varki A; Calcium-dependent oligonucleotide antagonists specific for L-selectin. Proc Natl Acad Sci USA 1996, 93:5883-5887. An excellent example of how selection methods can be devised to target specific binding epitopes on protein targets.
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Proc Natl Acad Sci USA
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O'Connell, D.1
Koenig, A.2
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Nuclease-resistant nucleic acid ligands to vascular permeability factor/vascular endothelial growth factor
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Green LS, Jellinek D, Bell C, Beebe LA, Feistner BD, Gill SC, Jucker FM, Janjic N: Nuclease-resistant nucleic acid ligands to vascular permeability factor/vascular endothelial growth factor. Chem Biol 1995, 2:683-695. Examples of exhaustive post-SELEX modification to improve the therapeutic potential of aptamers.
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Chem Biol
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Green, L.S.1
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Bell, C.3
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Janjic, N.8
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0028923775
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High-affinity RNA ligands to Escherichia coli ribosomes and ribosomal protein S1: Comparison of natural and unnatural binding sites
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Ringquist S, Jones T, Snyder EE, Gibson T, Boni I, Gold L: High-affinity RNA ligands to Escherichia coli ribosomes and ribosomal protein S1: comparison of natural and unnatural binding sites. Biochemistry 1995, 34:3640-3648.
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Biochemistry
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Ringquist, S.1
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Selection and characterization of RNAs replicated by Q replicase
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Brown D, Gold L: Selection and characterization of RNAs replicated by Q replicase. Biochemistry 1995, 34:14775-14782.
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Biochemistry
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Brown, D.1
Gold, L.2
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High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus
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Schneider DJ, Feigon J, Hostomsky Z, Gold L: High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. Biochemistry 1995, 34:9599-9610.
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Biochemistry
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Schneider, D.J.1
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Comprehensive chemical modification interference and nucleotide substitution analysis of an RNA pseudoknot inhibitor to HIV-1 reverse transcriptase
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Green L, Waugh S, Binkley JP, Hostomska Z, Hostomsky Z, Tuerk C: Comprehensive chemical modification interference and nucleotide substitution analysis of an RNA pseudoknot inhibitor to HIV-1 reverse transcriptase. J Mol Biol 1995, 247:60-68.
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J Mol Biol
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Green, L.1
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Potent 2′-amino-2′-deoxypyrimidine RNA inhibitors of basic fibroblast growth factor
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Jellinek D, Green LS, Bell C, Lynott CK, Gill N, Vargeese C, Kirschenheuter G, McGee DPC, Abesinghe P, Pieken WA et al.: Potent 2′-amino-2′-deoxypyrimidine RNA inhibitors of basic fibroblast growth factor. Biochemistry 1995, 34:11363-11372. An example of how including modified UTP and CTP derivatives can be used for selection of serum stable aptamers.
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Biochemistry
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Jellinek, D.1
Green, L.S.2
Bell, C.3
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0029062420
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In vitro selection of RNA ligands to substance P
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Nieuwlandt D, Wecker M, Gold L: In vitro selection of RNA ligands to substance P. Biochemistry 1995, 34:5651-5659.
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Biochemistry
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Nieuwlandt, D.1
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Characterization of antibody-binding RNAs selected from structurally constrained libraries
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Hamm J: Characterization of antibody-binding RNAs selected from structurally constrained libraries. Nucleic Acids Res 1996, 24:2220-2227.
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Nucleic Acids Res
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0029379551
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Let's get specific: The relationship between specificity and affinity
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Eaton BE, Gold L, Zichi DA: Let's get specific: the relationship between specificity and affinity. Chem Biol 1995, 2:633-638. A discussion provoking review of aptamers and how their affinities and specificities seem to be correlated despite the fact that there is no theoretical basis.
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Chem Biol
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Eaton, B.E.1
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Using in vitro selection to direct the covalent attachment of human immunodeficiency virus type 1 Rev protein to high-affinity RNA ligands
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Jensen KB, Atkinson BL, Willis MC, Koch TH, Gold L: Using in vitro selection to direct the covalent attachment of human immunodeficiency virus type 1 Rev protein to high-affinity RNA ligands. Proc Natl Acad Sci USA 1995, 92:12220-12224. An example of how the aptamer/target interface can drive chemical reactions.
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Proc Natl Acad Sci USA
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Jensen, K.B.1
Atkinson, B.L.2
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Ribonucleosides and RNA
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Eaton BE, Pieken WA: Ribonucleosides and RNA. Annu Rev Biochem 1995, 64:837-863. A review of modified ribonucleosides and RNA including examples of chemistries that impart nuclease resistance and cross-linking.
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Annu Rev Biochem
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Eaton, B.E.1
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Interpretation of oligonucleotide mass spectra for determination of sequence using electrospray ionization and tandem mass spectrometry
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Ni J, Pomerantz SC, Rozenski J, Zhang Y, McCloskey JA: Interpretation of oligonucleotide mass spectra for determination of sequence using electrospray ionization and tandem mass spectrometry. Anal Chem 1996, 68:1989-1999. With some imagination this paper can serve as the basis for structural deconvolution of aptamers derived from post-SELEX combinatorial libraries.
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Anal Chem
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Ni, J.1
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N7-cyanoborane-2′-deoxyguanosine 5′-triphosphate is a good substrate for DNa polymerase
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Biochemistry
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Porter, K.W.1
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Synthesis of 2′-deoxyuridine nucleosides with appended 5-position carbonyl cross-linking groups
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Crouch GJ, Eaton BE: Synthesis of 2′-deoxyuridine nucleosides with appended 5-position carbonyl cross-linking groups. Nucleosides Nucleotides 1994, 13:939-944.
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Nucleosides Nucleotides
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New uridine derivatives for use in systematic evolution of RNA ligands by exponential enrichment
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Dewey TM, Mundt A, Crouch GJ, Zyzniewski MC, Eaton BE: New uridine derivatives for use in systematic evolution of RNA ligands by exponential enrichment J Am Chem Soc 1995, 117:8474-8475. The facile synthesis of 5-position modified UTPs and testing of modified UTPs as T7 RNA polymerase substrates is described.
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J Am Chem Soc
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Dewey, T.M.1
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Dewey TM, Zyzniewski MC, Eaton BE: The RNA world: functional diversity in a nucleoside by carboxyamidation of uridine. Nucleosides Nucleotides 1996, 15:1611-1617. A generic methodology for the streamlined synthesis of modified uridines is described.
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Nucleosides Nucleotides
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Dewey, T.M.1
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0028829020
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Palladium catalysis in the synthesis of 8-position modified adenosine, 2′-deoxyadenosine and guanosine
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Tu C, Keane C, Eaton BE: Palladium catalysis in the synthesis of 8-position modified adenosine, 2′-deoxyadenosine and guanosine. Nucleosides Nucleotides 1995, 14:1631-1638.
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Nucleosides Nucleotides
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Carboxyamidation of purine nucleosides: New secondary 8-carboxamid-purine nucleosides
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Tu C, Keane C, Eaton BE: Carboxyamidation of purine nucleosides: new secondary 8-carboxamid-purine nucleosides. Nucleosides Nucleotides 1997, in press.
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Nucleosides Nucleotides
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