The new world of ribozymes

Current Opinion in Structural Biology

Volumn 7, Issue 3, 1997, Pages 324-335

  Jaeger, Luc ^a  

^a INST DE BIOL MOLEC ET CELLULAIRE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOZYME; RNA;

ARTICLE; CATALYSIS; ENZYME ACTIVITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; PRIORITY JOURNAL; RNA STRUCTURE; STRUCTURE ACTIVITY RELATION;

EID: 0030996755     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80047-4     Document Type: Article

References (79)

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28. Streicher B, Westhof E, Schroeder R. The environment of two metal ions surrounding the splice site of a group I intron. EMBO J. 15:1996;2556-2564 The authors use site-specific cleavage by divalent metal ions to identify a high affinity metal ion binding site within the catalytic core of a group I intron. On the basis of published and experimental data, they proposed a structural location for two magnesium ions surrounding the splice site in the context of the Michel and Westhof [79] 3D model of the group I ribozyme. of special interest.
29. Sjögren A-S, Pettersson E, Sjöberg B-M, Strömberg R. Metal ion interaction with cosubstrate in self-splicing of group I introns. Nucleic Acids Res. 25:1997;648-653.
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31. 2+ coordinated to the pro-Rp oxygen of the scissile bond. Biochemistry. 36:1997;2425-2438 This paper provides very good evidence for the direct involvement of a magnesium in the catalytic process of RNase P RNAs. of special interest.
32. Pan T, Long DM, Uhlenbeck OC. Divalent metal ions in RNA folding and catalysis. Gesteland RF, Atkins JF. The RNA World. 1993;271-302 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
33. Jacquier A. Group II introns: elaborate ribozymes. Biochimie. 78:1996;474-487 This is an up to date review about group II introns which emphasizes the ability of these very large ribozymes to perform complex tasks. of special interest.
34. Pan T, Loria A, Zhong K. Probing of tertiary interactions in RNA: 2'-hydroxyl-base contacts between the RNase P RNA and pre-tRNA. Proc Natl Acad Sci USA. 92:1995;12510-12514.
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37. Conn MM, Prudent JR, Schultz PG. Porphyrin metalation catalyzed by a small RNA molecule. J Am Chem Soc. 118:1996;7012-7013 The porphyrin metalation ribozyme is the second ribozyme to be produced by selection for binding a transition-state analog. See also [76]. of special interest of outstanding interest.
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40. Dai X, De Mesmaeker A, Joyce GF. Cleavage of an amide bond by a ribozyme. Science. 297:1995;237-240 See annotation [41]. of special interest.
41. Dai X, De Mesmaeker A, Joyce GF. Amide cleavage by a ribozyme: correction. Science. 272:1996;18-19 These two papers [40,41] show that a group I ribozyme selected for its DNA-cleavage catalytic activity also catalyzes the cleavage of an amide bond, albeit very modestly. of special interest.
42. 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. 2:1996;982-994 This paper describes the selection of a small sulfur alkylating ribozyme that can ligate, via the formation of a thioether bond, a small bromoacetylated peptide called bradykinin to a monophosphorothioate localized at its 5'-end. This ribozyme seems to act without chemical catalysis, essentially providing a template for the peptide and ribozyme 5'-end. of special interest.
43. Chapman KB, Szostak JW. Isolation of a ribozyme with 5′→5′ ligase activity. Chem Biol. 2:1995;325-333 This paper describes a rather simple ribozyme that forms 5′→5′ oligophosphate linkages. Interestingly, the selected ribozyme does not perform the initially desired template-directed 3′→5′ ligation. This suggests either that there are no ribozymes catalyzing the desired reaction in the initial random pool, or that 3′→5′ ligases, less efficient than 5′→5′ ligases, are so diluted in the final pool that they do not show up. of special interest.
44. Lorsch JR, Szostak JW. Kinetic and thermodynamic characterization of the reaction catalyzed by a polynucleotide kinase ribozyme. Biochemistry. 34:1995;15315-15327 This interesting paper describes a detailed kinetic and thermodynamic framework for the reaction catalyzed by a polynucleotide kinase ribozyme. This ribozyme was previously isolated from a biased RNA pool that consisted of an ATP-binding domain flanked by regions of random sequence. This enzyme operates in a rather simple manner - with independent substrate-binding sites and without changing the mechanism of the underlying chemical reaction. See also the excellent paper [47]. of outstanding interest.
45. Wilson C, Szostak JW. In vitro evolution of a self-alkylating ribozyme. Nature. 374:1995;777-782 This paper presents the selection of an autoalkylating ribozyme using a multistep selection procedure. First, a biotin aptamer is selected from a random N72 pool. The biotin aptamer is then used to create a new pool to select ribozymes capable of self-biotinylation. Interestingly, the initial biotin-binding motif does not seem to have a structure robust enough not to be destroyed by a few mutations in the course of the selection. Thus, whether it helps to bias the pool towards binding of the biotin is not clear. of special interest.
46. Tsang J, Joyce GF. In vitro evolution of randomized ribozymes. Methods Enzymol. 267:1996;410-426 This technical paper about in vitro evolution techniques is part of an issue of Methods in Enzymology that is dedicated to combinatorial chemistry. Readers interested by in vitro selection and evolution of nucleic acids should refer to this issue, which contains other interesting and practical SELEX papers. of special interest.
47. Lorsch JR, Szostak JW. In vitro evolution of new ribozymes with polynucleotide kinase activity. Nature. 371:1994;31-36.
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