title: Structural diversity of self-cleaving ribozymes.
abstract: In vitro selection was used to isolate Mg(2+)-dependent self-cleaving ribozymes from random sequence. Characterization of representative clones revealed the emergence of at least 12 classes of ribozymes that adopt distinct secondary structure motifs. Only one class corresponds to a previously known structural motif, that of the naturally occurring hammerhead ribozyme. Each ribozyme promotes self-cleavage via an internal phosphoester transfer reaction involving the adjacent 2'-hydroxyl group with a chemical rate enhancement of between 10(3)- and 10(6)-fold greater than the corresponding uncatalyzed rate. These findings indicate that RNA can form a multitude of secondary and tertiary structures that promote cleavage by internal phosphoester transfer. Upon further in vitro selection, a class I ribozyme that adopts an "X motif" structure dominates over all other ribozymes in the population. Thus, self-cleaving RNAs isolated by in vitro selection from random-sequence populations can rival the catalytic efficiency of natural ribozymes.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA.
authors.forename: J
authors.initials: J
authors.lastname: Tang
authors.forename: R R
authors.initials: RR
authors.lastname: Breaker
mesh_terms: D020816:Amino Acid Motifs; D001483:Base Sequence; D002384:Catalysis; D015195:Drug Design; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: D016337:RNA, Catalytic