title: Hammerhead ribozyme structure probed by cell extracts.
abstract: To examine hammerhead ribozyme structure and vulnerability to cellular nucleases, ribozymes were incubated with soluble extracts from Escherichia coli, and cleavage sites were identified by primer extension analysis. Mapping of endonuclease-sensitive sites revealed that the most sensitive were in the 3'-substrate-binding region of the ribozyme. The catalytic domain was much less susceptible, although some cleavage preference was seen at two positions known to be twisted out of parallel stacking in a ribozyme-substrate analogue complex. Changes in substrate-binding domain nucleotide sequence had no effect on cleavage patterns of catalytic domains. Hammerhead ribozymes, in solution and free from substrate, appear to have structurally independent, asymmetrically arranged domains.
authors.affiliation: Public Health Research Institute, New York, NY 10016, USA.
authors.forename: J Y
authors.initials: JY
authors.lastname: Wang
authors.forename: L
authors.initials: L
authors.lastname: Qiu
authors.forename: K
authors.initials: K
authors.lastname: Drlica
mesh_terms: D001483:Base Sequence; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry; D016337:RNA, Catalytic / Q000737:chemistry*; D012260:Ribonucleases / Q000378:metabolism
chemical_list: D012329:RNA, Bacterial; D016337:RNA, Catalytic; D012260:Ribonucleases