title: A selection system for identifying accessible sites in target RNAs.
abstract: Although ribozymes offer tremendous potential for posttranscriptionally controlling expression of targeted genes, their utility is often limited by the accessibility of the targeted regions within the RNA transcripts. Here we describe a method that identifies RNA regions that are accessible to oligonucleotides. Based on this selection protocol, we show that construction of hammerhead ribozymes targeted to the identified regions results in catalytic activities that are consistently and substantially greater than those of ribozymes designed on the basis of computer modeling. Identification of accessible sites should also be widely applicable to design of antisense oligonucleotides and DNAzymes.
authors.affiliation: Department of Pathology, Biochemistry and Molecular Biology, The Gittlen Cancer Research Institute, The Pennsylvania State University, Hershey 17033, USA.
authors.forename: W H
authors.initials: WH
authors.lastname: Pan
authors.forename: H F
authors.initials: HF
authors.lastname: Devlin
authors.forename: C
authors.initials: C
authors.lastname: Kelley
authors.forename: H C
authors.initials: HC
authors.lastname: Isom
authors.forename: G A
authors.initials: GA
authors.lastname: Clawson
mesh_terms: D001483:Base Sequence; D021881:DNA, Catalytic; D019020:Directed Molecular Evolution / Q000379:methods*; D006515:Hepatitis B virus / Q000187:drug effects*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016376:Oligonucleotides, Antisense; D012323:RNA Processing, Post-Transcriptional; D016337:RNA, Catalytic / Q000494:pharmacology; D012367:RNA, Viral / Q000378:metabolism*; D013379:Substrate Specificity; D058727:RNA, Small Untranslated
chemical_list: D021881:DNA, Catalytic; D016376:Oligonucleotides, Antisense; D016337:RNA, Catalytic; D012367:RNA, Viral; D058727:RNA, Small Untranslated