title: RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts.
abstract: The use of antisense oligodeoxyribonucleotides (ODN) or ribozymes to specifically suppress gene expression is simple in concept and relies on efficient binding of the antisense strand to the target RNA. Although the identification of target sites accessible to base pairing is gradually being overcome by different techniques, it remains a major problem in the antisense and ribozyme approaches. In this study we have investigated the potential of a recent experimental and theoretical approach to predict the local accessibility of murine DNA-methyltransferase (MTase) mRNA in a comparative way. The accessibility of the native target RNA was probed with antisense ODN in cellular extracts. The results strongly correlated with the theoretically predicted target accessibility. This work suggests an effective two-step procedure for predicting RNA accessibility: first, computer-aided selection of ODN binding sites defined by an accessibility score followed by a more detailed experimental procedure to derive information about target accessibility at the single nucleotide level.
authors.affiliation: Abteilung für Hämatologie und Onkologie, Medizinische Hochschule Hannover, Carl-Neuberg-Strasse 1, Hannover, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Scherr
authors.forename: J J
authors.initials: JJ
authors.lastname: Rossi
authors.forename: G
authors.initials: G
authors.lastname: Sczakiel
authors.forename: V
authors.initials: V
authors.lastname: Patzel
mesh_terms: D000818:Animals; D020029:Base Pairing / Q000235:genetics; D001665:Binding Sites; D002457:Cell Extracts / Q000235:genetics; D003198:Computer Simulation; D015254:DNA Modification Methylases / Q000235:genetics / Q000378:metabolism; D051379:Mice; D009690:Nucleic Acid Conformation; D015345:Oligonucleotide Probes / Q000235:genetics / Q000378:metabolism; D016376:Oligonucleotides, Antisense / Q000235:genetics / Q000378:metabolism*; D020871:RNA Stability; D016337:RNA, Catalytic / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016914:Ribonuclease H / Q000378:metabolism; D013816:Thermodynamics
chemical_list: D002457:Cell Extracts; D015345:Oligonucleotide Probes; D016376:Oligonucleotides, Antisense; D016337:RNA, Catalytic; D012333:RNA, Messenger; D015254:DNA Modification Methylases; D016914:Ribonuclease H