title: Theoretical and experimental selection parameters for HBV-directed antisense RNA are related to increased RNA-RNA annealing.
abstract: Annealing kinetics of antisense species against two different target regions of the hepatitis B virus (HBV) were measured by kinetic in vitro selection. Individual association rates were related to energies calculated for local sequence segments and predicted structures of the complete pregenomic target RNA. A relationship between the presence of external loops and joint sequences with fast pairing was observed whereas internal loops did not favor fast RNA-RNA annealing. The findings were used to predict a fast-annealing HBV-directed antisense oligodeoxyribonucleotide that turned out to pair with its target RNA at an association rate constant of k=9.2 x 10(4) M(-1) s(-1), which is substantially faster than the annealing rates of artificial antisense RNA so far included in in vitro selection assays.
authors.affiliation: Forschungsschwerpunkt Angewandte Tumorvirologie, Deutsches Krebsforschungszentrum, Heidelberg, Germany.
authors.forename: V
authors.initials: V
authors.lastname: Patzel
authors.forename: J
authors.initials: J
authors.lastname: zu Putlitz
authors.forename: S
authors.initials: S
authors.lastname: Wieland
authors.forename: H E
authors.initials: HE
authors.lastname: Blum
authors.forename: G
authors.initials: G
authors.lastname: Sczakiel
mesh_terms: D003198:Computer Simulation; D016679:Genome, Viral; D006515:Hepatitis B virus / Q000235:genetics* / Q000378:metabolism*; D006801:Humans; D007700:Kinetics; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D016376:Oligonucleotides, Antisense / Q000737:chemistry* / Q000378:metabolism*; D012367:RNA, Viral / Q000378:metabolism*; D017423:Sequence Analysis, RNA
chemical_list: D016376:Oligonucleotides, Antisense; D012367:RNA, Viral