title: Dissociation of long-chain duplex RNA can occur via strand displacement in vitro: biological implications.
abstract: Hammerhead ribozymes with long antisense flanks (>50 bases) have been used successfully to inhibit replication of human immunodeficiency virus type 1 (HIV-1) in living cells. To explain their increased efficacy versus antisense controls or catalytically inactive derivatives, one can consider dissociation of the ribozyme-product complex to allow a complete catalytic cycle. In this work we investigated the dissociation of a double-stranded RNA with 56 bp in vitro. Dissociation was observed in the presence of single-stranded RNA with sequence complementarity to one of the duplex strands. A displacement reaction between RNA single strands and the duplex, but not simple dissociation, was strongly suggested by the concentration dependence of this process, the influence of additional non-complementary sequences on the single strand and by the unusually low Arrhenius activation energy. The strand displacement reaction was slow in vitro at 37 degrees C and physiological ionic strength, but was increased to k approximately 10(3)-10(4)/M/s (approximately 10(4)-fold) at higher temperatures by cetyltrimethylammonium bromide. This compound is thought to enhance non-sequence-specific association of nucleic acids in a mechanistically similar way to that in which cellular hnRNP proteins are thought to act, indicating that strand displacement can be fast and, more importantly, could be tightly regulated in vivo.
authors.affiliation: Forschungsschwerpunkt Angewandte Tumorvirologie, Deutsches Krebsforschungszentrum, Heidelberg, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Homann
authors.forename: W
authors.initials: W
authors.lastname: Nedbal
authors.forename: G
authors.initials: G
authors.lastname: Sczakiel
mesh_terms: D000077286:Cetrimonium; D002593:Cetrimonium Compounds / Q000494:pharmacology; D003902:Detergents / Q000494:pharmacology; D015497:HIV-1 / Q000502:physiology; D006801:Humans; D007700:Kinetics; D016376:Oligonucleotides, Antisense / Q000378:metabolism; D009994:Osmolar Concentration; D016337:RNA, Catalytic / Q000378:metabolism; D012330:RNA, Double-Stranded / Q000378:metabolism*; D013696:Temperature; D014779:Virus Replication
chemical_list: D002593:Cetrimonium Compounds; D003902:Detergents; D016376:Oligonucleotides, Antisense; D016337:RNA, Catalytic; D012330:RNA, Double-Stranded; D000077286:Cetrimonium