Relative stabilities of RNA/DNA hybrids: Effect of RNA chain length in competitive hybridization

Escherichia coli DNA and fragmented rRNA were used as a model system to study the effect of RNA fragment size in hybridization-competition experiments. Though no difference in hybridization rates was observed, the relative stabilities of the RNA/DNA hybrids were found to be largely affected by the fragment size of the RNA molecule. Intact rRNA was shown to replace shorter homologous rRNA sequences in their hybrids, the rate of the displacement being dependent on the molecular size of the RNA fragments. Hybridization-competition experiments between molecules of different lengths are expected to be complicated by the displacement reaction. The synthesis of tRNA Tyr -like sequences transcribed in vitro on φ80p su 3 + bacteriophage DNA was measured by hybridization competition assays. Indirect competition with labelled E. coli tRNA Tyr hybridization revealed that the in vitro -synthesized RNA contained significant amounts of tRNA Tyr ; these sequences could not, however, be detected by the direct competition method in which labelled in vitro -synthesized RNA competes with E. coli tRNA Tyr for hybridization to φ80p su 3 + DNA. These contradictory results can be traced to the differences in size of the competing molecules in the hybridization-competition reaction. Indeed, in vitro -transcribed tRNA Tyr -like sequences, longer than mature tRNA, were found to displace efficiently E. coli tRNA Tyr from its hybrids with φ80p su 3 + DNA. These findings explain why such sequences could not be detected by direct competition with E. coli tRNA Tyr .