Characterization of several kinds of dimer minizyme: Simultaneous cleavage at two sites in HIV-1 tat mRNA by dimer minizymes

A minizyme is a hammerhead ribozyme with short oligonucleotide linkers instead of stem-loop II, In a previous study we demonstrated that a minizyme with high activity forms a dimeric structure with a common stem II, Because of their dimeric structure, minizymes are potentially capable of cleaving a substrate at two different sites simultaneously, In order to examine the properties of different kinds of minizyme, we constructed a number of minizymes with short oligonucleotide linkers (2-5 bases) instead of stem-loop II and examined their cleavage activities against HIV-1 tat mRNA, Analyses of melting curves, as well as Arrhenius plots, revealed that, in general, the longer the oligonucleotide linkers, the more stable and more active were the dimer minizymes, All minizymes examined cleaved the target substrate at two sites simultaneously. The activity of the dimer minizyme with a 5 nt linker was higher than that of the parental hammerhead ribozyme because the latter full-sized ribozyme was able to cleave at one site only.