INHIBITION OF REV-CENTER-DOT-RRE COMPLEXATION BY TRIPLEX TETHERED OLIGONUCLEOTIDE PROBES

We have described a class of molecules, called tethered oligonucleotid e probes (TOPs), that bind RNA on the basis of both sequence and struc ture. TOPs consist of two short oligonucleotides joined by a tether wh ose length and composition may be varied using chemical synthesis. In a triplex TOP, one oligonucleotide recognizes a short single-stranded region in a target RNA through the formation of Watson-Crick base pair s; the other oligonucleotide recognizes a short double-stranded region through the formation of Hoogsteen base pairs. Binding of tripler TOP s to an HIV-1 Rev Response Element RNA Variant (RREAU) was measured by competition electrophoretic mobility shift analysis. Tripler TOP.RREA U stabilities ranged between -9.6 and -6.1 kcal mol(-1) under physiolo gical conditions of pH, salt, and temperature. Although the most stabl e tripler TOP.RREAU complex contained 12 contiguous U.AU triple helica l base pairs, complexes containing only six or nine triple helical bas e pairs also formed. Tripler TOPs inhibited formation of the RRE.Rev c omplex with IC50 values that paralleled the dissociation constants of the analogous tripler TOP.RREAU complexes. In contrast to results obta ined with TOPs that target two single-stranded RRE regions, inhibition of Rev.RREAU complexation by tripler TOPs did not require pre-incubat ion of RREAU and a TOP: tripler TOPs competed efficiently with Rev for RREAU and inhibited RREAU.Rev complexation at equilibrium. (C) 1997 E lsevier Science Ltd.