Structural RNA mimetics: N3'-->P5' phosphoramidate DNA analogs of HIV-1 RRE and TAR RNA form A-type helices that bind specifically to Rev and Tat-related peptides.

Abstract

An attractive strategy for the development of anti-retroviral drugs is the exploration of compounds that mimic RNA control regions of the viral genome and act as "decoys" to sequester viral gene regulatory proteins. Decoys consisting of RNA, however, are chemically unstable and readily degraded by cellular nucleases. DNA decoys, which are slightly more stable, also might not be appropriate because of possible structural differences between RNA and DNA helices and the complexes they form with proteins. It was recently reported, however, that DNA analogs with modified N3'-->P5' phosphoramidate sugar-phosphate backbones are stable and nuclease-resistant and exist predominately as A-form helices in solution [Gryaznov, S., et al. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 5798-5802]. We now report that oligonucleotide N3'-->P5' phosphoramidates DNA analogs of HIV-1 RRE IIB and TAR RNA form stable duplexes that exist in the A form as judged by circular dichroism (CD). Moreover, gel shift assays demonstrate that these phosphoramidates can specifically bind to peptides derived from HIV-1 Rev and Tat proteins. Isosequential phosphodiester DNA duplexes, existing in the B form by CD, do not bind to the respective peptides under the experimental conditions used. These results suggest the possibility that nuclease-resistant oligonucleotide N3'-->P5' phosphoramidates might serve as RNA-like decoys and disrupt specific viral RNA/protein interactions such as RRE/Rev and TAR/Tat in HIV-1.