title: 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.
authors.affiliation: Department of Chemistry, Georgia State University, Atlanta 30303, USA.
authors.forename: C T
authors.initials: CT
authors.lastname: Rigl
authors.forename: D H
authors.initials: DH
authors.lastname: Lloyd
authors.forename: D S
authors.initials: DS
authors.lastname: Tsou
authors.forename: S M
authors.initials: SM
authors.lastname: Gryaznov
authors.forename: W D
authors.initials: WD
authors.lastname: Wilson
mesh_terms: D001665:Binding Sites; D002942:Circular Dichroism; D004591:Electrophoresis, Polyacrylamide Gel; D015694:Gene Products, rev / Q000737:chemistry* / Q000378:metabolism; D015696:Gene Products, tat / Q000737:chemistry* / Q000378:metabolism; D015497:HIV-1; D006358:Hot Temperature; D009687:Nuclear Proteins / Q000737:chemistry* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000378:metabolism; D012313:RNA / Q000378:metabolism; D054321:rev Gene Products, Human Immunodeficiency Virus; D054322:tat Gene Products, Human Immunodeficiency Virus
chemical_list: D015694:Gene Products, rev; D015696:Gene Products, tat; D009687:Nuclear Proteins; D009841:Oligonucleotides; C069802:nuclear factor, RRE binding; D054321:rev Gene Products, Human Immunodeficiency Virus; D054322:tat Gene Products, Human Immunodeficiency Virus; D012313:RNA