Inhibition of the HIV-1 rev-RRE complex formation by unfused aromatic cations.

RNA viruses cause a wide range of human diseases. Development of new agents to target such viruses is an active area of research. Towards this goal, a series of diphenylfuran cations as potential inhibitors of the Rev-RRE complex have been designed and synthesized. Analysis of the interaction of the diphenylfurans with RRE and TAR RNA model systems by gel shift assays indicates that they exhibit both sequence and structure-dependent binding modes. Our results show a strong interaction between the diphenylfuran ring system and RRE bases, while the TAR interactions are much weaker with the compounds that are the best inhibitors of Rev-RRE.

Design and analysis of molecular motifs for specific recognition of RNA.

Selective targeting of RNA has become a recent priority in drug design strategies due to the emergence of retroviruses, the need for new antibiotics to counter drug resistance, and our increased awareness of the essential role RNA and RNA structures play in the progression of disease. Most organic compounds known to specifically target RNA are complex, naturally occurring antibiotics that are difficult to synthesize or derivatize and modification of these compounds to optimize interactions with structurally unique RNAs is difficult. The de novo design of synthetically accessible analogues is one possible alternative; however, little is known about the RNA recognition principles on which to design new compounds and limited information on RNA structure in general is available. To contribute to the growing body of knowledge on RNA recognition principles, we have prepared two series of polycationic RNA-binding agents, one with a linear scaffold, the other with a macrocyclic scaffold. We evaluated these compounds for their ability to bind to DNA and RNA, as well as to a specific RNA, the regulatory sequence, RRE, derived from HIV-1, by using thermal melting, circular dichroism, and electrophoresis gel shift methods. Out results suggest that cationic charge centers of high pKa that are displayed along a scaffold of limited flexibility bind preferentially to RNA, most likely within the major groove. Related derivatives that bind more strongly to DNA more closely mimic classical DNA minor-groove binding agents. Several of the macrocyclic polycations expand on a new binding motif where purine bases in duplex RNA are complexed within the macrocyclic cavity, enhancing base-pair opening processes and ultimately destabilizing the RNA duplex. The results in this report should prove a helpful addition to the growing information on molecular motifs that specifically bind to RNA.

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.

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.

Automated quantification of thyrotropin by radial partition immunoassay.

We describe a radial partition enzyme immunoassay in which fully automated quantification of human thyrotropin (hTSH) takes less than 11 min. This "sandwich"-type assay involves two monoclonal antibodies, both specific for the intact hTSH molecule. The solid phase consists of tabs of glass-fiber filter paper containing a pre-immobilized monoclonal anti-hTSH antibody complexed with a goat antibody specific for the Fc region of mouse IgG. The patient's sample is first applied to the central "reaction zone" of the tab, wherein hTSH binds to the immobilized antibody. Application of a buffered solution containing enzyme-labeled Fab' fragments of the second monoclonal anti-hTSH antibody initiates "sandwich" formation. A wash buffer containing a fluorogenic substrate elutes unbound conjugate to the tab periphery. The bound enzyme conjugate is quantified by measuring the rate of increase in fluorescence in the reaction zone of the tab, then converting the rate to clinical units by comparison with a stored calibration curve. The clinical utility and performance of the present assay compare favorably with those of other sensitive assays for hTSH.

Radial partition immunoassay applied to automated quantification of human choriogonadotropin with use of two monoclonal antibodies.

We describe a novel application of radial partition immunoassay to quantification of human choriogonadotropin (hCG). In this "sandwich"-type assay, two monoclonal antibodies, specific for different sites on the intact molecule are used. The solid phase consists of tabs of glass-fiber filter paper containing a pre-immobilized antibody specific for the alpha subunit of hCG. The patient's sample is first applied directly to the central "reaction zone" of the tab, allowing hCG to bind to the solid-phase antibody. Then a buffered solution containing enzyme-labeled Fab' fragments of a monoclonal antibody specific for the beta subunit of hCG is applied, initiating "sandwich" formation. Finally, a wash buffer containing a fluorogenic substrate is applied, eluting unbound conjugate to the tab periphery. Bound enzyme conjugate is quantified by measuring the rate of increase in fluorescence. Rates are converted to clinical units by comparison with a stored calibration curve. Elapsed time from sample application to results is less than 8 min. Specific performance characteristics of this assay are reported.