{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T17:48:15Z","timestamp":1790272095901,"version":"4.1.0"},"reference-count":60,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2003,7,29]],"date-time":"2003-07-29T00:00:00Z","timestamp":1059436800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biopolymers"],"published-print":{"date-parts":[[2003,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>RNA plays a pivotal role in the replication of all organisms, including viral and bacterial pathogens. The development of small molecules that selectively interfere with undesired RNA activity is a promising new direction for drug design. Currently, there are no anti\u2010HIV treatments that target nucleic acids. This article presents the HIV\u20101 Rev response element (RRE) as an important focus for the development of antiviral agents that target RNA. The Rev binding site on the RRE is highly conserved, even between different groups of HIV\u20101 isolates. Compounds that inhibit HIV replication by binding to the RRE and displacing Rev are therefore expected to retain activity across groups of genetically diverse HIV infections. Systematic evaluations of both the RRE affinity and specificity of numerous small molecule inhibitors are essential for deciphering the parameters that govern effective RRE recognition. This article discusses fluorescence\u2010based techniques that are useful for probing a small molecule's RRE affinity and its ability to inhibit Rev\u2013RRE binding. Rev displacement experiments can be conducted by observing the fluorescence anisotropy of a fluorescein\u2010labeled Rev peptide, or by quantifying its displacement from a solid\u2010phase immobilized RRE. Experiments conducted in the presence of competing nucleic acids are useful for evaluating the RRE specificity of Rev\u2010RRE inhibitors. The discovery and characterization of new RRE ligands are described. Eilatin is a polycyclic aromatic heterocycle that has at least one binding site on the RRE (apparent <jats:italic>K<\/jats:italic><jats:sub>d<\/jats:sub> \u2248 0.13 \u03bc<jats:italic>M<\/jats:italic>), but it does not displace Rev upon binding the RRE (IC<jats:sub>50<\/jats:sub> &gt; 3 \u03bc<jats:italic>M<\/jats:italic>). In contrast, ethidium bromide and two eilatin\u2010containing metal complexes show better consistency between their RRE affinity and their ability to displace a fluorescent Rev peptide from the RRE. These results highlight the importance of conducting orthogonal binding assays that establish both the RNA affinity of a small molecule and its ability to inhibit the function of the RNA target. Some Rev\u2013RRE inhibitors, including ethidium bromide, \u039b\u2010[Ru(bpy)<jats:sub>2<\/jats:sub>eilatin]<jats:sup>2+<\/jats:sup>, and \u0394\u2010[Ru(bpy)<jats:sub>2<\/jats:sub>eilatin]<jats:sup>2+<\/jats:sup> also inhibit HIV\u20101 gene expression in cell cultures (IC<jats:sub>50<\/jats:sub> = 0.2\u20133 \u03bc<jats:italic>M<\/jats:italic>). These (and similar) results should facilitate the future discovery and implementation of anti\u2010HIV drugs that are targeted to viral RNA sites. In addition, a deeper general understanding of RNA\u2013small molecule recognition will assist in the effective targeting of other therapeutically important RNA sites. \u00a9 2003 Wiley Periodicals, Inc. Biopolymers, 2003<\/jats:p>","DOI":"10.1002\/bip.10428","type":"journal-article","created":{"date-parts":[[2003,8,22]],"date-time":"2003-08-22T13:35:13Z","timestamp":1061559313000},"page":"103-119","source":"Crossref","is-referenced-by-count":74,"title":["Fluorescence\u2010based methods for evaluating the RNA affinity and specificity of HIV\u20101 Rev\u2013RRE inhibitors"],"prefix":"10.1002","volume":"70","author":[{"given":"Nathan W.","family":"Luedtke","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yitzhak","family":"Tor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2003,8,13]]},"reference":[{"key":"e_1_2_12_2_2","volume-title":"The RNA World","author":"Gestland R. 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