Nucleic Acids Research Advance Access published online on October 12, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl533
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Methods Online |
Specific binding of a hexanucleotide to HIV-1 reverse transcriptase: a novel class of bioactive molecules
1 Kompetenzzentrum Drug Design and Target Monitoring Maria-Göppert-Strasse 1, D-23538 Lübeck, Germany 2 Institut für Molekulare Medizin, Universitätsklinikum Schleswig-Holstein and ZMSB, Universität zu Lübeck Ratzeburger Allee 160, D-23538 Lübeck, Germany
*To whom correspondence should be addressed. Tel: +49 451 500 2731l; Fax: +49 451 500 2729; Email: sczakiel{at}imm.uni-luebeck.de
Received May 18, 2006. Revised July 10, 2006. Accepted July 10, 2006.
Short oligonucleotides below 8–10 nt in length adopt relatively simple structures. Accordingly, they represent interesting and so far unexplored lead compounds as molecular tools and, potentially, for drug development as a rational improvement of efficacy seem to be less complex than for other classes of longer oligomeric nucleic acid. As a ‘proof of concept’, we describe the highly specific binding of the hexanucleotide UCGUGU (Hex-S3) to human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) as a model target. Ultraviolet (UV) cross-linking studies and competition experiments with primer/template substrates and a RT-directed aptamer suggest site-specific binding of Hex-S3 to the large subunit (p66) of the viral enzyme. The affinity of 5.3 µM is related to hexanucleotide-specific suppression of HIV-1 replication in human cells by up to three orders of magnitude indicating that Hex-S3 exerts specific and biologically relevant activity. Experimental evidence described here further suggests a systematic hexamer array-based search for new tools for molecular biology and novel lead compounds in nucleic acid-based drug development.