The objectives of this project are to design and synthesize small molecules which are able to recognize and stabilize RNA/DNA heteroduplexes (R/D). We hypothesize that molecules that are able to do this will be effective at inhibiting telomerase, a target for anticancer therapy. Telomerase is an enzyme which extends telomeres, the single C- rich strand at the end of chromosomes. It is hypothesized that the maintenance of telomeres by telomerase in cancerous cells allows uncontrolled cell division, and therefore tumor growth. Telomerase is a ribonucleoprotein which contains a single strand of RNA that has a sequence complementary to the G-rich telomere. The RNA from telomerase anneals to the DNA and acts as a template to extension of the telomere, thus forming an R/D. After synthesis of one repeat of the telomeric sequence, the RNA and DNA strands separate, translocate, reanneal and repeat the polymerization. We anticipate that the binding of a small molecule to the minor groove of the R/D that forms at the active site will stabilize the duplex structure and prevent separation of the two strands. This is what is observed with small molecules that recognize the minor groove of DNA/DNA duplexes (D/D). There are significant differences between R/D and D/D that should allow the tailoring of D/D specific molecules to be R/D specific molecules. The main differences identified are a decreased depth and increased width in the minor groove of R/D relative to D/D, as well as the presence of the 2' hydroxyl group. We will utilize molecular modeling techniques to design molecules which can exploit these differences and assess the validity of design through binding analysis to nucleotide targets and eventually telomerase inhibition.
