Targeting DNA and RNA using dimeric aminoglycoside

The discovery of the chemical structure of DNA duplex helped in understanding mechanism of biological processes at molecular level. The concept "central dogma of molecular biology" was coined by James Crick and is a framework for understanding the transfer of information from one biopolymer to another. This revolutionized the medical field because it enabled the development of drugs to combat theretofore incurable diseases.;For the past eleven years, our laboratory has been investigating recognition of nucleic acids using small molecules. Our group has discovered that neomycin; an aminoglycoside can recognize the A-form nucleic acids, including DNA (DNA triplex), RNA, and hybrid structures. A number of neomycin conjugates were synthesized where neomycin was covalently linked to intercalators and minor groove binders to specifically target DNA duplex and triplex.;A dimeric conjugate of neomycin surprisingly has shown high affinity towards B-form DNA, contrary to neomycin. We have performed a series of experiments using various analytical techniques including UV thermal denaturation, isothermal calorimetry titration (ITC), circular dichroism (CD), and fluorescent intercalator displacement (FID) assay. The neomycin dimer specifically targeted continuous AT rich DNA duplexes (B*-form DNA conformation) with high affinity (K a = 108 M-1). Following these experiments, a series of neomycin dimers was synthesized and screened against AT-rich DNA duplexes to determine the optimal length of neomycin dimer conjugate with highest affinity.;In a separate project, another series of neomycin dimers was synthesized using click chemistry to target HIV TAR RNA, a 31-mer RNA sequence that plays an important role in the replication of HIV by interacting with a ribonucleoprotein (TAT). The HIV TAR RNA has two binding sites for neomycin, which encouraged us to design and study neomycin dimers against HIV TAR RNA. Neomycin dimers have shown high binding affinity towards HIV TRA RNA (Ka = 10 8 M-1). In vitro assays were carried out with neomycin dimers against cells infected with HIV. The in vitro assays clearly showed that these compounds are potential candidates to target HIV.;We also have been conducting experiments for the dual recognition of nucleic acids. A series of neomycin dimer conjugates have been synthesized and the studies are ongoing and will be presented in the near future.;In summary, we have succeeded in targeting the B-form DNA as well as HIV TAR RNA.