| In this work, the three-dimensional structure of the bulge DNA complexed with glutathione post-activated neocarzinostatin chromophore (NCSi-glu) is elucidated using NMR spectroscopy complemented by molecular dynamics simulations. In this structure, NCSi-glu binds to a decamer DNA, d(GCCAGAGAGC), in the minor groove. The NCSi-glu binding triggers a conformational switch in DNA from a loose duplex in the free form to a single strand, tightly folded hairpin that contains an adenosine-bulge embedded in-between three base-paired stems. The naphthoate aromatic moiety of NCSi-glu intercalates into a GG step flanked by the bulge site, and its substituent groups of the 2-N-methylfucosainine ring and the tetrahydroindacene form a complementary minor groove binding surface, mostly interacting with the GCC strand in the duplex stem of DNA. The bulge site is stabilized by the interactions involving the NCSi-glu naphthoate and the GSH tripeptide. The positioning of NCSi-glu is such that only single chain cleavage via hydrogen abstraction at the 5'-position of C3, opposite to the bulge base, is possible, thus explaining the observed single chain cleavage specificity. Further comprehensive structural assessment has been performed between three post-activated NCS-chrom-containing complexes including two complexes previously determined in our laboratory. These efforts offer models for specific recognition of DNA bulges of various sizes through binding to either the minor or the major groove and for single chain cleavage of bulge DNA sequences.;This work also includes a study on another bulge-containing complex between a modified neomycin named PRN and HIV-1 Rev responsive element (RRE). Since the RRE binding to Rev protein is necessary for an HIV-1 viral replication, the inhibition of RRE-Rev complex formation is a promising approach for the development of potential antivirus drugs. |
