Chemical and biomolecular structures in recognition of DNA modification

Abstract

Formation of O6-alkylguanine adducts leads to potentially carcinogenic mutations in genes involved in carcinogenesis, despite the low abundance of these adducts. We intend to develop DNA hybridization probes specific for O6-alkylguanine adducts to probe the formation and persistence of these adducts in genes. For this purpose, a unique set of synthetically derived nucleoside analogs is proposed to be used in these hybridization probes. Structural design of these probes to specifically recognize O6-alkylguanine adducts requires an understanding of chemical and sequence related factors involved in base-pair interactions. We have evaluated thermal stabilities of duplex combinations containing structurally varied synthetic nucleosides paired with O6-alkylated DNA adducts. Influence of base structure, modified base pair position and/or neighboring base identity on stability of modified duplexes has been evaluated. Data indicate that favorable H-bonding rather than inter-strand stacking interactions dictate the stabilities of the modified base pairs. To understand the molecular basis of modified base pairing, oligonucleotides harboring site-specifically incorporated base pairs containing synthetic nucleoside probe Per were synthesized and subjected to NMR and X-ray crystallography analysis. The data provides structural insights into the interaction of a synthetic nucleoside with unmodified and O6-alkylated guanine. A sensitive O6-alkylguanine adduct recognition assay based on nanoparticle conjugates with modified oligonucleotides containing adduct specific synthetic nucleoside probe is proposed. Synthesis of modified oligonucleotides containing a chemically modified thiol-tethered Cytosine, to probe the enzyme active site structure of APOBEC3G through disulfide cross-linking, is reported.