A synthetic nucleoside probe that discerns a DNA adduct from unmodified DNA

Selective pairing of engineering nucleosides in DNA duplexes provides a potential means to probe structurally modified DNA bases (i.e., DNA adducts) and address challenges associated with correlating adduct chemical structure with biological impact. The current study provides the first example of a thermodynamically stable DNA base pair that is comprised of a biologically relevant carcinogen-DNA adduct and a synthetic nucleoside probe. O-6-Benzylguanine is a mutagenic DNA adduct; molecular modeling indicates that a novel diaminonaphthyl-derived nucleoside (dNap):O-6-benzylguanine base pair may be stabilized by a combination of hydrogen-bonding and hydrophobic interactions. The nucleoside dNap was synthetically incorporated into oligonucleotides, and a series of duplexes were evaluated by thermal denaturation studies. The bulky DNA adduct O-6-benzylguanine forms a highly stable and orthogonal base pair with dNap. Data indicate pi-stacking potential, self-pairing capacity, isomeric selectivity, 1:1 duplex stoichiometry, and a B-form DNA structure. Further studies are required to understand the physical determinants of adduct:probe pair stability for the design of probes for diverse forms of DNA damage and for the development of adduct-probe-based molecular techniques.