Structural and thermodynamic studies of the hairpins and duplexes formed by a DNA palindrome containing a 1,N(2)-propanodeoxyguanosine adduct

Conformational and thermodynamic studies were conducted on a thirteen base oligodeoxynucleotide palindrome sequence derived from the hisD3052 gene on Salmonella typhimurium. The oligodeoxynucleotide d(CGCGGTXTCCGCG) was studied in both the native form, where X = guanine, and in the adducted form, where X = 1,N2-propanodeoxyguanosine (PdG). The sequence was studied in the single stranded hairpin form as well as the duplex form when combined with the complementary strand d(CGCGGACACCGCG). Thermodynamic studies determined that the hairpins were unusually stable with melting temperatures (T_m) of 73°C and 74°C for the G Hairpin and PdG Hairpin, respectively, in phosphate buffer containing 10 mm NaCl. The PdG adduct had little effect upon the stability of the hairpin. The PdG adduct had a significant effect upon the stability of the double stranded duplex. The T_m's of the TGT and TXT Duplexes were 49°C and 35°C, respectively, in phosphate buffer containing 1 mM NaCl. The structures of the hairpins and duplexes were refined by restrained molecular dynamics calculation using distance and dihedral restraints determined from nuclear magnetic resonance spectroscopy (NMR) data. The hairpin structures consisted of a B-like DNA stem composed of five G·C base pairs and a three base loop composed of the three central bases (TXT). The unmodified duplex was similar to B-form DNA composed of thirteen Watson-Crick base pairs. At pH 5.2, the PdG base in the modified duplex rotated into the syn conformation with respect to the sugar and formed a Hoogsteen base pair with the N3 protonated cytosine, in the complimentary strand. The remaining bases in the TXT Duplex were similar to B-form DNA. Relationships between structural data and the mutagenic spectrum of this site-specifically modified oligonucleotide are discussed.