Synthesis, structure and thermodynamic properties of 8-methylguanine-containing oligonucleotides: Z-DNA under physiological salt conditions

Various oligonucleotides containing 8-methylguanine (m8G) have been synthesized and their structures and thermodynamic properties investigated. Introduction of m(8)G into DNA sequences markedly stabilizes the Z conformation under low salt conditions, The hexamer d(CGC[m(8)G]CG)(2) exhibits a CD spectrum characteristic of the Z conformation under physiological salt conditions. The NOE-restrained refinement unequivocally demonstrated that d(CGC[m(8)G]CG)2 adopts a Z structure with all guanines in the syn conformation. The refined NMR structure is very similar to the Z form crystal structure of d(CGCGCG)(2), with a root mean square deviation of 0.6 between the two structures, The contribution of m(8)G to the stabilization of Z-DNA has been estimated from the mid-point NaCl concentrations for the B-Z transition of various m(8)G-containing oligomers. The presence of m8G in d(CGC[m(8)G]CG)(2) stabilizes the Z conformation by at least Delta G = -0.8 kcal/mol relative to the unmodified hexamer. The Z conformation was further stabilized by increasing the number of m(8)Gs incorporated and destabilized by incorporating syn-A or syn-T found respectively in the (A,T)-containing alternating and non-alternating pyrimidine-purine sequences. The results suggest that the chemically less reactive m8G base is a useful agent for studying molecular interactions of Z-DNA or other DNA structures that incorporate syn-G conformation.