A Model for Interactions of Amino Acid Side Chains with Watson-Crick Base Pair of Guanine and Cytosine. Crystal Structures of 9-(2-Carboxyethyl)guanine and Its Crystalline Complex with 1-Methylcytosine

Abstract

Abstract A new compound, 9-(2-carboxyethyl)guanine, was successfully synthesized and its crystalline complex with 1-methylcytosine was prepared, in order to investigate the protein-nucleic acid interactions involving guanine base. The crystal structures of 9-(2-carboxyethyl)guanine (cx9G) and of the complex of cx9G with 1-methylcytosine (cx9G:m1C) were determined by the X-ray analysis. Crystal data: cx9G, P21/c, a=12.221(3), b=11.022(2), c=6.961(2) Å, β=100.22(2)°; cx9G:m1C, P\bar1, a=8.932(1), b=12.370(1), c=7.139(1) Å, α=85.01(1), β=99.21(1), γ=86.64(1)°. In cx9G, the carboxyl group is doubly hydrogen-bonded with N(2) and N(3) of the guanine moiety of the adjacent molecule, N(2)–H···O distance being 2.939(5) Å and N(3)···H–O 2.660(5) Å for N···O. In cx9G: m1C, the guanine moiety and 1-methylcytosine form a Watson-Crick base pair. The carboxyl group takes an O=C–OH antiperiplanar conformation and is hydrogen-bonded with N(7) of guanine in the adjacent base pair. This hydrogen bond distance is very short, 2.634(2) Å, though the unfavorable conformation of the carboxyl group. This may suggest the marked preference of the carboxyl group for N(7) of guanine in the Watson-Crick base pair. On the basis of the geometrical data found in the present crystals, some possible models of interactions were constructed and examined, for example, aspartic or glutamic acid residue in the major groove of double stranded DNA.