Elementary Patterns in Protein-Nucleic Acid Interactions. IV. Crystal Structure of 3-(Adenin-9-yl)propionamide : 1-Methylthymine (1 : 1) Complex Dihydrate

Abstract

Abstract As a ternary interaction model between adenine:thymine base pair and carbamoyl group, 3-(adenin-9-yl)-propionamide: 1-methylthymine complex was prepared and its crystal structure was examined. The crystal exhibits a disordered structure, and the structure unit is a monoclinic cell with dimensions a=11.368(1), b=6.909(1), c=12.708(2) Å, and β=114.49(1)°. The space group is P21 and the unit cell contains two complexes and four water molecules. The base pairing pattern between adenine and thymine is the Hoogsteen type. The carbamoyl group is hydrogen-bonded to N(A1) of adenine in this base pair, the distance NH···N(A1) being 2.94(2) Å. With two kinds of hydrogen bonds of the carbamoyl group, NH···N(A1) above-mentioned and NH···O(carbamoyl), the 3-(adenin-9-yl)propionamide molecules form a sheet extending perpendicular to the c axis; the base-paired thymine molecules extrude alternately from the sheet. Diffused spots along c* with half integers of l can be interpreted as a stacking disorder of the sheets.