CRYSTAL AND MOLECULAR-STRUCTURE OF D(GTCTAGAC)

d(GTCTAGAC), C78H92N30O46P7.3H2O, M(r) for DNA only = 2403, tetragonal, P4(3)2(1)2, a = 42.56 (11), c = 24.61 (11) angstrom, V = 44577 angstrom3, Z = 8, lambda(Cu Kalpha) = 1.5418 angstrom, mu(Cu Kalpha) = 9.7 cm-1, T = 295 K, R = 0.211 for 801 unique reflections with F > sigma(F) between 6 and 2.5 angstrom resolution. The asymmetric unit consists of a single strand of oligonucleotide and three well-defined solvent molecules. The structure is quasi-isomorphous with d(CTCTAGAG) [Hunter, Langlois d'Estaintot & Kennard (1989). Biochemistry, 28, 2444-2451] and was solved by molecular replacement. Restrained least-squares methods interspersed with computer-graphics manipulation were used to refine the structure. Two strands, related by a crystallographic dyad axis, coil about each other to form a right-handed helix. The mean helix rotation is 32-degrees resulting in 11.3 base pairs per turn. The average rise per base pair is 3.3 angstrom, most of the furanose rings adopt a C3'-endo conformation and the duplex shows a shallow minor groove and a deep major groove. These global features suggest classification of d(GTCTAGAC) as A-form DNA and tend to mask significant variations in conformational parameters at the base-pair level. In particular, the central TpA (= TpA) step displays extensive interstrand purine-purine overlap and an unusual sugar-phosphate backbone conformation.