CRYSTAL-STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCGCGCGCGC) IN THE Z-DNA CONFORMATION .1.

Alternating self-complementary oligonucleotides starting with a 5'-pyr imidine usually form left-handed Z-DNA; however, with a 5'-purine star t sequence they form the right-handed A-DNA. Here we report the crysta l structure of the decamer d(GCGCGCGCGC) with a 5'-purine start in the ;Z-DNA form, The decamer crystallizes in the hexagonal space group P6( 5)22, unit cell dimensions a = b = 18.08 and c = 43.10 Angstrom, with one of the following four dinucleotide diphosphates in the asymmetric unit: d(pGpC)/d(GpCp)/d(pCpG)/d(CpGp). The molecular replacement metho d, starting with d(pGpC) of the isomorphous Z-DNA hexamer d(araC-dG)(3 ) without the 2'-OH group of arabinose, was used in the structure anal ysis, The method gave the solution only after the sugar-phosphate conf ormation of the GpC step was manipulated, The refinement converged to a final R value of 18.6% for 340 unique reflections in the resolution range 8.0-1.9 Angstrom. A result of the sequence alternation is the al ternation in the nucleotide conformation; guanosine is C3'-endo, syn, and cytidine is C2'-endo, anti, The CpG step phosphodiester conformati on is the same as Z(I) or Z(II), whereas that of the GpC step phosphod iester is ''intermediate'' in the sense that zeta (O3'-P bond) is the same as Z(II) but alpha (P-O5' bond) is the same as Z(I). The duplexes generated from the dinucleotide asymmetric unit are stacked one on to p of the other in the crystal to form an infinite pseudocontinuous hel ix, This renders it a quasi-polymerlike structure that has assumed the Z-DNA conformation further strengthened by the long inner Z-forming s tretch d(CG)(4). An interesting feature of the structure is the presen ce of water strings in both the major and the minor grooves, In the mi nor groove the cytosine carbonyl oxygen atoms of the GpC and CpG steps are cross-bridged by water molecules that are not themselves hydrogen bonded but are enclosed by the water rings in the mouth of the minor groove. In the major groove three independent water molecules form a z igzagging continuous water string that runs throughout the duplex.