C. Ban et M. Sundaralingam, CRYSTAL-STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION .2., Biophysical journal, 71(3), 1996, pp. 1222-1227
The crystal structure of the alternating 5'-purine start decamer d(GCG
CGCGCGC) was found to be in the left-handed Z-DNA conformation. Inasmu
ch as the A . T base pair is known to resist Z-DNA formation, we subst
ituted A . T base pairs in the dyad-related positions of the decamer d
uplex. The alternating self-complementary decamer d(GCACGCGTGC) crysta
llizes in a different hexagonal space group, P6(1)22, with very differ
ent unit cell dimensions a = b = 38.97 and c = 77.34 Angstrom compared
with the all-G . C alternating decamer, The A . T-containing decamer
has one strand in the asymmetric unit, and because it is isomorphous t
o some other A-DNA decamers it was considered also to be right-handed,
The structure was refined, starting with the atomic coordinates of th
e A-DNA decamer d(GCGGGCCCGC), by use of 2491 unique reflections out t
o 1.9-Angstrom resolution. The refinement converged to an R value of 1
8.6% for a total of 202 nucleotide atoms and 32 water molecules. This
research further demonstrates that A . T base pairs not only resist th
e formation of Z-DNA but can also assist the formation of A-DNA by swi
tching the helix handedness when the oligomer starts with a 5'-purine:
also, the length of the inner Z-DNA stretch (d(CG)(n)) is reduced fro
m an octamer to a tetramer, It may be noted that these oligonucleotide
properties are in crystals and not necessarily in solutions.