Crystal structures of the two isomorphous A-DNA decamers d(GTACGCGTAC) and d(GGCCGCGGCC)

Abstract

To study the effect of sequence oil DNA structure, the two decamer crystal structures one alternating, d(GTACGCGTAC), and the other non-alternating, d(GGCCGCGGCC), were solved. Crystals of both decamers belong to the hexagonal space group P6(1)22, with one strand in the asymmetric unit. The unit cell constants of the alternating decamer are a = b 39.26 angstrom, c = 77.70 angstrom. The structure was refined with 1,828 reflections from 8.0 to 2.0 angstrom resolution to an R value of 21.3% with all DNA atoms and 63 water molecules. The isomorphous non-alternating decamer had unit cell dimensions of a = b = 39.05 angstrom, c = 82.15 angstrom. The structure was refined with 2,423 reflections from 8.0 to 2.0 angstrom resolution to a final R value of 22.2% for all DNA atoms and 65 water molecules. Although the average helical parameters of the decamers are typical of A-DNAs, there are some minor differences between them. The helical twist, rise, x-displacement, inclination and roll alternate in the alternating decamer, but do not in the non-alternating decamer. The backbone conformations in both structures show some differences; the residue G(7) of the alternating decamer is trans for alpha and gamma while the trans conformations are observed at the residue G(8) of the non-alternating decamer.