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Bulletin of the Korean Chemical Society (BKCS)

ISSN 0253-2964(Print)
ISSN 1229-5949(Online)
Volume 27, Number 4
BKCSDE 27(4)
April 20, 2006 

 
Title
Crystal Structures of the Two Isomorphous A-DNA Decamers d(GTACGCGTAC) and d(GGCCGCGGCC)
Author
Taegyun Kim, Taek Hun Kwon, Hyesun Jung, Ja Kang Ku, Muttaiya Sundaralingam, Changill Ban*
Keywords
X-Ray crystallography, A-DNA decamer, Conformational flexibility, Helical parameter
Abstract
To study the effect of sequence on 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 P6122, with one strand in the asymmetric unit. The unit cell constants of the alternating decamer are a = b = 39.26 A, c = 77.70 A. The structure was refined with 1,828 reflections from 8.0 to 2.0 A 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 A, c = 82.15 A. The structure was refined with 2,423 reflections from 8.0 to 2.0 A 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 ADNAs, 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 α and γ while the trans conformations are observed at the residue G(8) of the non-alternating decamer.
Page
568 - 572
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