260D

CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION-PART II

Summary for 260D

• Entry DOI: 10.2210/pdb260d/pdb
• Descriptor: DNA (5'-D(*GP*CP*AP*CP*GP*CP*GP*TP*GP*C)-3') (2 entities in total)
• Functional Keywords: a-dna, double helix, dna
• Total number of polymer chains: 1
• Total formula weight: 3045.99

Authors

Ban, C.,Sundaralingam, M. (deposition date: 1996-05-21, release date: 1996-06-27, Last modification date: 2024-02-14)

Primary citation

Ban, C.,Sundaralingam, M.
Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II.
Biophys.J., 71:1222-1227, 1996

PubMed Abstract: The crystal structure of the alternating 5'-purine start decamer d(GCGCGCGCGC) was found to be in the left-handed Z-DNA conformation. Inasmuch as the A.T base pair is known to resist Z-DNA formation, we substituted A.T base pairs in the dyad-related positions of the decamer duplex. The alternating self-complementary decamer d(GCACGCGTGC) crystallizes in a different hexagonal space group, P6(1)22, with very different unit cell dimensions a = b = 38.97 and c = 77.34 A 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 to some other A-DNA decamers it was considered also to be right-handed. The structure was refined, starting with the atomic coordinates of the A-DNA decamer d(GCGGGCCCGC), by use of 2491 unique reflections out to 1.9-A resolution. The refinement converged to an R value of 18.6% for a total of 202 nucleotide atoms and 32 water molecules. This research further demonstrates that A.T base pairs not only resist the formation of Z-DNA but can also assist the formation of A-DNA by switching 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 from an octamer to a tetramer. It may be noted that these oligonucleotide properties are in crystals and not necessarily in solutions.

PubMed: 8873996

Experimental method

X-RAY DIFFRACTION (1.9 Å)