1d16
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STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS
OverviewOverview
The synthetic DNA oligomer C-G-C-G-C-G-T-T-T-T-C-G-C-G-C-G crystallizes as, a Z-DNA hexamer, capped at one end by a T4 loop. The crystals are, monoclinic, space group C2, with a = 57.18 A, b = 21.63 A, c = 36.40 A, beta = 95.22 degrees, and one hairpin molecule per asymmetric unit. The, structure of the z-hexamer stem was determined by molecular replacement, and the T4 loop was positioned by difference map methods. The final R, factor at 2.1 A resolution for hairpin plus 70 water molecules is 20% for, 2 sigma data, with a root-mean-square error of 0.26 A. The (C-G)3 stem, resembles the free Z-DNA hexamer with minor crystal packing effects. The, T4 loop differs from that observed on a B-DNA stem in solution, or in, longer loops in tRNA, in that it shows intraloop and intermolecular, interactions rather than base stacking on the final base-pair of the stem., Bases T7, T8 and T9 stack with one another and with the sugar of T7. Two, T10 bases from different molecules stack between the C1-G12 terminal, base-pairs of a third and fourth molecule, to simulate a T.T "base-pair"., Distances between thymine N and O atoms suggest that the two thymine bases, are hydrogen bonded, and a keto-enol tautomer pair is favored over, disordered keto-keto wobble pairs. The hairpin molecules pack in the, crystal in herringbone columns in a manner that accounts well for the, observed relative crystal growth rates in a, b and c directions. Hydration, seems to be most extensive around the phosphate groups, with lesser, hydration within the grooves.
About this StructureAbout this Structure
1D16 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
Structure of a T4 hairpin loop on a Z-DNA stem and comparison with A-RNA and B-DNA loops., Chattopadhyaya R, Grzeskowiak K, Dickerson RE, J Mol Biol. 1990 Jan 5;211(1):189-210. PMID:2299669
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