1d16

[[Image:1d16.gif|left|200px]]<br /><applet load="1d16" size="450" color="white" frame="true" align="right" spinBox="true"

caption="1d16, resolution 2.100&Aring;" />

'''STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS'''<br />

==Overview==

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 Structure==

1D16 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D16 OCA].

 

==Reference==

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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2299669 2299669]

[[Category: Protein complex]]

[[Category: Chattopadhyaya, R.]]

[[Category: Dickerson, R.E.]]

[[Category: Grzeskowiak, K.]]

[[Category: hairpin loop]]

[[Category: single strand]]

[[Category: z-dna stem]]