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| | {{STRUCTURE_1d16| PDB=1d16 | SCENE= }} | | {{STRUCTURE_1d16| PDB=1d16 | SCENE= }} |
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| - | '''STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS'''
| + | ===STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS=== |
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| - | ==Overview==
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| - | 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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_2299669}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 2299669 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_2299669}} |
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| | ==About this Structure== | | ==About this Structure== |
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| | [[Category: Single strand]] | | [[Category: Single strand]] |
| | [[Category: Z-dna stem]] | | [[Category: Z-dna stem]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:20:01 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:01:30 2008'' |
Revision as of 19:01, 30 June 2008
Template:STRUCTURE 1d16
STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS
Template:ABSTRACT PUBMED 2299669
About this Structure
Full crystallographic information is available from 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:2299669
Page seeded by OCA on Mon Jun 30 22:01:30 2008
