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| [[Image:1dn9.gif|left|200px]]<br /><applet load="1dn9" size="450" color="white" frame="true" align="right" spinBox="true"
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| caption="1dn9, resolution 2.200Å" />
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| '''STRUCTURE OF AN ALTERNATING-B DNA HELIX AND ITS RELATIONSHIP TO A-TRACT DNA'''<br />
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| ==Overview== | | ==STRUCTURE OF AN ALTERNATING-B DNA HELIX AND ITS RELATIONSHIP TO A-TRACT DNA== |
| The crystal structure of the synthetic DNA dodecamer CGCATATATGCG has been, solved at 2.2-A resolution. Its central 6 base pairs adopt the, alternating-B-DNA helix structure proposed nearly a decade ago. This, alternating poly(AT) structure contrasts with the four known examples of, what can be termed a poly(A) subfamily of B-DNA structures: CGCAAAAAAGCG, CGCAAATTTGCG, CGCGAATTCGCG, and CGCGAATTbrCGCG, their defining, characteristic being a succession of two or more adenines along one, strand, in a region of 4 or more A.T base pairs. All five helices show a, characteristically narrow minor groove in their AT centers, but the mean, propeller twist at A.T base pairs is lower in the alternating poly(AT), helix than in the poly(A) subfamily of helices. Three general principles, emerge from x-ray analyses of B-DNA oligonucleotides: (i) GC and, mixed-sequence B-DNA have a wide minor groove, whereas the minor groove is, narrow in heteropolymer or homopolymer AT sequences. (ii) G.C base pairs, have low propeller twist; A.T pairs can adopt a high propeller twist but, need not do so. A high propeller twist can be stabilized by cross-strand, hydrogen bonds in the major or minor groove, examples being the minor, groove bonds seen in CCAAGATTGG and the major groove bonds that can, accompany AA sequences in the poly(A) family. (iii) Homopolymer poly(A), tracts may be stiffer than are alternating AT or general-sequence DNA, because of these cross-strand major groove hydrogen bonds. Poly(A) tracts, appear internally unbent, but bends may occur at junctions with, mixed-sequence DNA because of differences in propeller twist, base pair, inclination, and base stacking on the two sides of the junction. Bending, occurs most easily via base roll, favoring compression of the broad major, groove.
| | <StructureSection load='1dn9' size='340' side='right'caption='[[1dn9]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | | == Structural highlights == |
| ==About this Structure== | | <table><tr><td colspan='2'>[[1dn9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DN9 FirstGlance]. <br> |
| 1DN9 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=1DN9 OCA].
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dn9 OCA], [https://pdbe.org/1dn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dn9 RCSB], [https://www.ebi.ac.uk/pdbsum/1dn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dn9 ProSAT]</span></td></tr> |
| ==Reference== | | </table> |
| Structure of an alternating-B DNA helix and its relationship to A-tract DNA., Yoon C, Prive GG, Goodsell DS, Dickerson RE, Proc Natl Acad Sci U S A. 1988 Sep;85(17):6332-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=3413099 3413099]
| | __TOC__ |
| [[Category: Protein complex]] | | </StructureSection> |
| [[Category: Dickerson, R.E.]] | | [[Category: Large Structures]] |
| [[Category: Yoon, C.]] | | [[Category: Dickerson RE]] |
| [[Category: b-dna]] | | [[Category: Yoon C]] |
| [[Category: double helix]] | |
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| ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:22:11 2007''
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