|
|
| (10 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| [[Image:260d.gif|left|200px]]
| |
|
| |
|
| <!--
| | ==CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION-PART II== |
| The line below this paragraph, containing "STRUCTURE_260d", creates the "Structure Box" on the page.
| | <StructureSection load='260d' size='340' side='right'caption='[[260d]], [[Resolution|resolution]] 1.90Å' scene=''> |
| You may change the PDB parameter (which sets the PDB file loaded into the applet)
| | == Structural highlights == |
| or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| | <table><tr><td colspan='2'>[[260d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=260D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=260D FirstGlance]. <br> |
| or leave the SCENE parameter empty for the default display.
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</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=260d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=260d OCA], [https://pdbe.org/260d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=260d RCSB], [https://www.ebi.ac.uk/pdbsum/260d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=260d ProSAT]</span></td></tr> |
| {{STRUCTURE_260d| PDB=260d | SCENE= }}
| | </table> |
| | | __TOC__ |
| '''CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION-PART II'''
| | </StructureSection> |
| | | [[Category: Large Structures]] |
| | | [[Category: Ban C]] |
| ==Overview==
| | [[Category: Sundaralingam M]] |
| 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.
| |
| | |
| ==About this Structure== | |
| Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=260D OCA]. | |
| | |
| ==Reference== | |
| Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II., Ban C, Sundaralingam M, Biophys J. 1996 Sep;71(3):1222-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8873996 8873996]
| |
| [[Category: Ban, C.]] | |
| [[Category: Sundaralingam, M.]] | |
| [[Category: A-dna]] | |
| [[Category: Double helix]] | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 18:24:15 2008''
| |
