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| | ==STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS== |
| The line below this paragraph, containing "STRUCTURE_1bna", creates the "Structure Box" on the page.
| | <StructureSection load='1bna' size='340' side='right'caption='[[1bna]], [[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'>[[1bna]] is a 2 chain structure. The November 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''DNA'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_11 10.2210/rcsb_pdb/mom_2001_11]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BNA 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=1bna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bna OCA], [https://pdbe.org/1bna PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bna RCSB], [https://www.ebi.ac.uk/pdbsum/1bna PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bna ProSAT]</span></td></tr> |
| {{STRUCTURE_1bna| PDB=1bna | SCENE= }}
| | </table> |
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| '''STRUCTURE OF A B-DNA DODECAMER. CONFORMATION AND DYNAMICS'''
| | ==See Also== |
| | | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| | | __TOC__ |
| ==Overview==
| | </StructureSection> |
| The crystal structure of the synthetic DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG) has been refined to a residual error of R = 17.8% at 1.9-A resolution (two-sigma data). The molecule forms slightly more than one complete turn of right-handed double-stranded B helix. The two ends of the helix overlap and interlock minor grooves with neighboring molecules up and down a 2(1) screw axis, producing a 19 degrees bend in helix axis over the 11-base-pair steps of the dodecamer. In the center of the molecule, where perturbation is least, the helix has a mean rotation of 36.9 degrees per step, or 9.8 base pairs per turn. The mean propeller twist (total dihedral angle between base planes) between A . T base pairs in the center of the molecule is 17.3 degrees, and that between C . G pairs on the two ends averages 11.5 degrees. Individual deoxyribose ring conformations as measured by the C5'-C4'-C3'-O3' torsion angle delta, exhibit an approximately Gaussian distribution centered around the C1'-exo position with delta avg = 123 degrees and a range of 79 degrees to 157 degrees. Purine sugars cluster at high delta values, and pyrimidine sugars cluster at lower delta. A tendency toward 2-fold symmetry in sugar conformation about the center of the molecule is detectable in spite of the destruction of ideal 2-fold symmetry by the molecular bending. More strikingly, sugar conformations of paired based appear to follow a "principle of anticorrelation," with delta values lying approximately the same distance to either side of the center value, delta = 123 degrees. This same anticorrelation is also observed in other DNA and DNA . RNA structures.
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| ==About this Structure== | |
| The following page contains interesting information on the relation of 1BNA with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb23_1.html DNA]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BNA OCA].
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| ==Reference==
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| Structure of a B-DNA dodecamer: conformation and dynamics., Drew HR, Wing RM, Takano T, Broka C, Tanaka S, Itakura K, Dickerson RE, Proc Natl Acad Sci U S A. 1981 Apr;78(4):2179-83. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/6941276 6941276]
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| [[Category: DNA]] | | [[Category: DNA]] |
| [[Category: Broka, C.]] | | [[Category: Large Structures]] |
| [[Category: Dickerson, R E.]] | | [[Category: RCSB PDB Molecule of the Month]] |
| [[Category: Drew, H R.]] | | [[Category: Broka C]] |
| [[Category: Itakura, K.]] | | [[Category: Dickerson RE]] |
| [[Category: Takano, T.]] | | [[Category: Drew HR]] |
| [[Category: Tanaka, S.]] | | [[Category: Itakura K]] |
| [[Category: Wing, R M.]] | | [[Category: Takano T]] |
| [[Category: B-dna]] | | [[Category: Tanaka S]] |
| [[Category: Double helix]] | | [[Category: Wing RM]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 11:43:38 2008''
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