1d80: Difference between revisions

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==CRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE DUPLEX CONTAINING G.G BASE-PAIRS: THE INFLUENCE OF MISPAIRING ON DNA BACKBONE CONFORMATION==
The line below this paragraph, containing "STRUCTURE_1d80", creates the "Structure Box" on the page.
<StructureSection load='1d80' size='340' side='right'caption='[[1d80]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1d80]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D80 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D80 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d80 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d80 OCA], [https://pdbe.org/1d80 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d80 RCSB], [https://www.ebi.ac.uk/pdbsum/1d80 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d80 ProSAT]</span></td></tr>
{{STRUCTURE_1d80|  PDB=1d80  |  SCENE= }}
</table>
 
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'''CRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE DUPLEX CONTAINING G.G BASE-PAIRS: THE INFLUENCE OF MISPAIRING ON DNA BACKBONE CONFORMATION'''
</StructureSection>
 
[[Category: Large Structures]]
 
[[Category: Edwards KJ]]
==Overview==
[[Category: Jenkins TC]]
The structure of the G.G mispaired dodecanucleotide d(CGCGAATTGGCG)2 has been solved by x-ray crystallography and refined to an R factor of 18.8% at 2.2 A resolution for 3513 reflections. The dodecamer crystallizes as a B-type DNA double helix. It contains two G(anti).G(syn) base pairs--i.e., G-4/G-16(anti).G-21/G-9(syn). The Hoogsteen base pairing involves atoms O-6 and N-7 of the guanine in the syn conformation with atoms N-1 and N-2 of the anti-paired purine. One G.G base pair has a bifurcated hydrogen bond between G-4(N-1)...G-21(N-7) and G-4(N-1)...G-21(O-6). There is little overall structural distortion of the double helix induced as a consequence of the mispairing. The helical width is significantly increased by comparison with the structure of the native duplex, and the minor groove width in the 5'-AATT region is decreased. The G.G base pairing induces high-BII phosphate conformations at residues G-9 and T-20 in addition to more normal BII conformations at G-10 and G-22. It is suggested that these backbone aberrations provide signals for the facile repairability of G.G mispairs in DNA.
[[Category: Neidle S]]
 
[[Category: Skelly JV]]
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D80 OCA].  
 
==Reference==
Crystal structure of an oligonucleotide duplex containing G.G base pairs: influence of mispairing on DNA backbone conformation., Skelly JV, Edwards KJ, Jenkins TC, Neidle S, Proc Natl Acad Sci U S A. 1993 Feb 1;90(3):804-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8430089 8430089]
[[Category: Edwards, K J.]]
[[Category: Jenkins, T C.]]
[[Category: Neidle, S.]]
[[Category: Skelly, J V.]]
[[Category: B-dna]]
[[Category: Double helix]]
[[Category: Mismatched]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:33:11 2008''

Latest revision as of 09:50, 7 February 2024

CRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE DUPLEX CONTAINING G.G BASE-PAIRS: THE INFLUENCE OF MISPAIRING ON DNA BACKBONE CONFORMATIONCRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE DUPLEX CONTAINING G.G BASE-PAIRS: THE INFLUENCE OF MISPAIRING ON DNA BACKBONE CONFORMATION

Structural highlights

1d80 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1d80, resolution 2.20Å

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