1exl

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[[Image:1exl.gif|left|200px]]
 
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==STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING THE CARBOCYCLIC NUCLEOTIDE ANALOG: 2'-DEOXYARISTEROMYCIN==
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The line below this paragraph, containing "STRUCTURE_1exl", creates the "Structure Box" on the page.
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<StructureSection load='1exl' size='340' side='right'caption='[[1exl]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1exl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EXL 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">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2AR:2-DEOXYARISTEROMYCIN-5-PHOSPHATE'>2AR</scene></td></tr>
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{{STRUCTURE_1exl| PDB=1exl | SCENE= }}
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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=1exl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1exl OCA], [https://pdbe.org/1exl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1exl RCSB], [https://www.ebi.ac.uk/pdbsum/1exl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1exl ProSAT]</span></td></tr>
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</table>
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'''STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING THE CARBOCYCLIC NUCLEOTIDE ANALOG: 2'-DEOXYARISTEROMYCIN'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Johnson F]]
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2'-deoxyaristeromycin (dAr) is a nucleoside analogue that is resistant to the action of DNA glycosylases. High-resolution NMR spectroscopy and molecular dynamics simulations were used to determine the three-dimensional structure of an 11-mer DNA containing a single dAr.T base pair at its center. Analysis of the spectra revealed the existence of a right-handed duplex in solution, stabilized by Watson-Crick hydrogen bonding and base-stacking interactions. The carbocyclic sugar adopted a C1'-exo conformation and sugars of the 3'-flanking base pair had puckers in the O4'-endo range. The dAr.T base pair was mildly propeller twisted, and the dAr analogue showed a positive roll with the 3'-flanking base. Our findings indicate that the observed resistance of dAr-containing oligodeoxynucleotides to the catalytic action of DNA glycosylases relates to its electronic properties rather than structure, and validate the use of dAr and related carbocyclic nucleoside analogues for biological and structure/function relationship studies.
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[[Category: Marumoto R]]
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[[Category: Smirnov S]]
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==About this Structure==
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[[Category: De los Santos C]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EXL OCA].
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==Reference==
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Structure of an 11-mer DNA duplex containing the carbocyclic nucleotide analog: 2'-deoxyaristeromycin., Smirnov S, Johnson F, Marumoto R, de los Santos C, J Biomol Struct Dyn. 2000 Jun;17(6):981-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10949165 10949165]
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[[Category: Johnson, F.]]
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[[Category: Marumoto, R.]]
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[[Category: Santos, C de los.]]
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[[Category: Smirnov, S.]]
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[[Category: 2'-deoxyaristeromycin]]
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[[Category: Dna]]
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[[Category: Modified nucleotide]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 15:38:30 2008''
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Current revision

STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING THE CARBOCYCLIC NUCLEOTIDE ANALOG: 2'-DEOXYARISTEROMYCIN

PDB ID 1exl

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