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1oo7

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[[Image:1oo7.gif|left|200px]]
 
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==DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURINE-RICH RNA STRAND, NMR, 4 STRUCTURES==
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The line below this paragraph, containing "STRUCTURE_1oo7", creates the "Structure Box" on the page.
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<StructureSection load='1oo7' size='340' side='right'caption='[[1oo7]]' 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'>[[1oo7]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OO7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OO7 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=5PC:5(1-PROPYNYL)-2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>5PC</scene>, <scene name='pdbligand=PDU:5(1-PROPYNYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>PDU</scene></td></tr>
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{{STRUCTURE_1oo7| PDB=1oo7 | 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=1oo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oo7 OCA], [https://pdbe.org/1oo7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oo7 RCSB], [https://www.ebi.ac.uk/pdbsum/1oo7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oo7 ProSAT]</span></td></tr>
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</table>
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'''DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURINE-RICH RNA STRAND, NMR, 4 STRUCTURES'''
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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: Brown T]]
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The addition of the propynyl group at the 5 position of pyrimidine nucleotides is highly stabilising. We have determined the thermodynamic stability of the DNA.RNA hybrid r(GAAGAGAAGC)*d(GC(p)U(p)U(p)C(p)U(p) C(p)U(p)U(p)C) where p is the propynyl group at the 5 position and compared it with that of the unmodified duplex and the effects of methyl substitutions. The incorporation of the propyne group at the 5 position gives rise to a very large stabilisation of the hybrid duplex compared with the analogous 5-Me modification. The duplexes have been characterised by gel electrophoresis and NMR spectroscopy, which indicate that methyl substitutions have a smaller influence on local and global conformation than the propynyl groups. The increased NMR spectral dispersion of the propyne-modified duplex allowed a larger number of experimental restraints to be measured. Restrained molecular dynamics in a fully solvated system showed that the propyne modification leads to substantial conformational rearrangements stabilising a more A-like structure. The propynyl groups occupy a large part of the major groove and make favourable van der Waals interactions with their nearest neighbours and the atoms of the rings. This enhanced overlap may account at least in part for the increased thermodynamic stability. Furthermore, the simulations show a spine of hydration in the major groove as well as in the minor groove involving the RNA hydroxyl groups.
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[[Category: Conn GL]]
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[[Category: Gao D]]
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==About this Structure==
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[[Category: Gyi JI]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OO7 OCA].
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[[Category: Lane AN]]
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[[Category: Trent JO]]
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==Reference==
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The solution structure of a DNA*RNA duplex containing 5-propynyl U and C; comparison with 5-Me modifications., Gyi JI, Gao D, Conn GL, Trent JO, Brown T, Lane AN, Nucleic Acids Res. 2003 May 15;31(10):2683-93. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12736318 12736318]
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[[Category: Brown, T.]]
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[[Category: Conn, G L.]]
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[[Category: Gao, D.]]
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[[Category: Gyi, J I.]]
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[[Category: Lane, A N.]]
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[[Category: Trent, J O.]]
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[[Category: Antisense]]
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[[Category: Dna rna hybrid]]
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[[Category: Purine/pyrimidine-rich strand]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 04:05:40 2008''
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Current revision

DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURINE-RICH RNA STRAND, NMR, 4 STRUCTURES

PDB ID 1oo7

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