2icz

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[[Image:2icz.png|left|200px]]
 
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==NMR Structures of the Expanded DNA 10bp xTGxTAxCxGCxAxGT:xACTxGCGxTAxCA==
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The line below this paragraph, containing "STRUCTURE_2icz", creates the "Structure Box" on the page.
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<StructureSection load='2icz' size='340' side='right'caption='[[2icz]]' 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'>[[2icz]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ICZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ICZ 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=XAE:3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-3H-IMIDAZO[4,5-G]QUINAZOLIN-8-AMINE'>XAE</scene>, <scene name='pdbligand=XCS:(1R)-1-(4-AMINO-6-METHYL-2-OXO-1,2-DIHYDROQUINAZOLIN-8-YL)-1,4-ANHYDRO-2-DEOXY-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>XCS</scene>, <scene name='pdbligand=XGA:6-AMINO-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-3,7-DIHYDRO-8H-IMIDAZO[4,5-G]QUINAZOLIN-8-ONE'>XGA</scene>, <scene name='pdbligand=XTY:(1R)-1,4-ANHYDRO-2-DEOXY-1-(6-METHYL-2,4-DIOXO-1,2,3,4-TETRAHYDROQUINAZOLIN-8-YL)-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>XTY</scene></td></tr>
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{{STRUCTURE_2icz| PDB=2icz | 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=2icz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2icz OCA], [https://pdbe.org/2icz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2icz RCSB], [https://www.ebi.ac.uk/pdbsum/2icz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2icz ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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We describe the NMR-derived solution structure of the double-helical form of a designed eight-base genetic pairing system, termed xDNA. The benzo-homologous xDNA design contains base pairs that are wider than natural DNA pairs by ca. 2.4 A (the width of a benzene ring). The eight component bases of this xDNA helix are A, C, G, T, xA, xT, xC, and xG. The structure was solved in aqueous buffer using 1D and 2D NMR methods combined with restrained molecular dynamics. The data show that the decamer duplex is right-handed and antiparallel, and hydrogen-bonded in a way analogous to that of Watson-Crick DNA. The sugar-phosphate backbone adopts a regular conformation similar to that of B-form DNA, with small dihedral adjustments due to the larger circumference of the helix. The grooves are much wider and more shallow than those of B-form DNA, and the helix turn is slower, with ca. 12 base pairs per 360 degrees turn. There is an extensive intra- and interstrand base stacking surface area, providing an explanation for the greater stability of xDNA relative to natural DNA. There is also evidence for greater motion in this structure compared to a previous two-base-expanded helix; possible chemical and structural reasons for this are discussed. The results confirm paired self-assembly of the designed xDNA system. This suggests the possibility that other genetic system structures besides the natural one might be functional in encoding information and transferring it to new complementary strands.
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===NMR Structures of the Expanded DNA 10bp xTGxTAxCxGCxAxGT:xACTxGCGxTAxCA===
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Toward a designed, functioning genetic system with expanded-size base pairs: solution structure of the eight-base xDNA double helix.,Lynch SR, Liu H, Gao J, Kool ET J Am Chem Soc. 2006 Nov 15;128(45):14704-11. PMID:17090058<ref>PMID:17090058</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_17090058}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2icz" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 17090058 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17090058}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ICZ OCA].
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[[Category: Lynch SR]]
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==Reference==
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Toward a designed, functioning genetic system with expanded-size base pairs: solution structure of the eight-base xDNA double helix., Lynch SR, Liu H, Gao J, Kool ET, J Am Chem Soc. 2006 Nov 15;128(45):14704-11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17090058 17090058]
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[[Category: Lynch, S R.]]
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[[Category: Expanded dna]]
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[[Category: Xdna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 09:03:47 2008''
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Current revision

NMR Structures of the Expanded DNA 10bp xTGxTAxCxGCxAxGT:xACTxGCGxTAxCA

PDB ID 2icz

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