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1c2q

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[[Image:1c2q.png|left|200px]]
 
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==SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC THYMIDINE AND POLARITY REVERSALS==
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The line below this paragraph, containing "STRUCTURE_1c2q", creates the "Structure Box" on the page.
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<StructureSection load='1c2q' size='340' side='right'caption='[[1c2q]]' 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'>[[1c2q]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C2Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C2Q 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=T3P:THYMIDINE-3-PHOSPHATE'>T3P</scene></td></tr>
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{{STRUCTURE_1c2q| PDB=1c2q | 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=1c2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c2q OCA], [https://pdbe.org/1c2q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c2q RCSB], [https://www.ebi.ac.uk/pdbsum/1c2q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c2q 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 report the thermodynamic and structural properties of an alpha-containing DNA.RNA nonamer hybrid duplex, d(ATGG-3'-3'-alphaT-5'-5'-GCTC).r(gagcaccau). The RNA strand corresponds to the core of the initiation sequence for the transcript of the erbB-2 oncogene. The tandem anomeric and polarity changes in the DNA strand result in a slight decrease in thermostability (DeltaT(m) = -2.8 degrees C) compared to the unmodified control hybrid. The three-dimensional solution structure determination of the alpha-containing DNA.RNA hybrid, conducted via restrained molecular dynamics using interproton distance (nuclear Overhauser enhancement) and furanose ring torsion angle (J-based) restraints, converged to a final ensemble of structures from unique starting models. In agreement with hyperchromicity and circular dichroism data, the final average structure derived from this ensemble is consistent with an overall A-like motif featuring Watson-Crick base pairing and base stacking across the entire sequence, albeit with localized B-like traits within the DNA strand. Comparative pseudorotation analyses of the J-coupling data for this hybrid and its unmodified control reveal a surprising increase in S-puckering for two nucleotides immediately upstream of the 3'-3' linkage, and the associated narrowing of the minor groove in this portion of the hybrid. Other structural perturbations are localized to and diagnostic of the central alpha-nucleotide and juxtaposed polarity reversals. The structural information presented here has direct relevance to the design of future antisense oligonucleotides composed of these modifications.
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===SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC THYMIDINE AND POLARITY REVERSALS===
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Solution structure of a DNA.RNA hybrid containing an alpha-anomeric thymidine and polarity reversals: d(ATGG-3'-3'-alphaT-5'-5'-GCTC). r(gagcaccau).,Aramini JM, Germann MW Biochemistry. 1999 Nov 23;38(47):15448-58. PMID:10569927<ref>PMID:10569927</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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<div class="pdbe-citations 1c2q" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 10569927 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_10569927}}
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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=1C2Q OCA].
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[[Category: Aramini JM]]
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[[Category: Germann MW]]
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==Reference==
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Solution structure of a DNA.RNA hybrid containing an alpha-anomeric thymidine and polarity reversals: d(ATGG-3'-3'-alphaT-5'-5'-GCTC). r(gagcaccau)., Aramini JM, Germann MW, Biochemistry. 1999 Nov 23;38(47):15448-58. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10569927 10569927]
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[[Category: Aramini, J M.]]
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[[Category: Germann, M W.]]
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[[Category: 3'-3'/5'-5' phosphodiester linkage]]
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[[Category: Alphat-anomeric thymidine]]
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[[Category: Dna/rna hybrid]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 20:07:50 2008''
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Current revision

SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC THYMIDINE AND POLARITY REVERSALS

PDB ID 1c2q

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