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New page: left|200px<br /><applet load="1c2q" size="450" color="white" frame="true" align="right" spinBox="true" caption="1c2q" /> '''SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTA...
 
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[[Image:1c2q.gif|left|200px]]<br /><applet load="1c2q" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1c2q" />
'''SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC THYMIDINE AND POLARITY REVERSALS'''<br />


==Overview==
==SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC THYMIDINE AND POLARITY REVERSALS==
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.
<StructureSection load='1c2q' size='340' side='right'caption='[[1c2q]]' scene=''>
== Structural highlights ==
<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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<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>
<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>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==About this Structure==
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>
1C2Q is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1C2Q OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=10569927 10569927]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 1c2q" style="background-color:#fffaf0;"></div>
[[Category: Aramini, J.M.]]
== References ==
[[Category: Germann, M.W.]]
<references/>
[[Category: 3'-3'/5'-5' phosphodiester linkages]]
__TOC__
[[Category: alphat-anomeric thymidine]]
</StructureSection>
[[Category: dna/rna hybrid]]
[[Category: Large Structures]]
 
[[Category: Aramini JM]]
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 00:58:19 2007''
[[Category: Germann MW]]
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