1d3x
From Proteopedia
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| - | [[Image:1d3x.gif|left|200px]]<br /><applet load="1d3x" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1d3x" /> | ||
| - | '''INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES'''<br /> | ||
| - | == | + | ==INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES== |
| + | <StructureSection load='1d3x' size='340' side='right'caption='[[1d3x]]' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1d3x]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D3X 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d3x OCA], [https://pdbe.org/1d3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d3x RCSB], [https://www.ebi.ac.uk/pdbsum/1d3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d3x ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
A DNA molecule was designed and synthesized with three octanucleotide stretches linked by two hexakis(ethylene glycol) chains to form an intramolecular triplex in solution. The structural data obtained from a series of NMR NOESY spectra yielded interproton distances, and COSY experiments provided dihedral angle information for analysis of deoxyribose ring pucker. Using distance geometry followed by simulated annealing with restrained molecular dynamics and relaxation matrix refinement, a well-refined ensemble of conformations was calculated. Although some NOE cross-peaks involving protons of the hexakis(ethylene glycol) linker could be identified, most could not be assigned and the conformations of the linkers were not determined. The deoxyribose conformations are predominantly of the S type, except for the protonated cytosine residues in the third strand which show hybrid N and S character. Overall, the duplex part of the molecule resembles a B-DNA double helix with the third strand bound in its major groove by Hoogsteen hydrogen bonds. This structure provides a basis for comparison with triplexes containing noncanonical or nonnatural nucleotides. | A DNA molecule was designed and synthesized with three octanucleotide stretches linked by two hexakis(ethylene glycol) chains to form an intramolecular triplex in solution. The structural data obtained from a series of NMR NOESY spectra yielded interproton distances, and COSY experiments provided dihedral angle information for analysis of deoxyribose ring pucker. Using distance geometry followed by simulated annealing with restrained molecular dynamics and relaxation matrix refinement, a well-refined ensemble of conformations was calculated. Although some NOE cross-peaks involving protons of the hexakis(ethylene glycol) linker could be identified, most could not be assigned and the conformations of the linkers were not determined. The deoxyribose conformations are predominantly of the S type, except for the protonated cytosine residues in the third strand which show hybrid N and S character. Overall, the duplex part of the molecule resembles a B-DNA double helix with the third strand bound in its major groove by Hoogsteen hydrogen bonds. This structure provides a basis for comparison with triplexes containing noncanonical or nonnatural nucleotides. | ||
| - | + | Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT).,Tarkoy M, Phipps AK, Schultze P, Feigon J Biochemistry. 1998 Apr 28;37(17):5810-9. PMID:9558314<ref>PMID:9558314</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | [[Category: | + | <div class="pdbe-citations 1d3x" style="background-color:#fffaf0;"></div> |
| - | [[Category: Feigon | + | == References == |
| - | [[Category: Phipps | + | <references/> |
| - | [[Category: Schultze | + | __TOC__ |
| - | [[Category: Tarkoy | + | </StructureSection> |
| - | + | [[Category: Large Structures]] | |
| - | + | [[Category: Feigon J]] | |
| - | + | [[Category: Phipps AK]] | |
| - | + | [[Category: Schultze P]] | |
| - | + | [[Category: Tarkoy M]] | |
Current revision
INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES
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