1d3x: Difference between revisions
New page: left|200px<br /><applet load="1d3x" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d3x" /> '''INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTUR... |
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[[Image:1d3x.gif|left|200px]]<br /><applet load="1d3x" size=" | [[Image:1d3x.gif|left|200px]]<br /><applet load="1d3x" size="350" color="white" frame="true" align="right" spinBox="true" | ||
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'''INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES'''<br /> | '''INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES'''<br /> | ||
==Overview== | ==Overview== | ||
A DNA molecule was designed and synthesized with three octanucleotide | 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. | ||
==About this Structure== | ==About this Structure== | ||
1D3X 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:// | 1D3X 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3X OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Feigon, J.]] | [[Category: Feigon, J.]] | ||
[[Category: Phipps, A | [[Category: Phipps, A K.]] | ||
[[Category: Schultze, P.]] | [[Category: Schultze, P.]] | ||
[[Category: Tarkoy, M.]] | [[Category: Tarkoy, M.]] | ||
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[[Category: triplex]] | [[Category: triplex]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:12:42 2008'' | ||
Revision as of 13:12, 21 February 2008
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INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES
OverviewOverview
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.
About this StructureAbout this Structure
1D3X is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
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
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