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==INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES==
The line below this paragraph, containing "STRUCTURE_1d3x", creates the "Structure Box" on the page.
<StructureSection load='1d3x' size='340' side='right'caption='[[1d3x]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<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>
or leave the SCENE parameter empty for the default display.
</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='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>
{{STRUCTURE_1d3x| PDB=1d3x  |  SCENE= }}
</table>
 
<div style="background-color:#fffaf0;">
'''INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES'''
== Publication Abstract from PubMed ==
 
 
==Overview==
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.


==About this Structure==
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>
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D3X OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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:[http://www.ncbi.nlm.nih.gov/pubmed/9558314 9558314]
</div>
[[Category: Feigon, J.]]
<div class="pdbe-citations 1d3x" style="background-color:#fffaf0;"></div>
[[Category: Phipps, A K.]]
== References ==
[[Category: Schultze, P.]]
<references/>
[[Category: Tarkoy, M.]]
__TOC__
[[Category: Oligonucleotide]]
</StructureSection>
[[Category: Rna third strand]]
[[Category: Large Structures]]
[[Category: Triplex]]
[[Category: Feigon J]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:25:28 2008''
[[Category: Phipps AK]]
[[Category: Schultze P]]
[[Category: Tarkoy M]]

Latest revision as of 14:42, 22 November 2023

INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURESINTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES

Structural highlights

1d3x is a 3 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Tarkoy M, Phipps AK, Schultze P, Feigon J. Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT). Biochemistry. 1998 Apr 28;37(17):5810-9. PMID:9558314 doi:http://dx.doi.org/10.1021/bi9728102
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