1bwg: Difference between revisions
New page: left|200px<br /><applet load="1bwg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bwg" /> '''DNA TRIPLEX WITH 5' AND 3' JUNCTIONS, NMR, 1... |
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== | ==DNA TRIPLEX WITH 5' AND 3' JUNCTIONS, NMR, 10 STRUCTURES== | ||
BACKGROUND: Polypurine x polypyrimidine sequences of DNA can form parallel | <StructureSection load='1bwg' size='340' side='right'caption='[[1bwg]]' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1bwg]] is a 3 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BWG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BWG 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=1bwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bwg OCA], [https://pdbe.org/1bwg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bwg RCSB], [https://www.ebi.ac.uk/pdbsum/1bwg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bwg ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
BACKGROUND: Polypurine x polypyrimidine sequences of DNA can form parallel triple helices via Hoogsteen hydrogen bonds with a third DNA strand that is complementary to the purine strand. The triplex prevents transcription and could therefore potentially be used to regulate specific genes. The determination of the structures of triplex-duplex junctions can help us to understand the structural basis of specificity, and aid in the design of optimal antigene oligonucleotides. RESULTS: The solution structures of the junction triplexes d(GAGAGACGTA)-X-(TACGTCTCTC)-X-(CTCTCT) and d(CTCTCT)-X-(TCTCTCAGTC)-X-(GACTGAGAGA) (where X is bis(octylphosphate) and nucleotides in the triplex regions are underlined) have been solved using nuclear magnetic resonance (NMR) spectroscopy. The structure is characterised by significant changes in the conformation of the purine residues, asymmetry of the 5' and 3' junctions, and variations in groove widths associated with the positive charge of the protonated cytosine residues in the third strand. The thermodynamic stability of triplexes with either a 5' or a 3'CH+ is higher than those with a terminal thymidine. CONCLUSIONS: The observed sequence dependence of the triplex structure, and the distortions of the DNA at the 5' and 3' termini has implications for the design of optimal triplex-forming sequences, both in terms of the terminal bases and the importance of including positive charges in the third strand. Thus, triplex-stabilising ligands might be designed that can discriminate between TA x T-rich and CG x C+-rich sequences that depend not only on charge, but also on local groove widths. This could improve the stabilisation and specificity of antigene triplex formation. | |||
Solution conformation of a parallel DNA triple helix with 5' and 3' triplex-duplex junctions.,Asensio JL, Brown T, Lane AN Structure. 1999 Jan 15;7(1):1-11. PMID:10368268<ref>PMID:10368268</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 1bwg" style="background-color:#fffaf0;"></div> | ||
[[Category: Asensio | == References == | ||
[[Category: Brown | <references/> | ||
[[Category: Lane | __TOC__ | ||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Asensio JL]] | |||
[[Category: Brown T]] | |||
[[Category: Lane AN]] | |||
Latest revision as of 14:37, 22 November 2023
DNA TRIPLEX WITH 5' AND 3' JUNCTIONS, NMR, 10 STRUCTURESDNA TRIPLEX WITH 5' AND 3' JUNCTIONS, NMR, 10 STRUCTURES
Structural highlights
Publication Abstract from PubMedBACKGROUND: Polypurine x polypyrimidine sequences of DNA can form parallel triple helices via Hoogsteen hydrogen bonds with a third DNA strand that is complementary to the purine strand. The triplex prevents transcription and could therefore potentially be used to regulate specific genes. The determination of the structures of triplex-duplex junctions can help us to understand the structural basis of specificity, and aid in the design of optimal antigene oligonucleotides. RESULTS: The solution structures of the junction triplexes d(GAGAGACGTA)-X-(TACGTCTCTC)-X-(CTCTCT) and d(CTCTCT)-X-(TCTCTCAGTC)-X-(GACTGAGAGA) (where X is bis(octylphosphate) and nucleotides in the triplex regions are underlined) have been solved using nuclear magnetic resonance (NMR) spectroscopy. The structure is characterised by significant changes in the conformation of the purine residues, asymmetry of the 5' and 3' junctions, and variations in groove widths associated with the positive charge of the protonated cytosine residues in the third strand. The thermodynamic stability of triplexes with either a 5' or a 3'CH+ is higher than those with a terminal thymidine. CONCLUSIONS: The observed sequence dependence of the triplex structure, and the distortions of the DNA at the 5' and 3' termini has implications for the design of optimal triplex-forming sequences, both in terms of the terminal bases and the importance of including positive charges in the third strand. Thus, triplex-stabilising ligands might be designed that can discriminate between TA x T-rich and CG x C+-rich sequences that depend not only on charge, but also on local groove widths. This could improve the stabilisation and specificity of antigene triplex formation. Solution conformation of a parallel DNA triple helix with 5' and 3' triplex-duplex junctions.,Asensio JL, Brown T, Lane AN Structure. 1999 Jan 15;7(1):1-11. PMID:10368268[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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