136d: Difference between revisions
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== | ==SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES== | ||
<StructureSection load='136d' size='340' side='right'caption='[[136d]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[136d]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=136D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=136D 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=136d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=136d OCA], [https://pdbe.org/136d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=136d RCSB], [https://www.ebi.ac.uk/pdbsum/136d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=136d ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
BACKGROUND: Oligonucleotide-directed triple helix formation allows sequence specific recognition of double helical DNA. This powerful approach has been used to inhibit gene transcription in vitro and to mediate single site specific cleavage of a human chromosome. RESULTS: Using a combined NMR and molecular dynamics approach (including relaxation matrix refinement), we have determined the solution structure of an intramolecular purine.purine.pyrimidine (R.RY) DNA triplex containing guanines and thymines in the third strand to high resolution. Our studies define the G.GC and T.AT base triple pairing alignments in the R.RY triplex and identify the structural discontinuities in the third strand associated with the non-isomorphism of the base triples. The 5'-d(TpG)-3' base steps exhibit a pronounced increase in axial rise and reduction in helical twist, while the reverse is observed, to a lesser extent at 5'-d(GpT)-3' steps. A third groove is formed between the purine-rich third strand and the pyrimidine strand. It is wider and deeper than the other two grooves. CONCLUSIONS: Our structure of the R.RY DNA triplex will be important in the design of oligonucleotide probes with enhanced specificity and affinity for targeting in the genome. The third groove presents a potential target for binding additional ligands. | BACKGROUND: Oligonucleotide-directed triple helix formation allows sequence specific recognition of double helical DNA. This powerful approach has been used to inhibit gene transcription in vitro and to mediate single site specific cleavage of a human chromosome. RESULTS: Using a combined NMR and molecular dynamics approach (including relaxation matrix refinement), we have determined the solution structure of an intramolecular purine.purine.pyrimidine (R.RY) DNA triplex containing guanines and thymines in the third strand to high resolution. Our studies define the G.GC and T.AT base triple pairing alignments in the R.RY triplex and identify the structural discontinuities in the third strand associated with the non-isomorphism of the base triples. The 5'-d(TpG)-3' base steps exhibit a pronounced increase in axial rise and reduction in helical twist, while the reverse is observed, to a lesser extent at 5'-d(GpT)-3' steps. A third groove is formed between the purine-rich third strand and the pyrimidine strand. It is wider and deeper than the other two grooves. CONCLUSIONS: Our structure of the R.RY DNA triplex will be important in the design of oligonucleotide probes with enhanced specificity and affinity for targeting in the genome. The third groove presents a potential target for binding additional ligands. | ||
Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples.,Radhakrishnan I, Patel DJ Structure. 1993 Oct 15;1(2):135-52. PMID:8069626<ref>PMID:8069626</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: | <div class="pdbe-citations 136d" style="background-color:#fffaf0;"></div> | ||
[[Category: Patel | == References == | ||
[[Category: Radhakrishnan | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Patel DJ]] | |||
[[Category: Radhakrishnan I]] | |||
Latest revision as of 04:17, 28 December 2023
SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLESSOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES
Structural highlights
Publication Abstract from PubMedBACKGROUND: Oligonucleotide-directed triple helix formation allows sequence specific recognition of double helical DNA. This powerful approach has been used to inhibit gene transcription in vitro and to mediate single site specific cleavage of a human chromosome. RESULTS: Using a combined NMR and molecular dynamics approach (including relaxation matrix refinement), we have determined the solution structure of an intramolecular purine.purine.pyrimidine (R.RY) DNA triplex containing guanines and thymines in the third strand to high resolution. Our studies define the G.GC and T.AT base triple pairing alignments in the R.RY triplex and identify the structural discontinuities in the third strand associated with the non-isomorphism of the base triples. The 5'-d(TpG)-3' base steps exhibit a pronounced increase in axial rise and reduction in helical twist, while the reverse is observed, to a lesser extent at 5'-d(GpT)-3' steps. A third groove is formed between the purine-rich third strand and the pyrimidine strand. It is wider and deeper than the other two grooves. CONCLUSIONS: Our structure of the R.RY DNA triplex will be important in the design of oligonucleotide probes with enhanced specificity and affinity for targeting in the genome. The third groove presents a potential target for binding additional ligands. Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples.,Radhakrishnan I, Patel DJ Structure. 1993 Oct 15;1(2):135-52. PMID:8069626[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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