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| - | [[Image:134d.jpg|left|200px]] | |
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| - | {{Structure
| + | ==SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES== |
| - | |PDB= 134d |SIZE=350|CAPTION= <scene name='initialview01'>134d</scene>
| + | <StructureSection load='134d' size='340' side='right'caption='[[134d]]' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>
| + | <table><tr><td colspan='2'>[[134d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=134D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=134D FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | |GENE=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=134d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=134d OCA], [https://pdbe.org/134d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=134d RCSB], [https://www.ebi.ac.uk/pdbsum/134d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=134d ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=[[135d|135D]], [[136d|136D]]
| + | __TOC__ |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=134d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=134d OCA], [http://www.ebi.ac.uk/pdbsum/134d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=134d RCSB]</span>
| + | </StructureSection> |
| - | }}
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Synthetic construct]] |
| - | '''SOLUTION STRUCTURE OF A PURINE(DOT)PURINE(DOT)PYRIMIDINE DNA TRIPLEX CONTAINING G(DOT)GC AND T(DOT)AT TRIPLES'''
| + | [[Category: Patel DJ]] |
| - | | + | [[Category: Radhakrishnan I]] |
| - | | + | |
| - | ==Overview==
| + | |
| - | 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.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 134D is a [[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=134D OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | 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:[http://www.ncbi.nlm.nih.gov/pubmed/8069626 8069626]
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| - | [[Category: Protein complex]]
| + | |
| - | [[Category: Patel, D J.]]
| + | |
| - | [[Category: Radhakrishnan, I.]] | + | |
| - | [[Category: dna]] | + | |
| - | [[Category: nmr]] | + | |
| - | [[Category: triplex]] | + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:27:41 2008''
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