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| - | [[Image:1p3x.gif|left|200px]] | |
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| - | {{Structure
| + | ==INTRAMOLECULAR DNA TRIPLEX WITH 1-PROPYNYL DEOXYURIDINE IN THE THIRD STRAND, NMR, 10 STRUCTURES== |
| - | |PDB= 1p3x |SIZE=350|CAPTION= <scene name='initialview01'>1p3x</scene>
| + | <StructureSection load='1p3x' size='340' side='right'caption='[[1p3x]]' 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=DCM:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DCM</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=PDU:5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONOPHOSPHATE'>PDU</scene>
| + | <table><tr><td colspan='2'>[[1p3x]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P3X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P3X 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCM:2-DEOXYCYTIDINE-5-MONOPHOSPHATE'>DCM</scene>, <scene name='pdbligand=PDU:5(1-PROPYNYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>PDU</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1p3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p3x OCA], [https://pdbe.org/1p3x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p3x RCSB], [https://www.ebi.ac.uk/pdbsum/1p3x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p3x ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1p3x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p3x OCA], [http://www.ebi.ac.uk/pdbsum/1p3x PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1p3x RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''INTRAMOLECULAR DNA TRIPLEX WITH 1-PROPYNYL DEOXYURIDINE IN THE THIRD STRAND, NMR, 10 STRUCTURES'''
| + | [[Category: Feigon J]] |
| - | | + | [[Category: Phipps AK]] |
| - | | + | [[Category: Schultze P]] |
| - | ==Overview==
| + | [[Category: Tarkoy M]] |
| - | Incorporation of the modified base 5-(1-propynl)-2'-deoxyuridine (propynylU) in the third strand of a triplex leads to enhanced triplex stabilization. To investigate effects of the propyne nucleotide on triplex structure and the factors underlying the increased stability, we have determined the solution structure of the intramolecular DNA pyrmidine-purine-pyrimdine d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-PCPCPCPP) (PDD-EG), which contains 5-(1-propynl)-2'-deoxyuridine (P) in the third strand and hexakis(ethylene glycol) linkers [(EG)6]. The structure was calculated using X-PLOR with distance and dihedral angle restraints obtained from two-dimensional NMR experiments and refined with the direct relaxation matrix method. The structures show that the extended aromatic electron cloud of the propynylU nucleotide stacks well over the 5'-neighboring nucleotides, resulting in increased stabilization. The propynylU nucleotides also affect the overall structure of the triple helix. A comparison of the structure to that of the nonmodified intramolecular DNA triplex of the same sequence, d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT) (DDD-EG), shows that PDD-EG has a more A-DNA like X displacement and inclination than DDD-EG yet still maintains predominantly S-type sugar puckers as found in DDD-EG and other DNA triplexes.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1P3X 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=1P3X OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Solution structure of an intramolecular DNA triplex containing 5-(1-propynyl)-2'-deoxyuridine residues in the third strand., Phipps AK, Tarkoy M, Schultze P, Feigon J, Biochemistry. 1998 Apr 28;37(17):5820-30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9558315 9558315]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Feigon, J.]] | + | |
| - | [[Category: Phipps, A K.]] | + | |
| - | [[Category: Schultze, P.]] | + | |
| - | [[Category: Tarkoy, M.]] | + | |
| - | [[Category: oligonucleotide]]
| + | |
| - | [[Category: propyne]]
| + | |
| - | [[Category: triplex]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:54:28 2008''
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