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| [[Image:1cvy.gif|left|200px]]
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| <!--
| | ==CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG== |
| The line below this paragraph, containing "STRUCTURE_1cvy", creates the "Structure Box" on the page.
| | <StructureSection load='1cvy' size='340' side='right'caption='[[1cvy]], [[Resolution|resolution]] 2.15Å' 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'>[[1cvy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CVY 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">X-ray diffraction, [[Resolution|Resolution]] 2.15Å</td></tr> |
| -->
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPY:IMIDAZOLE-PYRROLE+POLYAMIDE'>IPY</scene></td></tr> |
| {{STRUCTURE_1cvy| PDB=1cvy | SCENE= }}
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cvy OCA], [https://pdbe.org/1cvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cvy RCSB], [https://www.ebi.ac.uk/pdbsum/1cvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cvy ProSAT]</span></td></tr> |
| | | </table> |
| '''CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYPYPYBETADP)2 BOUND TO CCAGATCTGG'''
| | __TOC__ |
| | | </StructureSection> |
| | | [[Category: Large Structures]] |
| ==Overview== | | [[Category: Baird EE]] |
| Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole (Hp) bind specific DNA sequences as antiparallel dimers in the minor groove. The side-by-side pairings of aromatic rings in the dimer afford a general recognition code that allows all four base-pairs to be distinguished. To examine the structural consequences of changing the DNA sequence context on T.A recognition by Hp/Py pairs in the minor groove, crystal structures of polyamide dimers (ImPyHpPy)(2) and the pyrrole counterpart (ImPyPyPy)(2) bound to the six base-pair target site 5'-AGATCT-3' in a ten base-pair oligonucleotide have been determined to a resolution of 2.27 and 2.15 A, respectively. The structures demonstrate that the principles of Hp/Py recognition of T.A are consistent between different sequence contexts. However, a general structural explanation for the non-additive reduction in binding affinity due to introduction of the hydroxyl group is less clear. Comparison with other polyamide-DNA cocrystal structures reveals structural themes and differences that may relate to sequence preference.
| | [[Category: Bremer RE]] |
| | | [[Category: Dervan PB]] |
| ==About this Structure== | | [[Category: Kielkopf CL]] |
| Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CVY OCA]. | | [[Category: Rees DC]] |
| | | [[Category: White S]] |
| ==Reference== | |
| Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove., Kielkopf CL, Bremer RE, White S, Szewczyk JW, Turner JM, Baird EE, Dervan PB, Rees DC, J Mol Biol. 2000 Jan 21;295(3):557-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10623546 10623546]
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| [[Category: Baird, E. E.]] | |
| [[Category: Bremer, R. E.]]
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| [[Category: Dervan, P. B.]]
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| [[Category: Kielkopf, C. L.]] | |
| [[Category: Rees, D. C.]] | |
| [[Category: White, S.]] | |
| [[Category: Double drug in minor groove]] | |
| [[Category: Imidazole-pyrrole polyamide]] | |
| [[Category: Minor groove recognition]] | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:10:07 2008''
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