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| | ==Dodecamer DNA containing the synthetic base pair P-Z== | | ==Dodecamer DNA containing the synthetic base pair P-Z== |
| - | <StructureSection load='6i4o' size='340' side='right'caption='[[6i4o]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | + | <StructureSection load='6i4o' size='340' side='right'caption='[[6i4o]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6i4o]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I4O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I4O FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6i4o]] is a 2 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=6I4O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I4O FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DP:DISOPYRAMIDE'>DP</scene>, <scene name='pdbligand=DZ:N-(3,5-DIBROMO-4-HYDROXYPHENYL)-2,6-DIMETHYLBENZAMIDE'>DZ</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DP:DISOPYRAMIDE'>DP</scene>, <scene name='pdbligand=DZ:N-(3,5-DIBROMO-4-HYDROXYPHENYL)-2,6-DIMETHYLBENZAMIDE'>DZ</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6i4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i4o OCA], [http://pdbe.org/6i4o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i4o RCSB], [http://www.ebi.ac.uk/pdbsum/6i4o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i4o ProSAT]</span></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=6i4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i4o OCA], [https://pdbe.org/6i4o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i4o RCSB], [https://www.ebi.ac.uk/pdbsum/6i4o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i4o ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Burley, G A]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Padroni, G]] | + | [[Category: Burley GA]] |
| - | [[Category: Parkinson, J A]] | + | [[Category: Padroni G]] |
| - | [[Category: Reichenbach, L F]] | + | [[Category: Parkinson JA]] |
| - | [[Category: Dna]] | + | [[Category: Reichenbach LF]] |
| - | [[Category: Synthetic base pair]]
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| Structural highlights
Publication Abstract from PubMed
The structural basis of minor groove recognition of a DNA duplex containing synthetic genetic information by hairpin pyrrole-imidazole polyamides is described. Hairpin polyamides induce a higher melting stabilization of a DNA duplex containing the unnatural P.Z base-pair when an imidazole unit is aligned with a P nucleotide. An NMR structural study showed that the incorporation of two isolated P.Z pairs enlarges the minor groove and slightly narrows the major groove at the site of this synthetic genetic information, relative to a DNA duplex consisting entirely of Watson-Crick base-pairs. Pyrrole-imidazole polyamides bind to a P.Z-containing DNA duplex to form a stable complex, effectively mimicking a G.C pair. A structural hallmark of minor groove recognition of a P.Z pair by a polyamide is the reduced level of allosteric distortion induced by binding of a polyamide to a DNA duplex. Understanding the molecular determinants that influence minor groove recognition of DNA containing synthetic genetic components provides the basis to further develop unnatural base-pairs for synthetic biology applications.
Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components.,Padroni G, Withers JM, Taladriz-Sender A, Reichenbach LF, Parkinson JA, Burley GA J Am Chem Soc. 2019 Jun 4. doi: 10.1021/jacs.8b12444. PMID:31117639[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Padroni G, Withers JM, Taladriz-Sender A, Reichenbach LF, Parkinson JA, Burley GA. Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components. J Am Chem Soc. 2019 Jun 4. doi: 10.1021/jacs.8b12444. PMID:31117639 doi:http://dx.doi.org/10.1021/jacs.8b12444
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