7kzl

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<table><tr><td colspan='2'>[[7kzl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KZL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KZL FirstGlance]. <br>
<table><tr><td colspan='2'>[[7kzl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KZL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KZL FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene>, <scene name='pdbligand=XDD:N-[(1S,2S)-2-aminocyclopentyl]-N-[(6-amino-9H-purin-9-yl)acetyl]glycine'>XDD</scene>, <scene name='pdbligand=XDJ:N-[(1S,2S)-2-aminocyclopentyl]-N-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)acetyl]glycine'>XDJ</scene>, <scene name='pdbligand=XDV:2-[2-(2-aminoethoxy)ethoxy]acetamide'>XDV</scene>, <scene name='pdbligand=XDY:N-[(1S,2S)-2-aminocyclopentyl]-N-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]glycine'>XDY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MOH:METHANOL'>MOH</scene>, <scene name='pdbligand=XDD:N-[(1S,2S)-2-aminocyclopentyl]-N-[(6-amino-9H-purin-9-yl)acetyl]glycine'>XDD</scene>, <scene name='pdbligand=XDJ:2-[[(1~{S},2~{S})-2-azanylcyclopentyl]-[2-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)ethanoyl]amino]ethanoic+acid'>XDJ</scene>, <scene name='pdbligand=XDV:2-[2-(2-azanylethoxy)ethoxy]ethanamide'>XDV</scene>, <scene name='pdbligand=XDY:2-[[(1~{S},2~{S})-2-azanylcyclopentyl]-[2-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]ethanoyl]amino]ethanoic+acid'>XDY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=7kzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kzl OCA], [https://pdbe.org/7kzl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kzl RCSB], [https://www.ebi.ac.uk/pdbsum/7kzl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kzl 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=7kzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kzl OCA], [https://pdbe.org/7kzl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kzl RCSB], [https://www.ebi.ac.uk/pdbsum/7kzl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kzl ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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We report a series of synthetic, nucleic acid mimics with highly customizable thermodynamic binding to DNA. Incorporation of helix-promoting cyclopentanes into peptide nucleic acids (PNAs) increases the melting temperatures (Tm) of PNA+DNA duplexes by approximately +5 degrees C per cyclopentane. Sequential addition of cyclopentanes allows the Tm of PNA + DNA duplexes to be systematically fine-tuned from +5 to +50 degrees C compared with the unmodified PNA. Containing only nine nucleobases and an equal number of cyclopentanes, cpPNA-9 binds to complementary DNA with a Tm around 90 degrees C. Additional experiments reveal that the cpPNA-9 sequence specifically binds to DNA duplexes containing its complementary sequence and functions as a PCR clamp. An X-ray crystal structure of the cpPNA-9-DNA duplex revealed that cyclopentanes likely induce a right-handed helix in the PNA with conformations that promote DNA binding.
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Conformational constraints of cyclopentane peptide nucleic acids facilitate tunable binding to DNA.,Zheng H, Botos I, Clausse V, Nikolayevskiy H, Rastede EE, Fouz MF, Mazur SJ, Appella DH Nucleic Acids Res. 2021 Jan 25;49(2):713-725. doi: 10.1093/nar/gkaa1249. PMID:33406227<ref>PMID:33406227</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 7kzl" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
__TOC__
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</StructureSection>
</StructureSection>

Current revision

Cyclopentane peptide nucleic acid in complex with DNA

PDB ID 7kzl

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