7kzl - Revision history

OCA at 07:17, 3 April 2024

2024-04-03T07:17:58Z

←Older revision		Revision as of 07:17, 3 April 2024
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	<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>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	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.
-
-	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>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7kzl" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:58, 15 November 2023

2023-11-15T10:58:49Z

←Older revision		Revision as of 10:58, 15 November 2023
Line 1:		Line 1:

-	====	+	==Cyclopentane peptide nucleic acid in complex with DNA==
-	<StructureSection load='7kzl' size='340' side='right'caption='[[7kzl]]' scene=''>	+	<StructureSection load='7kzl' size='340' side='right'caption='[[7kzl]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= 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='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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.3Å</td></tr>
		+	<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>
		+	<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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.
		+
		+	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>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7kzl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Synthetic construct]]
		+	[[Category: Appella DH]]
		+	[[Category: Botos I]]

OCA at 11:18, 3 February 2021

2021-02-03T11:18:09Z

←Older revision		Revision as of 11:18, 3 February 2021
Line 3:		Line 3:
	<StructureSection load='7kzl' size='340' side='right'caption='[[7kzl]]' scene=''>		<StructureSection load='7kzl' size='340' side='right'caption='[[7kzl]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=7kzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kzl OCA], [~~http~~://pdbe.org/7kzl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7kzl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7kzl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7kzl ProSAT]</span></td></tr>	+	</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>
	__TOC__		__TOC__

OCA at 10:42, 24 December 2020

2020-12-24T10:42:32Z

←Older revision		Revision as of 10:42, 24 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7kzl ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7kzl' size='340' side='right'caption='[[7kzl]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=7kzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kzl OCA], [http://pdbe.org/7kzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7kzl RCSB], [http://www.ebi.ac.uk/pdbsum/7kzl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7kzl ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA: Protected "7kzl" [edit=sysop:move=sysop]

2020-12-16T11:18:00Z

Protected "7kzl" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:18, 16 December 2020

OCA: New page: '''Unreleased structure''' The entry 7kzl is ON HOLD Authors: Description: Category: Unreleased Structures

2020-12-16T11:17:59Z

New page: '''Unreleased structure''' The entry 7kzl is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7kzl is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]