OCA at 07:41, 19 January 2022

OCA — Wed, 19 Jan 2022 07:41:03 GMT

←Older revision		Revision as of 07:41, 19 January 2022
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	==Parallel Q-D hybrid with 3' duplex stem-loop as a lateral snapback loop==		==Parallel Q-D hybrid with 3' duplex stem-loop as a lateral snapback loop==
-	<StructureSection load='7pne' size='340' side='right'caption='[[7pne]]' scene=''>	+	<StructureSection load='7pne' size='340' side='right'caption='[[7pne]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' 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=7PNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PNE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7pne]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PNE 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=7pne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pne OCA], [https://pdbe.org/7pne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pne RCSB], [https://www.ebi.ac.uk/pdbsum/7pne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pne ProSAT]</span></td></tr>	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=THM:THYMIDINE'>THM</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=7pne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pne OCA], [https://pdbe.org/7pne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pne RCSB], [https://www.ebi.ac.uk/pdbsum/7pne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pne ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Quadruplex-duplex (Q-D) junctions are increasingly considered promising targets for medicinal and technological applications. Here, a Q-D hybrid with a hairpin-type snapback loop coaxially stacked onto the quadruplex 3'-outer tetrad was designed and employed as a target structure for the indoloquinoline ligand SYUIQ-5. NMR spectral analysis demonstrated high-affinity binding of the ligand at the quadruplex-duplex interface with association constants determined by isothermal titration calorimetry of about 10 7 M -1 and large exothermicities Delta H degrees of -14 kcal/mol in a 120 mM K + buffer at 40 degrees C. Determination of the ligand-bound hybrid structure revealed intercalation of SYUIQ-5 between 3'-outer tetrad and the neighboring CG base pair, maximizing pi-pi stacking as well as electrostatic interactions with guanine carbonyl groups in close vicinity to the positively charged protonated quinoline nitrogen of the tetracyclic indoloquinoline. Exhibiting considerable flexibility, the SYUIQ-5 sidechain resides in the duplex minor groove. Based on comparative binding studies with the non-substituted N 5-methylated indoloquinoline cryptolepine, the sidechain is suggested to confer additional affinity and to fix the alignment of the intercalated indoloquinoline aromatic core. However, selectivity for the Q-D junction mostly relies on the geometry and charge distribution of the indoloquinoline ring system. The presented results are expected to provide valuable guidelines for the design of ligands specifically targeting Q-D interfaces.
		+
		+	Indoloquinoline Ligands Favor Intercalation at Quadruplex-Duplex Interfaces.,Vianney YM, Weisz K Chemistry. 2021 Dec 14. doi: 10.1002/chem.202103718. PMID:34905232<ref>PMID:34905232</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7pne" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Vianney YM]]	+	[[Category: Vianney, Y M]]
-	[[Category: Weisz K]]	+	[[Category: Weisz, K]]
		+	[[Category: Dna]]
		+	[[Category: Duplex]]
		+	[[Category: G-quadruplex]]
		+	[[Category: Quadruplex-duplex junction]]

OCA at 14:10, 29 December 2021

OCA — Wed, 29 Dec 2021 14:10:41 GMT

←Older revision		Revision as of 14:10, 29 December 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7pne ~~is ON HOLD until Paper Publication~~	+	==Parallel Q-D hybrid with 3' duplex stem-loop as a lateral snapback loop==
-		+	<StructureSection load='7pne' size='340' side='right'caption='[[7pne]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PNE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PNE FirstGlance]. <br>
-	~~Description~~:	+	</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=7pne FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pne OCA], [https://pdbe.org/7pne PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pne RCSB], [https://www.ebi.ac.uk/pdbsum/7pne PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pne ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Vianney YM]]
		+	[[Category: Weisz K]]

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

OCA — Wed, 15 Sep 2021 08:11:42 GMT

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

←Older revision

Revision as of 08:11, 15 September 2021

OCA: New page: '''Unreleased structure''' The entry 7pne is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 15 Sep 2021 08:11:41 GMT

New page: '''Unreleased structure''' The entry 7pne is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7pne is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]

7pne - Revision history

OCA at 07:41, 19 January 2022

OCA at 14:10, 29 December 2021

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

OCA: New page: '''Unreleased structure''' The entry 7pne is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures