2n2d - Revision history

OCA at 06:13, 15 May 2024

2024-05-15T06:13:44Z

← Older revision		Revision as of 06:13, 15 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2n2d]] is a 1 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=2N2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2n2d]] is a 1 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=2N2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N2D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</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=2n2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2d OCA], [https://pdbe.org/2n2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n2d RCSB], [https://www.ebi.ac.uk/pdbsum/2n2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n2d 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=2n2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2d OCA], [https://pdbe.org/2n2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n2d RCSB], [https://www.ebi.ac.uk/pdbsum/2n2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n2d ProSAT]</span></td></tr>
	</table>		</table>

OCA at 09:53, 14 June 2023

2023-06-14T09:53:25Z

← Older revision		Revision as of 09:53, 14 June 2023
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	==Structure of DNA G-quadruplex adopted by ALS and FTD related GGGGCC repeat with G21 to Br-G21 substitution==		==Structure of DNA G-quadruplex adopted by ALS and FTD related GGGGCC repeat with G21 to Br-G21 substitution==
	<StructureSection load='2n2d' size='340' side='right'caption='[[2n2d~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>		<StructureSection load='2n2d' size='340' side='right'caption='[[2n2d]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2n2d]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2n2d]] is a 1 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=2N2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N2D FirstGlance]. <br>
	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</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=2n2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2d OCA], [https://pdbe.org/2n2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n2d RCSB], [https://www.ebi.ac.uk/pdbsum/2n2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n2d 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=2n2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2d OCA], [https://pdbe.org/2n2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n2d RCSB], [https://www.ebi.ac.uk/pdbsum/2n2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n2d ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Brcic, J~~]]		[[Category: Synthetic construct]]
	[[Category: ~~Plavec,~~ J]]		[[Category: Brcic J]]
	[[Category: ~~Antiparallel]]~~		[[Category: Plavec J]]
	~~[[Category: Dna]]~~
	~~[[Category: G-quadruplex~~]]

OCA at 20:49, 20 October 2021

2021-10-20T20:49:51Z

← Older revision		Revision as of 20:49, 20 October 2021
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	<StructureSection load='2n2d' size='340' side='right'caption='[[2n2d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2n2d' size='340' side='right'caption='[[2n2d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2n2d]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2N2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2n2d]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N2D FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</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=2n2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2d OCA], [~~http~~://pdbe.org/2n2d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2n2d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2n2d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2n2d 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=2n2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2d OCA], [https://pdbe.org/2n2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n2d RCSB], [https://www.ebi.ac.uk/pdbsum/2n2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n2d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:30, 21 August 2019

2019-08-21T07:30:46Z

← Older revision		Revision as of 07:30, 21 August 2019
Line 1:		Line 1:

	==Structure of DNA G-quadruplex adopted by ALS and FTD related GGGGCC repeat with G21 to Br-G21 substitution==		==Structure of DNA G-quadruplex adopted by ALS and FTD related GGGGCC repeat with G21 to Br-G21 substitution==
	<StructureSection load='2n2d' size='340' side='right' caption='[[2n2d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2n2d' size='340' side='right'caption='[[2n2d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2n2d]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2N2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2n2d]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2N2D FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Brcic, J]]		[[Category: Brcic, J]]
	[[Category: Plavec, J]]		[[Category: Plavec, J]]

OCA at 15:04, 16 November 2017

2017-11-16T15:04:13Z

← Older revision		Revision as of 15:04, 16 November 2017
Line 1:		Line 1:

	==Structure of DNA G-quadruplex adopted by ALS and FTD related GGGGCC repeat with G21 to Br-G21 substitution==		==Structure of DNA G-quadruplex adopted by ALS and FTD related GGGGCC repeat with G21 to Br-G21 substitution==
	<StructureSection load='2n2d' size='340' side='right' caption='[[2n2d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2n2d' size='340' side='right' caption='[[2n2d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2n2d]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2N2D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2n2d]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2N2D FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</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=2n2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2d OCA], [http://pdbe.org/2n2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2n2d RCSB], [http://www.ebi.ac.uk/pdbsum/2n2d PDBsum]</span></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=2n2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2d OCA], [http://pdbe.org/2n2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2n2d RCSB], [http://www.ebi.ac.uk/pdbsum/2n2d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2n2d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:21, 15 October 2015

2015-10-15T21:21:42Z

← Older revision		Revision as of 21:21, 15 October 2015
Line 1:		Line 1:
	'''~~Unreleased~~ structure'''		==Structure of DNA G-quadruplex adopted by ALS and FTD related GGGGCC repeat with G21 to Br-G21 substitution==
			<StructureSection load='2n2d' size='340' side='right' caption='[[2n2d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2n2d]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N2D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2N2D FirstGlance]. <br>
			</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGM:8-BROMO-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>BGM</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=2n2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n2d OCA], [http://pdbe.org/2n2d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2n2d RCSB], [http://www.ebi.ac.uk/pdbsum/2n2d PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			A prolonged expansion of GGGGCC repeat within non-coding region of C9orf72 gene has been identified as the most common cause of familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which are devastating neurodegenerative disorders. Formation of unusual secondary structures within expanded GGGGCC repeat, including DNA and RNA G-quadruplexes and R-loops was proposed to drive ALS and FTD pathogenesis. Initial NMR investigation on DNA oligonucleotides with four repeat units as the shortest model with the ability to form an unimolecular G-quadruplex indicated their folding into multiple G-quadruplex structures in the presence of K(+) ions. Single dG to 8Br-dG substitution at position 21 in oligonucleotide d[(G4C2)3G4] and careful optimization of folding conditions enabled formation of mostly a single G-quadruplex species, which enabled determination of a high-resolution structure with NMR. G-quadruplex structure adopted by d[(G4C2)3GG(Br)GG] is composed of four G-quartets, which are connected by three edgewise C-C loops. All four strands adopt antiparallel orientation to one another and have alternating syn-anti progression of glycosidic conformation of guanine residues. One of the cytosines in every loop is stacked upon the G-quartet contributing to a very compact and stable structure.

	~~The entry 2n2d is ON HOLD until Paper Publication~~		Solution structure of a DNA quadruplex containing ALS and FTD related GGGGCC repeat stabilized by 8-bromodeoxyguanosine substitution.,Brcic J, Plavec J Nucleic Acids Res. 2015 Sep 30;43(17):8590-600. doi: 10.1093/nar/gkv815. Epub, 2015 Aug 7. PMID:26253741<ref>PMID:26253741</ref>

	~~Authors: Brcic~~, J.~~, Plavec, J~~.		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~Description~~:		<div class="pdbe-citations 2n2d" style="background-color:#fffaf0;"></div>
	~~[[Category: Unreleased Structures]]~~		== References ==
			<references/>
			__TOC__
			</StructureSection>
	[[Category: Brcic, J]]		[[Category: Brcic, J]]
	[[Category: Plavec, J]]		[[Category: Plavec, J]]
			[[Category: Antiparallel]]
			[[Category: Dna]]
			[[Category: G-quadruplex]]

OCA at 08:14, 10 June 2015

2015-06-10T08:14:57Z

← Older revision		Revision as of 08:14, 10 June 2015
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 2n2d is ON HOLD		The entry 2n2d is ON HOLD until Paper Publication

	Authors: Brcic, J., Plavec, J.		Authors: Brcic, J., Plavec, J.

OCA: Protected "2n2d" [edit=sysop:move=sysop]

2015-05-13T06:50:05Z

Protected "2n2d" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:50, 13 May 2015
(No difference)

OCA: New page: '''Unreleased structure''' The entry 2n2d is ON HOLD Authors: Brcic, J., Plavec, J. Description: Category: Unreleased Structures Category: Brcic, J Category: Plavec, J

2015-05-13T06:50:04Z

New page: '''Unreleased structure''' The entry 2n2d is ON HOLD Authors: Brcic, J., Plavec, J. Description: Category: Unreleased Structures Category: Brcic, J Category: Plavec, J

New page

'''Unreleased structure'''

The entry 2n2d is ON HOLD

Authors: Brcic, J., Plavec, J.

Description:
[[Category: Unreleased Structures]]
[[Category: Brcic, J]]
[[Category: Plavec, J]]