5uzi - Revision history

OCA at 10:27, 14 June 2023

OCA — Wed, 14 Jun 2023 10:27:31 GMT

←Older revision		Revision as of 10:27, 14 June 2023
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	==Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A6-DNAm1A16 structure==		==Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A6-DNAm1A16 structure==
-	<StructureSection load='5uzi' size='340' side='right'caption='[[5uzi~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='5uzi' size='340' side='right'caption='[[5uzi]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uzi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UZI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uzi]] 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=5UZI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UZI FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uzd\|5uzd]], [[5uzf\|5uzf]]~~</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=5uzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uzi OCA], [https://pdbe.org/5uzi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uzi RCSB], [https://www.ebi.ac.uk/pdbsum/5uzi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uzi ProSAT]</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=5uzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uzi OCA], [~~http~~://pdbe.org/5uzi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5uzi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5uzi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5uzi 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: Al-Hashimi~~, H M~~]]	+	[[Category: Synthetic construct]]
-	[[Category: Sathyamoorthy, B]]	+	[[Category: Al-Hashimi HM]]
-	[[Category: Shi, H]]	+	[[Category: Sathyamoorthy B]]
-	[[Category: Xue, Y]]	+	[[Category: Shi H]]
-	~~[[Category: Damage recognition and repair]]~~	+	[[Category: Xue Y]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna structure and dynamic]]~~	+
-	~~[[Category: Hoogsteen base pair]]~~	+
-	~~[[Category: N1-methyladenine]]~~	+
-	~~[[Category: Nmr structure and dynamic ensemble~~]]	+

OCA at 09:25, 1 January 2020

OCA — Wed, 01 Jan 2020 09:25:12 GMT

←Older revision		Revision as of 09:25, 1 January 2020
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	==Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A6-DNAm1A16 structure==		==Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A6-DNAm1A16 structure==
-	<StructureSection load='5uzi' size='340' side='right' caption='[[5uzi]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>	+	<StructureSection load='5uzi' size='340' side='right'caption='[[5uzi]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5uzi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UZI FirstGlance]. <br>		<table><tr><td colspan='2'>[[5uzi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UZI FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Al-Hashimi, H M]]		[[Category: Al-Hashimi, H M]]
	[[Category: Sathyamoorthy, B]]		[[Category: Sathyamoorthy, B]]

OCA at 07:37, 27 April 2017

OCA — Thu, 27 Apr 2017 07:37:51 GMT

←Older revision		Revision as of 07:37, 27 April 2017
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	<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=5uzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uzi OCA], [http://pdbe.org/5uzi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uzi RCSB], [http://www.ebi.ac.uk/pdbsum/5uzi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uzi ProSAT]</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=5uzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uzi OCA], [http://pdbe.org/5uzi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uzi RCSB], [http://www.ebi.ac.uk/pdbsum/5uzi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uzi ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated ( approximately 0.02-0.4%) and short-lived (lifetimes approximately 0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A*T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking ( approximately 9 degrees ); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair.
		+
		+	Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.,Sathyamoorthy B, Shi H, Zhou H, Xue Y, Rangadurai A, Merriman DK, Al-Hashimi HM Nucleic Acids Res. 2017 Mar 21. doi: 10.1093/nar/gkx186. PMID:28369571<ref>PMID:28369571</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5uzi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:31, 5 April 2017

OCA — Wed, 05 Apr 2017 13:31:38 GMT

←Older revision		Revision as of 13:31, 5 April 2017
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-	'''Unreleased structure'''

-	~~The entry 5uzi is ON HOLD~~	+	==Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A - A6-DNAm1A16 structure==
-		+	<StructureSection load='5uzi' size='340' side='right' caption='[[5uzi]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
-	~~Authors: Sathyamoorthy, B., Shi, H., Xue, Y., Al-Hashimi, H.M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5uzi]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UZI FirstGlance]. <br>
-	~~Description:~~ Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A -A6-DNAm1A16 structure	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MA7:1N-METHYLADENOSINE-5-MONOPHOSPHATE'>MA7</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uzd\|5uzd]], [[5uzf\|5uzf]]</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=5uzi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uzi OCA], [http://pdbe.org/5uzi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uzi RCSB], [http://www.ebi.ac.uk/pdbsum/5uzi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uzi ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Al-Hashimi, H M]]
	[[Category: Sathyamoorthy, B]]		[[Category: Sathyamoorthy, B]]
		+	[[Category: Shi, H]]
	[[Category: Xue, Y]]		[[Category: Xue, Y]]
-	[[Category: Al-~~Hashimi, H.M~~]]	+	[[Category: Damage recognition and repair]]
-	[[Category: ~~Shi, H~~]]	+	[[Category: Dna]]
		+	[[Category: Dna structure and dynamic]]
		+	[[Category: Hoogsteen base pair]]
		+	[[Category: N1-methyladenine]]
		+	[[Category: Nmr structure and dynamic ensemble]]

OCA at 19:33, 15 March 2017

OCA — Wed, 15 Mar 2017 19:33:07 GMT

←Older revision		Revision as of 19:33, 15 March 2017
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	The entry 5uzi is ON HOLD		The entry 5uzi is ON HOLD

-	Authors: Sathyamoorthy, B, Shi, H, Xue, Y, Al-Hashimi, HM	+	Authors: Sathyamoorthy, B., Shi, H., Xue, Y., Al-Hashimi, H.M.

	Description: Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A -A6-DNAm1A16 structure		Description: Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A -A6-DNAm1A16 structure
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Sathyamoorthy, B~~, Shi, H,~~ Xue, Y, Al-Hashimi, Hm]]	+	[[Category: Sathyamoorthy, B]]
		+	[[Category: Xue, Y]]
		+	[[Category: Al-Hashimi, H.M]]
		+	[[Category: Shi, H]]

OCA: Protected "5uzi" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:08:33 GMT

Protected "5uzi" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:08, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5uzi is ON HOLD Authors: Sathyamoorthy, B, Shi, H, Xue, Y, Al-Hashimi, HM Description: Insights into Watson-Crick/Hoogsteen Breathing Dynamics and ...

OCA — Thu, 09 Mar 2017 15:08:32 GMT

New page: '''Unreleased structure''' The entry 5uzi is ON HOLD Authors: Sathyamoorthy, B, Shi, H, Xue, Y, Al-Hashimi, HM Description: Insights into Watson-Crick/Hoogsteen Breathing Dynamics and ...

New page

'''Unreleased structure'''

The entry 5uzi is ON HOLD

Authors: Sathyamoorthy, B, Shi, H, Xue, Y, Al-Hashimi, HM

Description: Insights into Watson-Crick/Hoogsteen Breathing Dynamics and Damage Repair from the Solution Structure and Dynamic Ensemble of DNA Duplexes containing m1A -A6-DNAm1A16 structure
[[Category: Unreleased Structures]]
[[Category: Sathyamoorthy, B, Shi, H, Xue, Y, Al-Hashimi, Hm]]