6alu - Revision history

OCA at 07:29, 1 May 2024

OCA — Wed, 01 May 2024 07:29:24 GMT

←Older revision		Revision as of 07:29, 1 May 2024
Line 1:		Line 1:

	==Solution structure of a DNA dodecamer with 5-methylcytosine at the 3rd and 8-oxoguanine at the 4th position==		==Solution structure of a DNA dodecamer with 5-methylcytosine at the 3rd and 8-oxoguanine at the 4th position==
-	<StructureSection load='6alu' size='340' side='right'caption='[[6alu~~]], [[NMR_Ensembles_of_Models \| 11 NMR models~~]]' scene=''>	+	<StructureSection load='6alu' size='340' side='right'caption='[[6alu]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6alu]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ALU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ALU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6alu]] 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=6ALU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ALU FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=DCZ:2-DEOXYCYTIDINE'>DCZ</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='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=6alu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alu OCA], [~~http~~://pdbe.org/6alu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6alu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6alu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6alu ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=DCZ:2-DEOXYCYTIDINE'>DCZ</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=6alu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alu OCA], [https://pdbe.org/6alu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6alu RCSB], [https://www.ebi.ac.uk/pdbsum/6alu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6alu ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	DNA damage can affect various regulatory elements of the genome, with the consequences for DNA structure, dynamics, and interaction with proteins remaining largely unexplored. We used solution NMR spectroscopy, restrained and free molecular dynamics to obtain the structures and investigate dominant motions for a set of DNA duplexes containing CpG sites permuted with combinations of 5-methylcytosine (mC), the primary epigenetic base, and 8-oxoguanine (oxoG), an abundant DNA lesion. Guanine oxidation significantly changed the motion in both hemimethylated and fully methylated DNA, increased base pair breathing, induced BI-->BII transition in the backbone 3' to the oxoG and reduced the variability of shift and tilt helical parameters. UV melting experiments corroborated the NMR and molecular dynamics results, showing significant destabilization of all methylated contexts by oxoG. Notably, some dynamic and thermodynamic effects were not additive in the fully methylated oxidized CpG, indicating that the introduced modifications interact with each other. Finally, we show that the presence of oxoG biases the recognition of methylated CpG dinucleotides by ROS1, a plant enzyme involved in epigenetic DNA demethylation, in favor of the oxidized DNA strand. Thus, the conformational and dynamic effects of spurious DNA oxidation in the regulatory CpG dinucleotide can have far-reaching biological consequences.
-
-	Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation.,Gruber DR, Toner JJ, Miears HL, Shernyukov AV, Kiryutin AS, Lomzov AA, Endutkin AV, Grin IR, Petrova DV, Kupryushkin MS, Yurkovskaya AV, Johnson EC, Okon M, Bagryanskaya EG, Zharkov DO, Smirnov SL Nucleic Acids Res. 2018 Nov 16;46(20):10827-10839. doi: 10.1093/nar/gky893. PMID:30289469<ref>PMID:30289469</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6alu" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bagryanskaya, E G~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Endutkin, A V~~]]	+	[[Category: Bagryanskaya EG]]
-	[[Category: ~~Gruber, D R~~]]	+	[[Category: Endutkin AV]]
-	[[Category: ~~Shernyukov, A V~~]]	+	[[Category: Gruber DR]]
-	[[Category: ~~Smirnov, S L~~]]	+	[[Category: Shernyukov AV]]
-	[[Category: ~~Zharkov, D O~~]]	+	[[Category: Smirnov SL]]
-	[[Category: ~~Dna]]~~	+	[[Category: Zharkov DO]]
-	~~[[Category: Dna adduct]]~~	+
-	~~[[Category: Dna damage]]~~	+
-	~~[[Category: Drew-dickerson]]~~	+
-	~~[[Category: Lesion]]~~	+
-	~~[[Category: Modified dna]]~~	+
-	~~[[Category: Non-canonical]]~~	+
-	~~[[Category: Oxidized dna~~]]	+

OCA at 08:14, 27 November 2019

OCA — Wed, 27 Nov 2019 08:14:59 GMT

←Older revision		Revision as of 08:14, 27 November 2019
Line 1:		Line 1:

	==Solution structure of a DNA dodecamer with 5-methylcytosine at the 3rd and 8-oxoguanine at the 4th position==		==Solution structure of a DNA dodecamer with 5-methylcytosine at the 3rd and 8-oxoguanine at the 4th position==
-	<StructureSection load='6alu' size='340' side='right' caption='[[6alu]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>	+	<StructureSection load='6alu' size='340' side='right'caption='[[6alu]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6alu]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ALU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALU FirstGlance]. <br>		<table><tr><td colspan='2'>[[6alu]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ALU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALU FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bagryanskaya, E G]]		[[Category: Bagryanskaya, E G]]
	[[Category: Endutkin, A V]]		[[Category: Endutkin, A V]]

OCA at 08:47, 19 December 2018

OCA — Wed, 19 Dec 2018 08:47:36 GMT

←Older revision		Revision as of 08:47, 19 December 2018
Line 7:		Line 7:
	<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=6alu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alu OCA], [http://pdbe.org/6alu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6alu RCSB], [http://www.ebi.ac.uk/pdbsum/6alu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6alu 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=6alu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alu OCA], [http://pdbe.org/6alu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6alu RCSB], [http://www.ebi.ac.uk/pdbsum/6alu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6alu ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA damage can affect various regulatory elements of the genome, with the consequences for DNA structure, dynamics, and interaction with proteins remaining largely unexplored. We used solution NMR spectroscopy, restrained and free molecular dynamics to obtain the structures and investigate dominant motions for a set of DNA duplexes containing CpG sites permuted with combinations of 5-methylcytosine (mC), the primary epigenetic base, and 8-oxoguanine (oxoG), an abundant DNA lesion. Guanine oxidation significantly changed the motion in both hemimethylated and fully methylated DNA, increased base pair breathing, induced BI-->BII transition in the backbone 3' to the oxoG and reduced the variability of shift and tilt helical parameters. UV melting experiments corroborated the NMR and molecular dynamics results, showing significant destabilization of all methylated contexts by oxoG. Notably, some dynamic and thermodynamic effects were not additive in the fully methylated oxidized CpG, indicating that the introduced modifications interact with each other. Finally, we show that the presence of oxoG biases the recognition of methylated CpG dinucleotides by ROS1, a plant enzyme involved in epigenetic DNA demethylation, in favor of the oxidized DNA strand. Thus, the conformational and dynamic effects of spurious DNA oxidation in the regulatory CpG dinucleotide can have far-reaching biological consequences.
		+
		+	Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation.,Gruber DR, Toner JJ, Miears HL, Shernyukov AV, Kiryutin AS, Lomzov AA, Endutkin AV, Grin IR, Petrova DV, Kupryushkin MS, Yurkovskaya AV, Johnson EC, Okon M, Bagryanskaya EG, Zharkov DO, Smirnov SL Nucleic Acids Res. 2018 Nov 16;46(20):10827-10839. doi: 10.1093/nar/gky893. PMID:30289469<ref>PMID:30289469</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6alu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA: Protected "6alu" [edit=sysop:move=sysop]

OCA — Wed, 13 Sep 2017 09:46:40 GMT

Protected "6alu" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:46, 13 September 2017

OCA: New page: ==Solution structure of a DNA dodecamer with 5-methylcytosine at the 3rd and 8-oxoguanine at the 4th position== == Structural highlights ==
<table><tr><td colspan='2'>[[6alu]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ALU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALU FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=DCZ:2-DEOXYCYTIDINE'>DCZ</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=6alu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alu OCA], [http://pdbe.org/6alu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6alu RCSB], [http://www.ebi.ac.uk/pdbsum/6alu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6alu ProSAT]</span></td></tr>
</table>
TOC
</StructureSection>
[[Category: Bagryanskaya, E G]]
[[Category: Endutkin, A V]]
[[Category: Gruber, D R]]
[[Category: Shernyukov, A V]]
[[Category: Smirnov, S L]]
[[Category: Zharkov, D O]]
[[Category: Dna]]
[[Category: Dna adduct]]
[[Category: Dna damage]]
[[Category: Drew-dickerson]]
[[Category: Lesion]]
[[Category: Modified dna]]
[[Category: Non-canonical]]
[[Category: Oxidized dna]]