1axl - Revision history

OCA at 11:34, 22 November 2023

2023-11-22T11:34:19Z

←Older revision		Revision as of 11:34, 22 November 2023
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	==SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES==		==SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES==
-	<StructureSection load='1axl' size='340' side='right'caption='[[1axl~~]], [[NMR_Ensembles_of_Models \| 6 NMR models~~]]' scene=''>	+	<StructureSection load='1axl' size='340' side='right'caption='[[1axl]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AXL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AXL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</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=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</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=1axl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1axl OCA], [https://pdbe.org/1axl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1axl RCSB], [https://www.ebi.ac.uk/pdbsum/1axl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1axl 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=1axl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1axl OCA], [https://pdbe.org/1axl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1axl RCSB], [https://www.ebi.ac.uk/pdbsum/1axl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1axl ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Broyde, S]]	+	[[Category: Broyde S]]
-	[[Category: Feng, B]]	+	[[Category: Feng B]]
-	[[Category: Geacintov~~, N E~~]]	+	[[Category: Geacintov NE]]
-	[[Category: Gorin~~, A A~~]]	+	[[Category: Gorin AA]]
-	[[Category: Hingerty~~, B E~~]]	+	[[Category: Hingerty BE]]
-	[[Category: Kolbanovskiy, A]]	+	[[Category: Kolbanovskiy A]]
-	[[Category: Patel~~, D J]]~~	+	[[Category: Patel DJ]]
-	~~[[Category: Carcinogen]]~~	+
-	~~[[Category: Deoxyribonucleic acid]]~~	+
-	~~[[Category: Dna~~]]	+

OCA at 06:55, 24 February 2021

2021-02-24T06:55:19Z

←Older revision		Revision as of 06:55, 24 February 2021
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	<StructureSection load='1axl' size='340' side='right'caption='[[1axl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>		<StructureSection load='1axl' size='340' side='right'caption='[[1axl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1AXL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AXL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</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=1axl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1axl OCA], [~~http~~://pdbe.org/1axl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1axl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1axl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1axl 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=1axl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1axl OCA], [https://pdbe.org/1axl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1axl RCSB], [https://www.ebi.ac.uk/pdbsum/1axl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1axl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:26, 21 May 2019

2019-05-21T09:26:51Z

←Older revision		Revision as of 09:26, 21 May 2019
Line 1:		Line 1:

	==SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES==		==SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES==
-	<StructureSection load='1axl' size='340' side='right' caption='[[1axl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>	+	<StructureSection load='1axl' size='340' side='right'caption='[[1axl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AXL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AXL FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Broyde, S]]		[[Category: Broyde, S]]
	[[Category: Feng, B]]		[[Category: Feng, B]]

OCA at 06:16, 17 August 2017

2017-08-17T06:16:53Z

←Older revision		Revision as of 06:16, 17 August 2017
Line 1:		Line 1:
		+
	==SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES==		==SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES==
	<StructureSection load='1axl' size='340' side='right' caption='[[1axl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>		<StructureSection load='1axl' size='340' side='right' caption='[[1axl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AXL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AXL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</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=1axl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1axl OCA], [http://pdbe.org/1axl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1axl RCSB], [http://www.ebi.ac.uk/pdbsum/1axl 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=1axl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1axl OCA], [http://pdbe.org/1axl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1axl RCSB], [http://www.ebi.ac.uk/pdbsum/1axl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1axl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:34, 11 September 2015

2015-09-11T06:34:03Z

←Older revision		Revision as of 06:34, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AXL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AXL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</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=1axl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1axl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1axl RCSB], [http://www.ebi.ac.uk/pdbsum/1axl 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=1axl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1axl OCA], [http://pdbe.org/1axl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1axl RCSB], [http://www.ebi.ac.uk/pdbsum/1axl PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 14:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1axl" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:19, 22 December 2014

2014-12-22T11:19:05Z

←Older revision		Revision as of 11:19, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AXL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AXL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1axl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1axl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1axl RCSB], [http://www.ebi.ac.uk/pdbsum/1axl 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=1axl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1axl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1axl RCSB], [http://www.ebi.ac.uk/pdbsum/1axl PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Broyde, S.]]	+	[[Category: Broyde, S]]
-	[[Category: Feng, B.]]	+	[[Category: Feng, B]]
-	[[Category: Geacintov, N E.]]	+	[[Category: Geacintov, N E]]
-	[[Category: Gorin, A A.]]	+	[[Category: Gorin, A A]]
-	[[Category: Hingerty, B E.]]	+	[[Category: Hingerty, B E]]
-	[[Category: Kolbanovskiy, A.]]	+	[[Category: Kolbanovskiy, A]]
-	[[Category: Patel, D J.]]	+	[[Category: Patel, D J]]
	[[Category: Carcinogen]]		[[Category: Carcinogen]]
	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
	[[Category: Dna]]		[[Category: Dna]]

OCA at 03:24, 7 August 2014

2014-08-07T03:24:30Z

←Older revision		Revision as of 03:24, 7 August 2014
Line 1:		Line 1:
-	[[~~Image:~~1axl.~~png~~\|~~left\|200px~~]]	+	==SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES==
		+	<StructureSection load='1axl' size='340' side='right' caption='[[1axl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1AXL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BAP:1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE'>BAP</scene><br>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1axl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1axl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1axl RCSB], [http://www.ebi.ac.uk/pdbsum/1axl PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A combined NMR-computational approach was employed to determine the solution structure of the (-)-trans-anti-[BP]dG adduct positioned opposite a -1 deletion site in the d(C1-C2-A3-T4-C5- [BP]G6-C7-T8-A9-C10-C11).d(G12-G13-T14-A15-G1 6-G17-A18-T19-G20-G21) sequence context. The (-)-trans-anti-[BP]dG moiety is derived from the binding of the (-)-anti-benzo[a]pyrene diol epoxide [(-)-anti-BPDE] to N2 of dG6 and has a 10R absolute configuration at the [BP]dG linkage site. The exchangeable and non-exchangeable protons of the benzo[a]pyrenyl moiety and the nucleic acid were assigned following analysis of two-dimensional NMR data sets in H2O and D2O solution. The solution conformation has been determined by incorporating intramolecular and intermolecular proton-proton distances defined by lower and upper bounds deduced from NOESY spectra as restraints in molecular mechanics computations in torsion angle space followed by restrained molecular dynamics calculations based on a NOE distance and intensity refinement protocol. Our structural studies establish that the aromatic BP ring system intercalates into the helix opposite the deletion site, while the modified deoxyguanosine residue is displaced into the minor groove with its face parallel to the helix axis. The intercalation site is wedge-shaped and the BP aromatic ring system stacks over intact flanking Watson-Crick dG.dC base pairs. The modified deoxyguanosine stacks over the minor groove face of the sugar ring of the 5'-flanking dC5 residue. The BP moiety is positioned with the benzylic ring oriented toward the minor groove and the distal pyrenyl aromatic ring directed toward the major groove. This conformation strikingly contrasts with the corresponding structure in the full duplex with the same 10R (-)-trans-anti-[BP]dG lesion positioned opposite a complementary dC residue [de los Santos et al. (1992) Biochemistry 31, 5245-5252); in this case the aromatic BP ring system is located in the minor groove, and there is no disruption of the [BP]dG.dC Watson-Crick base pairing alignment. The intercalation-base displacement features of the 10R (-)-trans-anti-[BP]dG adduct opposite a deletion site have features in common to those of the 10S (+)-trans-anti-[BP]dG adduct opposite a deletion site previously reported by Cosman et al. [(1994)(Biochemistry 33, 11507-11517], except that there is a nearly 180 degrees rotation of the BP residue about the axis of the helix at the base-displaced intercalation site and the modified deoxyguanosine is positioned in the opposite groove. In the 10S adduct, the benzylic ring is in the major groove and the aromatic ring systems point toward the minor groove. This work extends the theme of opposite orientations of adducts derived from chiral pairs of (+)- and (-)-anti-BPDE enantiomers; both 10S and 10R adducts can be positioned with opposite orientations either in the minor groove or at base displaced intercalation sites, depending on the presence or absence of the partner dC base in the complementary strand.

-	~~{{STRUCTURE_1axl\| PDB=1axl \| SCENE= }}~~	+	Solution conformation of the (-)-trans-anti-[BP]dG adduct opposite a deletion site in a DNA duplex: intercalation of the covalently attached benzo[a]pyrene into the helix with base displacement of the modified deoxyguanosine into the minor groove.,Feng B, Gorin A, Kolbanovskiy A, Hingerty BE, Geacintov NE, Broyde S, Patel DJ Biochemistry. 1997 Nov 11;36(45):13780-90. PMID:9374854<ref>PMID:9374854</ref>

-	~~===SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG)~~, ~~NMR, 6 STRUCTURES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9374854}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[1axl]] is a 2 chain structure. Full experimental information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA].~~	+	</StructureSection>
	[[Category: Broyde, S.]]		[[Category: Broyde, S.]]
	[[Category: Feng, B.]]		[[Category: Feng, B.]]

OCA: Protected "1axl" [edit=sysop:move=sysop]

2012-10-21T12:22:23Z

Protected "1axl" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:22, 21 October 2012

OCA at 12:22, 21 October 2012

2012-10-21T12:22:16Z

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	{{STRUCTURE_1axl\| PDB=1axl \| SCENE= }}		{{STRUCTURE_1axl\| PDB=1axl \| SCENE= }}

	===SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES===		===SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES===

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	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA].	+	[[1axl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA].
-		+
-	~~==Reference==~~	+
-	Solution conformation of the (-)-trans-anti-[BP]dG adduct opposite a deletion site in a DNA duplex: intercalation of the covalently attached benzo[a]pyrene into the helix with base displacement of the modified deoxyguanosine into the minor groove., Feng B, Gorin A, Kolbanovskiy A, Hingerty BE, Geacintov NE, Broyde S, Patel DJ, Biochemistry. 1997 Nov 11;36(45):13780-90. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9374854 9374854]	+
	[[Category: Broyde, S.]]		[[Category: Broyde, S.]]
	[[Category: Feng, B.]]		[[Category: Feng, B.]]
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	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
	[[Category: Dna]]		[[Category: Dna]]
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OCA at 14:48, 30 June 2008

2008-06-30T14:48:38Z

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-	~~'''~~SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES~~'''~~	+	===SOLUTION CONFORMATION OF THE (-)-TRANS-ANTI-[BP]DG ADDUCT OPPOSITE A DELETION SITE IN DNA DUPLEX D(CCATC-[BP]G-CTACC)D(GGTAG--GATGG), NMR, 6 STRUCTURES===


-	~~==Overview==~~	+	<!--
-	~~A combined NMR~~-~~computational approach was employed to determine the solution structure of the (~~-~~)-trans-anti-[BP]dG adduct positioned opposite a -1 deletion site in the d(C1-C2-A3-T4-C5- [BP]G6-C7-T8-A9-C10-C11).d(G12-G13-T14-A15-G1 6-G17-A18-T19-G20-G21) sequence context.~~ The ~~(-)-trans-anti-[BP]dG moiety is derived from~~ the ~~binding of~~ the (-)-anti-benzo[a]pyrene diol epoxide [(-)-anti-BPDE] to N2 of dG6 and has a 10R absolute configuration at the [BP]dG linkage site. The exchangeable and non-exchangeable protons of the benzo[a]pyrenyl moiety and the nucleic acid were assigned following analysis of two-dimensional NMR data sets in H2O and D2O solution. The solution conformation has been determined by incorporating intramolecular and intermolecular proton-proton distances defined by lower and upper bounds deduced from NOESY spectra as ~~restraints in molecular mechanics computations in torsion angle space followed by restrained molecular dynamics calculations based~~ on ~~a NOE distance and intensity refinement protocol~~. Our structural studies establish that the aromatic BP ring system intercalates into the helix opposite the deletion site, while the modified deoxyguanosine residue is displaced into the minor groove with its face parallel to the helix axis. The intercalation site is wedge-shaped and the BP aromatic ring system stacks over intact flanking Watson-Crick dG.dC base pairs. The modified deoxyguanosine stacks over the minor groove face of the sugar ring of the 5'-flanking dC5 residue. The BP moiety is positioned with the benzylic ring oriented toward the minor groove and the distal pyrenyl aromatic ring directed toward the major groove. This conformation strikingly contrasts with the corresponding structure in the full duplex with the same 10R (-)~~-trans-anti-[BP]dG lesion positioned opposite a complementary dC residue [de los Santos et al. (1992) Biochemistry 31~~, ~~5245-5252); in this case the aromatic BP ring system~~ is ~~located in~~ the ~~minor groove, and there is no disruption of the [BP]dG~~.~~dC Watson~~-~~Crick base pairing alignment. The intercalation~~-base displacement features of the 10R (-)-trans-anti-[BP]dG adduct opposite a deletion site have features in common to those of the 10S (+)-trans-anti-[BP]dG adduct opposite a deletion site previously reported by Cosman et al. [(1994)(Biochemistry 33, 11507-11517], except that there is a nearly 180 degrees rotation of the BP residue about the axis of the helix at the base-displaced intercalation site and the modified deoxyguanosine is positioned in the opposite groove. In the 10S adduct, the benzylic ring is in the major groove and the aromatic ring systems point toward the minor groove. This work extends the theme of opposite orientations of adducts derived from chiral pairs of (+)- and (-)-anti-BPDE enantiomers; both 10S and 10R adducts can be positioned with opposite orientations either in the minor groove or at base displaced intercalation sites, depending on the presence or absence of the partner dC base in the complementary strand.	+	The line below this paragraph, {{ABSTRACT_PUBMED_9374854}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9374854 is the PubMed ID number.
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		+	{{ABSTRACT_PUBMED_9374854}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AXL OCA].

	==Reference==		==Reference==
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	[[Category: Deoxyribonucleic acid]]		[[Category: Deoxyribonucleic acid]]
	[[Category: Dna]]		[[Category: Dna]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May 2 10~~:48:47 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 17:48:37 2008''