1la8 - Revision history

OCA at 18:47, 29 November 2023

2023-11-29T18:47:47Z

←Older revision		Revision as of 18:47, 29 November 2023
Line 1:		Line 1:

	==Solution structure of the DNA hairpin 13-mer CGCGGTGTCCGCG==		==Solution structure of the DNA hairpin 13-mer CGCGGTGTCCGCG==
-	<StructureSection load='1la8' size='340' side='right'caption='[[1la8~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='1la8' size='340' side='right'caption='[[1la8]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'>[[1lae\|1lae]], [[1lai\|1lai]], [[1laq\|1laq]], [[1las\|1las]]</div~~></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'>[https://proteopedia.org/fgij/fg.htm?mol=1la8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1la8 OCA], [https://pdbe.org/1la8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1la8 RCSB], [https://www.ebi.ac.uk/pdbsum/1la8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1la8 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=1la8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1la8 OCA], [https://pdbe.org/1la8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1la8 RCSB], [https://www.ebi.ac.uk/pdbsum/1la8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1la8 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Marnett~~, L J~~]]	+	[[Category: Marnett LJ]]
-	[[Category: Reddy~~, G R~~]]	+	[[Category: Reddy GR]]
-	[[Category: Stone~~, M P~~]]	+	[[Category: Stone MP]]
-	[[Category: Weisenseel~~, J P]]~~	+	[[Category: Weisenseel JP]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Hairpin]]~~	+
-	~~[[Category: Three base loop~~]]	+

OCA at 05:53, 28 April 2021

2021-04-28T05:53:06Z

←Older revision		Revision as of 05:53, 28 April 2021
Line 3:		Line 3:
	<StructureSection load='1la8' size='340' side='right'caption='[[1la8]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1la8' size='340' side='right'caption='[[1la8]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lae\|1lae]], [[1lai\|1lai]], [[1laq\|1laq]], [[1las\|1las]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lae\|1lae]], [[1lai\|1lai]], [[1laq\|1laq]], [[1las\|1las]]</div></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=1la8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1la8 OCA], [~~http~~://pdbe.org/1la8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1la8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1la8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1la8 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=1la8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1la8 OCA], [https://pdbe.org/1la8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1la8 RCSB], [https://www.ebi.ac.uk/pdbsum/1la8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1la8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:11, 24 July 2019

2019-07-24T09:11:23Z

←Older revision		Revision as of 09:11, 24 July 2019
Line 1:		Line 1:

	==Solution structure of the DNA hairpin 13-mer CGCGGTGTCCGCG==		==Solution structure of the DNA hairpin 13-mer CGCGGTGTCCGCG==
-	<StructureSection load='1la8' size='340' side='right' caption='[[1la8]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='1la8' size='340' side='right'caption='[[1la8]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Marnett, L J]]		[[Category: Marnett, L J]]
	[[Category: Reddy, G R]]		[[Category: Reddy, G R]]

OCA at 10:51, 18 October 2017

2017-10-18T10:51:17Z

←Older revision		Revision as of 10:51, 18 October 2017
Line 1:		Line 1:
		+
	==Solution structure of the DNA hairpin 13-mer CGCGGTGTCCGCG==		==Solution structure of the DNA hairpin 13-mer CGCGGTGTCCGCG==
	<StructureSection load='1la8' size='340' side='right' caption='[[1la8]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1la8' size='340' side='right' caption='[[1la8]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lae\|1lae]], [[1lai\|1lai]], [[1laq\|1laq]], [[1las\|1las]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lae\|1lae]], [[1lai\|1lai]], [[1laq\|1laq]], [[1las\|1las]]</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=1la8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1la8 OCA], [http://pdbe.org/1la8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1la8 RCSB], [http://www.ebi.ac.uk/pdbsum/1la8 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=1la8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1la8 OCA], [http://pdbe.org/1la8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1la8 RCSB], [http://www.ebi.ac.uk/pdbsum/1la8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1la8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:38, 11 September 2015

2015-09-11T10:38:22Z

←Older revision		Revision as of 10:38, 11 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lae\|1lae]], [[1lai\|1lai]], [[1laq\|1laq]], [[1las\|1las]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lae\|1lae]], [[1lai\|1lai]], [[1laq\|1laq]], [[1las\|1las]]</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=1la8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1la8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1la8 RCSB], [http://www.ebi.ac.uk/pdbsum/1la8 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=1la8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1la8 OCA], [http://pdbe.org/1la8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1la8 RCSB], [http://www.ebi.ac.uk/pdbsum/1la8 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 1la8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:15, 22 December 2014

2014-12-22T05:15:53Z

←Older revision		Revision as of 05:15, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lae\|1lae]], [[1lai\|1lai]], [[1laq\|1laq]], [[1las\|1las]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lae\|1lae]], [[1lai\|1lai]], [[1laq\|1laq]], [[1las\|1las]]</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=1la8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1la8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1la8 RCSB], [http://www.ebi.ac.uk/pdbsum/1la8 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=1la8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1la8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1la8 RCSB], [http://www.ebi.ac.uk/pdbsum/1la8 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Marnett, L J.]]	+	[[Category: Marnett, L J]]
-	[[Category: Reddy, G R.]]	+	[[Category: Reddy, G R]]
-	[[Category: Stone, M P.]]	+	[[Category: Stone, M P]]
-	[[Category: Weisenseel, J P.]]	+	[[Category: Weisenseel, J P]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Hairpin]]		[[Category: Hairpin]]
	[[Category: Three base loop]]		[[Category: Three base loop]]

OCA at 05:49, 8 June 2014

2014-06-08T05:49:46Z

←Older revision		Revision as of 05:49, 8 June 2014
Line 1:		Line 1:
-	[[~~Image:~~1la8.~~png~~\|~~left~~\|~~200px~~]]	+	==Solution structure of the DNA hairpin 13-mer CGCGGTGTCCGCG==
		+	<StructureSection load='1la8' size='340' side='right' caption='[[1la8]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LA8 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lae\|1lae]], [[1lai\|1lai]], [[1laq\|1laq]], [[1las\|1las]]</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=1la8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1la8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1la8 RCSB], [http://www.ebi.ac.uk/pdbsum/1la8 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The solution structure of the 1,N(2)-propanodeoxyguanosine (PdG) adduct was determined in a 3-base hairpin loop formed by d(CGCGGTXTCCGCG) (X = PdG). This sequence is contained within the Salmonella typhimurium hisD3052 gene, a hotspot for frameshift mutagenesis. PdG provides a structural model for the primary adduct induced in DNA by malondialdehyde, the 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)pyrimido[1,2-a]-purin-10(3H)-one (M(1)G) lesion. The solution structure of the PdG-containing hairpin was refined by molecular dynamics calculations restrained by a combination of NMR-derived distances and dihedral angles, using a simulated annealing protocol. The structure of the PdG-modified hairpin consisted of a five-base-pair stem and a three-base loop consisting of T(6), X(7), and T(8). T(6) projected into the minor groove of the stem adjacent to G(4). The modified base X(7) stacked on top of the duplex stem and wedged between bases T(8) and C(9). The PdG moiety was oriented such that the imidazole proton was facing the minor groove of the stem and the exocyclic protons projected into the major groove. The structure of the adducted hairpin was compared with the structure of the corresponding unmodified oligodeoxynucleotide, and was found to be similar. There was a minor difference in the backbone angles of the G and PdG Hairpins at the phosphate linkage between G(5) and T(6) involving the G(5) epsilon angle and T(6) alpha and beta angles. The PdG-modified hairpin exhibited an increase in T(m) of approximately 2 degrees C compared to the unmodified hairpin. The structural and thermodynamic similarities suggested that PdG does not stabilize this hairpin and thus may not promote its extrusion in duplex DNA. The structural results are correlated with the results of site-specific mutagenesis experiments in the same sequence, which do not show evidence of frameshift mutations associated with hairpin loop formation. The geometry of this three-base loop is similar to that of other DNA hairpins containing three-base loops, and suggests a common motif for the folding of these loops.

-	~~{{STRUCTURE_1la8\| PDB=1la8 \| SCENE= }}~~	+	Structure of the 1,N(2)-propanodeoxyguanosine adduct in a three-base DNA hairpin loop derived from a palindrome in the Salmonella typhimurium hisD3052 gene.,Weisenseel JP, Reddy GR, Marnett LJ, Stone MP Chem Res Toxicol. 2002 Feb;15(2):140-52. PMID:11849039<ref>PMID:11849039</ref>

-	~~===Solution structure~~ of the ~~DNA hairpin 13-mer CGCGGTGTCCGCG===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11849039}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1la8]] is a 1 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1LA8 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011849039<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Marnett, L J.]]		[[Category: Marnett, L J.]]
	[[Category: Reddy, G R.]]		[[Category: Reddy, G R.]]

OCA: Protected "1la8" [edit=sysop:move=sysop]

2012-08-14T15:22:38Z

Protected "1la8" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:22, 14 August 2012

OCA at 15:22, 14 August 2012

2012-08-14T15:22:36Z

←Older revision		Revision as of 15:22, 14 August 2012
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-	{{Seed}}
	[[Image:1la8.png\|left\|200px]]		[[Image:1la8.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_1la8\| PDB=1la8 \| SCENE= }}		{{STRUCTURE_1la8\| PDB=1la8 \| SCENE= }}

	===Solution structure of the DNA hairpin 13-mer CGCGGTGTCCGCG===		===Solution structure of the DNA hairpin 13-mer CGCGGTGTCCGCG===

-
-	<!--
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	{{ABSTRACT_PUBMED_11849039}}		{{ABSTRACT_PUBMED_11849039}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA].	+	[[1la8]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA].

	==Reference==		==Reference==
-	Structure of the 1,N(2)-propanodeoxyguanosine adduct in a three-base DNA hairpin loop derived from a palindrome in the Salmonella typhimurium hisD3052 gene., Weisenseel JP, Reddy GR, Marnett LJ, Stone MP, Chem Res Toxicol. 2002 Feb;15(2):140-52. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~11849039 11849039]~~	+	<ref group="xtra">PMID:011849039</ref><references group="xtra"/>
	[[Category: Marnett, L J.]]		[[Category: Marnett, L J.]]
	[[Category: Reddy, G R.]]		[[Category: Reddy, G R.]]
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	[[Category: Hairpin]]		[[Category: Hairpin]]
	[[Category: Three base loop]]		[[Category: Three base loop]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 12:06:01 2008''

OCA at 09:06, 2 July 2008

2008-07-02T09:06:08Z

←Older revision		Revision as of 09:06, 2 July 2008
Line 1:		Line 1:
-	[[Image:1la8.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1la8.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1la8\| PDB=1la8 \| SCENE= }}		{{STRUCTURE_1la8\| PDB=1la8 \| SCENE= }}

-	~~'''~~Solution structure of the DNA hairpin 13-mer CGCGGTGTCCGCG~~'''~~	+	===Solution structure of the DNA hairpin 13-mer CGCGGTGTCCGCG===


-	~~==Overview==~~	+	<!--
-	~~The solution structure of the 1,N(2)~~-~~propanodeoxyguanosine (PdG) adduct was determined in a 3~~-base hairpin loop formed by d(CGCGGTXTCCGCG) (X = PdG). This sequence is contained within the Salmonella typhimurium hisD3052 gene, a hotspot for frameshift mutagenesis. PdG provides a structural model for the primary adduct induced in DNA by malondialdehyde, the 3-(2'-deoxy-beta-D-erythro-pentofuranosyl)pyrimido[1,2-a]-purin-10(3H)-one (M(1)G) lesion. The ~~solution structure of the PdG-containing hairpin was refined by molecular dynamics calculations restrained by a combination of NMR-derived distances and dihedral angles~~, ~~using a simulated annealing protocol. The structure of the PdG-modified hairpin consisted of a five-base-pair stem and a three-base loop consisting of T(6)~~, ~~X(7), and T(8). T(6) projected into~~ the ~~minor groove of~~ the ~~stem adjacent to G~~(~~4). The modified base X(7) stacked~~ on ~~top of the duplex stem and wedged between bases T(8) and C(9)~~. ~~The PdG moiety was oriented such that the imidazole proton was facing the minor groove of the stem and the exocyclic protons projected into the major groove~~. ~~The structure of the adducted hairpin was compared with the structure of the corresponding unmodified oligodeoxynucleotide~~, ~~and was found to be similar. There was a minor difference in~~ the ~~backbone angles of the G and PdG Hairpins at the phosphate linkage between G(5) and T(6) involving the G(5) epsilon angle and T(6) alpha and beta angles~~. ~~The PdG~~-modified hairpin exhibited an increase in T(m) of approximately 2 degrees C compared to the unmodified hairpin. The structural and thermodynamic similarities suggested that PdG does not stabilize this hairpin and thus may not promote its extrusion in duplex DNA. The structural results are correlated with the results of site-specific mutagenesis experiments in the same sequence, which do not show evidence of frameshift mutations associated with hairpin loop formation. The geometry of this three-base loop is similar to that of other DNA hairpins containing three-base loops, and suggests a common motif for the folding of these loops.	+	The line below this paragraph, {{ABSTRACT_PUBMED_11849039}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 11849039 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_11849039}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LA8 OCA].

	==Reference==		==Reference==
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	[[Category: Hairpin]]		[[Category: Hairpin]]
	[[Category: Three base loop]]		[[Category: Three base loop]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May~~ 2 23:43:10 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 12:06:01 2008''