1fzl - Revision history

OCA at 18:36, 29 November 2023

2023-11-29T18:36:35Z

←Older revision		Revision as of 18:36, 29 November 2023
Line 1:		Line 1:

	==DNA WITH PYRENE PAIRED AT ABASIC SITES==		==DNA WITH PYRENE PAIRED AT ABASIC SITES==
-	<StructureSection load='1fzl' size='340' side='right'caption='[[1fzl~~]], [[NMR_Ensembles_of_Models \| 6 NMR models~~]]' scene=''>	+	<StructureSection load='1fzl' size='340' side='right'caption='[[1fzl]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1fzl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FZL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fzl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FZL FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</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='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height~~: ~~3em;~~'>~~[[1fzs\|1fzs]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</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=1fzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzl OCA], [https://pdbe.org/1fzl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fzl RCSB], [https://www.ebi.ac.uk/pdbsum/1fzl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzl 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=1fzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzl OCA], [https://pdbe.org/1fzl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fzl RCSB], [https://www.ebi.ac.uk/pdbsum/1fzl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzl ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kool~~, E T~~]]	+	[[Category: Kool ET]]
-	[[Category: Matray~~, T J]]~~	+	[[Category: Matray TJ]]
-	~~[[Category: Santos, C de los~~]]	+	[[Category: Smirnov S]]
-	[[Category: Smirnov, S]]	+	[[Category: De los Santos C]]
-	[[Category: ~~Dna]]~~	+
-	~~[[Category: Non-hydrogen bonded dna base pair]]~~	+
-	~~[[Category: Pyrene]]~~	+
-	~~[[Category: Tetrahydrofuran~~]]	+

OCA at 07:10, 24 March 2021

2021-03-24T07:10:13Z

←Older revision		Revision as of 07:10, 24 March 2021
Line 3:		Line 3:
	<StructureSection load='1fzl' size='340' side='right'caption='[[1fzl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>		<StructureSection load='1fzl' size='340' side='right'caption='[[1fzl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1fzl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1FZL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1fzl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FZL FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</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=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzs\|1fzs]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fzs\|1fzs]]</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=1fzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzl OCA], [~~http~~://pdbe.org/1fzl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1fzl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1fzl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzl 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=1fzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzl OCA], [https://pdbe.org/1fzl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fzl RCSB], [https://www.ebi.ac.uk/pdbsum/1fzl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:27, 19 June 2019

2019-06-19T07:27:50Z

←Older revision		Revision as of 07:27, 19 June 2019
Line 1:		Line 1:

	==DNA WITH PYRENE PAIRED AT ABASIC SITES==		==DNA WITH PYRENE PAIRED AT ABASIC SITES==
-	<StructureSection load='1fzl' size='340' side='right' caption='[[1fzl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>	+	<StructureSection load='1fzl' size='340' side='right'caption='[[1fzl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1fzl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fzl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZL FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Kool, E T]]		[[Category: Kool, E T]]
	[[Category: Matray, T J]]		[[Category: Matray, T J]]

OCA at 10:51, 13 September 2017

2017-09-13T10:51:37Z

←Older revision		Revision as of 10:51, 13 September 2017
Line 1:		Line 1:
		+
	==DNA WITH PYRENE PAIRED AT ABASIC SITES==		==DNA WITH PYRENE PAIRED AT ABASIC SITES==
	<StructureSection load='1fzl' size='340' side='right' caption='[[1fzl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>		<StructureSection load='1fzl' size='340' side='right' caption='[[1fzl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</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=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzs\|1fzs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzs\|1fzs]]</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=1fzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzl OCA], [http://pdbe.org/1fzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fzl RCSB], [http://www.ebi.ac.uk/pdbsum/1fzl 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=1fzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzl OCA], [http://pdbe.org/1fzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fzl RCSB], [http://www.ebi.ac.uk/pdbsum/1fzl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1fzl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:49, 12 September 2015

2015-09-12T01:49:35Z

←Older revision		Revision as of 01:49, 12 September 2015
Line 5:		Line 5:
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</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=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzs\|1fzs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzs\|1fzs]]</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=1fzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fzl RCSB], [http://www.ebi.ac.uk/pdbsum/1fzl 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=1fzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzl OCA], [http://pdbe.org/1fzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fzl RCSB], [http://www.ebi.ac.uk/pdbsum/1fzl PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	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 1fzl" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:54, 22 December 2014

2014-12-22T23:54:13Z

←Older revision		Revision as of 23:54, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1fzl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1fzl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</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=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzs\|1fzs]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzs\|1fzs]]</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=1fzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fzl RCSB], [http://www.ebi.ac.uk/pdbsum/1fzl 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=1fzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fzl RCSB], [http://www.ebi.ac.uk/pdbsum/1fzl 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 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Kool, E T.]]	+	[[Category: Kool, E T]]
-	[[Category: Matray, T J.]]	+	[[Category: Matray, T J]]
-	[[Category: Santos, C de los.]]	+	[[Category: Santos, C de los]]
-	[[Category: Smirnov, S.]]	+	[[Category: Smirnov, S]]
	[[Category: Dna]]		[[Category: Dna]]
	[[Category: Non-hydrogen bonded dna base pair]]		[[Category: Non-hydrogen bonded dna base pair]]
	[[Category: Pyrene]]		[[Category: Pyrene]]
	[[Category: Tetrahydrofuran]]		[[Category: Tetrahydrofuran]]

OCA at 13:39, 28 September 2014

2014-09-28T13:39:23Z

←Older revision		Revision as of 13:39, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1fzl.~~png~~\|~~left~~\|~~200px~~]]	+	==DNA WITH PYRENE PAIRED AT ABASIC SITES==
		+	<StructureSection load='1fzl' size='340' side='right' caption='[[1fzl]], [[NMR_Ensembles_of_Models \| 6 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1fzl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FZL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=PYP:2-DEOXYRIBOFURANOSYLPYRENE-5-MONOPHOSPHATE'>PYP</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1fzs\|1fzs]]</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=1fzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fzl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1fzl RCSB], [http://www.ebi.ac.uk/pdbsum/1fzl PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA polymerases specifically insert the hydrophobic pyrene deoxynucleotide (P) opposite tetrahydrofuran (F), an stable abasic site analog, and DNA duplexes containing this non-hydrogen-bonded pair possess a high degree of thermodynamic stability. These observations support the hypothesis that steric complementarity and stacking interactions may be sufficient for maintaining stability of DNA structure and specificity of DNA replication, even in the absence of hydrogen bonds across the base pair. Here we report the NMR characterization and structure determination of two DNA molecules containing pyrene residues. The first is a 13mer duplex with a pyrene.tetrahydrofuran pair (P.F pair) at the ninth position and the second mimics a replication intermediate right after incorporation of a pyrene nucleoside opposite an abasic site. Our data indicate that both molecules adopt right-handed helical conformations with Watson- Crick alignments for all canonical base pairs. The pyrene ring stays inside the helix close to its baseless partner in both molecules. The single-stranded region of the replication intermediate folds back over the opposing strand, sheltering the hydrophobic pyrene moiety from water exposure. The results support the idea that the stability and replication of a P.F pair is due to its ability to mimic Watson-Crick structure.

-	~~{{STRUCTURE_1fzl\| PDB=1fzl \| SCENE= }}~~	+	Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites.,Smirnov S, Matray TJ, Kool ET, de los Santos C Nucleic Acids Res. 2002 Dec 15;30(24):5561-9. PMID:12490724<ref>PMID:12490724</ref>

-	~~===DNA WITH PYRENE PAIRED AT ABASIC SITES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12490724}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1fzl]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1FZL OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012490724<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Kool, E T.]]		[[Category: Kool, E T.]]
	[[Category: Matray, T J.]]		[[Category: Matray, T J.]]

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

2012-11-21T10:10:55Z

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

←Older revision

Revision as of 10:10, 21 November 2012

OCA at 10:10, 21 November 2012

2012-11-21T10:10:52Z

←Older revision		Revision as of 10:10, 21 November 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1fzl.png\|left\|200px]]		[[Image:1fzl.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_1fzl\| PDB=1fzl \| SCENE= }}		{{STRUCTURE_1fzl\| PDB=1fzl \| SCENE= }}

	===DNA WITH PYRENE PAIRED AT ABASIC SITES===		===DNA WITH PYRENE PAIRED AT ABASIC SITES===

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-	(as it appears on PubMed at http://www.pubmed.gov), where 12490724 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_12490724}}		{{ABSTRACT_PUBMED_12490724}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZL OCA].	+	[[1fzl]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FZL OCA].

	==Reference==		==Reference==
-	~~Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites., Smirnov S, Matray TJ, Kool ET, de los Santos C, Nucleic Acids Res. 2002 Dec 15;30(24):5561-9.~~ PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~12490724 12490724]~~	+	<ref group="xtra">PMID:012490724</ref><references group="xtra"/>
	[[Category: Kool, E T.]]		[[Category: Kool, E T.]]
	[[Category: Matray, T J.]]		[[Category: Matray, T J.]]
	[[Category: Santos, C de los.]]		[[Category: Santos, C de los.]]
	[[Category: Smirnov, S.]]		[[Category: Smirnov, S.]]
		+	[[Category: Dna]]
	[[Category: Non-hydrogen bonded dna base pair]]		[[Category: Non-hydrogen bonded dna base pair]]
	[[Category: Pyrene]]		[[Category: Pyrene]]
	[[Category: Tetrahydrofuran]]		[[Category: Tetrahydrofuran]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 04:10:40 2008''

OCA at 01:10, 1 July 2008

2008-07-01T01:10:42Z

←Older revision		Revision as of 01:10, 1 July 2008
Line 1:		Line 1:
-	[[Image:1fzl.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1fzl.png\|left\|200px]]

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	{{STRUCTURE_1fzl\| PDB=1fzl \| SCENE= }}		{{STRUCTURE_1fzl\| PDB=1fzl \| SCENE= }}

-	~~'''~~DNA WITH PYRENE PAIRED AT ABASIC SITES~~'''~~	+	===DNA WITH PYRENE PAIRED AT ABASIC SITES===


-	~~==Overview==~~	+	<!--
-	~~DNA polymerases specifically insert the hydrophobic pyrene deoxynucleotide (P) opposite tetrahydrofuran (F)~~, ~~an stable abasic site analog~~, ~~and DNA duplexes containing this non-hydrogen-bonded pair possess a high degree of thermodynamic stability. These observations support~~ the ~~hypothesis that steric complementarity and stacking interactions may be sufficient for maintaining stability of DNA structure and specificity of DNA replication, even in~~ the absence of hydrogen bonds across the base pair. Here we report the NMR characterization and structure determination of two DNA molecules containing pyrene residues. The first is a 13mer duplex with a pyrene.tetrahydrofuran pair (~~P.F pair)~~ at ~~the ninth position and the second mimics a replication intermediate right after incorporation of a pyrene nucleoside opposite an abasic site~~. ~~Our data indicate that both molecules adopt right-handed helical conformations with Watson- Crick alignments for all canonical base pairs~~. ~~The pyrene ring stays inside the helix close to its baseless partner in both molecules. The single-stranded region of the replication intermediate folds back over the opposing strand~~, ~~sheltering~~ the ~~hydrophobic pyrene moiety from water exposure~~. ~~The results support the idea that the stability and replication of a P.F pair is due to its ability to mimic Watson~~-~~Crick structure.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_12490724}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 12490724 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_12490724}}

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

	==Reference==		==Reference==
Line 27:		Line 31:
	[[Category: Pyrene]]		[[Category: Pyrene]]
	[[Category: Tetrahydrofuran]]		[[Category: Tetrahydrofuran]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri May~~ ~~2 16~~:56:37 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 04:10:40 2008''