1y8d - Revision history

OCA at 09:30, 6 December 2023

2023-12-06T09:30:34Z

←Older revision		Revision as of 09:30, 6 December 2023
Line 1:		Line 1:

	==Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad==		==Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad==
-	<StructureSection load='1y8d' size='340' side='right'caption='[[1y8d~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>	+	<StructureSection load='1y8d' size='340' side='right'caption='[[1y8d]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y8D FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y8D 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;'>[[1eeg\|1eeg]], [[1jjp\|1jjp]]</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=1y8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8d OCA], [https://pdbe.org/1y8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y8d RCSB], [https://www.ebi.ac.uk/pdbsum/1y8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y8d 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=1y8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8d OCA], [https://pdbe.org/1y8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y8d RCSB], [https://www.ebi.ac.uk/pdbsum/1y8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y8d ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Andreola, M L]]	+	[[Category: Andreola M-L]]
-	[[Category: Faure, A]]	+	[[Category: Faure A]]
-	[[Category: Kuryavyi~~, V V~~]]	+	[[Category: Kuryavyi VV]]
-	[[Category: Ma, J B]]	+	[[Category: Ma J-B]]
-	[[Category: Patel~~, D J~~]]	+	[[Category: Patel DJ]]
-	[[Category: Phan~~, A T]]~~	+	[[Category: Phan AT]]
-	~~[[Category: 3+1 g-tetrad]]~~	+
-	~~[[Category: Dimeric parallel-stranded quadruplex]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Dna aptamer]]~~	+
-	~~[[Category: Gag triad]]~~	+
-	~~[[Category: Hiv-1 integrase inhibitor design]]~~	+
-	~~[[Category: Single nucleotide chain reversal loop~~]]	+

OCA at 16:24, 3 November 2021

2021-11-03T16:24:40Z

←Older revision		Revision as of 16:24, 3 November 2021
Line 3:		Line 3:
	<StructureSection load='1y8d' size='340' side='right'caption='[[1y8d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1y8d' size='340' side='right'caption='[[1y8d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Y8D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y8D FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1eeg\|1eeg]], [[1jjp\|1jjp]]</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;'>[[1eeg\|1eeg]], [[1jjp\|1jjp]]</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=1y8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8d OCA], [~~http~~://pdbe.org/1y8d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1y8d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1y8d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1y8d 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=1y8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8d OCA], [https://pdbe.org/1y8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y8d RCSB], [https://www.ebi.ac.uk/pdbsum/1y8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y8d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:33, 29 January 2020

2020-01-29T16:33:29Z

←Older revision		Revision as of 16:33, 29 January 2020
Line 1:		Line 1:

	==Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad==		==Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad==
-	<StructureSection load='1y8d' size='340' side='right' caption='[[1y8d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>	+	<StructureSection load='1y8d' size='340' side='right'caption='[[1y8d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y8D FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y8D FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Andreola, M L]]		[[Category: Andreola, M L]]
	[[Category: Faure, A]]		[[Category: Faure, A]]

OCA at 06:21, 25 April 2018

2018-04-25T06:21:30Z

←Older revision		Revision as of 06:21, 25 April 2018
Line 1:		Line 1:
		+
	==Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad==		==Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad==
	<StructureSection load='1y8d' size='340' side='right' caption='[[1y8d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='1y8d' size='340' side='right' caption='[[1y8d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y8D FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y8D FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1eeg\|1eeg]], [[1jjp\|1jjp]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1eeg\|1eeg]], [[1jjp\|1jjp]]</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=1y8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8d OCA], [http://pdbe.org/1y8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y8d RCSB], [http://www.ebi.ac.uk/pdbsum/1y8d 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=1y8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8d OCA], [http://pdbe.org/1y8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y8d RCSB], [http://www.ebi.ac.uk/pdbsum/1y8d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1y8d ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:15, 10 September 2015

2015-09-10T22:15:28Z

←Older revision		Revision as of 22:15, 10 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y8D FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y8D FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1eeg\|1eeg]], [[1jjp\|1jjp]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1eeg\|1eeg]], [[1jjp\|1jjp]]</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=1y8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y8d RCSB], [http://www.ebi.ac.uk/pdbsum/1y8d 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=1y8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8d OCA], [http://pdbe.org/1y8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1y8d RCSB], [http://www.ebi.ac.uk/pdbsum/1y8d 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 1y8d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:45, 22 December 2014

2014-12-22T04:45:18Z

←Older revision		Revision as of 04:45, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y8D FirstGlance]. <br>		<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y8D FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1eeg\|1eeg]], [[1jjp\|1jjp]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1eeg\|1eeg]], [[1jjp\|1jjp]]</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=1y8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y8d RCSB], [http://www.ebi.ac.uk/pdbsum/1y8d 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=1y8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y8d RCSB], [http://www.ebi.ac.uk/pdbsum/1y8d 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: Andreola, M L.]]	+	[[Category: Andreola, M L]]
-	[[Category: Faure, A.]]	+	[[Category: Faure, A]]
-	[[Category: Kuryavyi, V V.]]	+	[[Category: Kuryavyi, V V]]
-	[[Category: Ma, J B.]]	+	[[Category: Ma, J B]]
-	[[Category: Patel, D J.]]	+	[[Category: Patel, D J]]
-	[[Category: Phan, A T.]]	+	[[Category: Phan, A T]]
	[[Category: 3+1 g-tetrad]]		[[Category: 3+1 g-tetrad]]
	[[Category: Dimeric parallel-stranded quadruplex]]		[[Category: Dimeric parallel-stranded quadruplex]]

OCA at 06:44, 9 June 2014

2014-06-09T06:44:33Z

←Older revision		Revision as of 06:44, 9 June 2014
Line 1:		Line 1:
-	[[~~Image:~~1y8d.~~png~~\|~~left~~\|~~200px~~]]	+	==Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad==
		+	<StructureSection load='1y8d' size='340' side='right' caption='[[1y8d]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Y8D FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1eeg\|1eeg]], [[1jjp\|1jjp]]</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=1y8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y8d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1y8d RCSB], [http://www.ebi.ac.uk/pdbsum/1y8d PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We report on the NMR-based solution structure of the 93del d(GGGGTGGGAGGAGGGT) aptamer, a potent nanomolar inhibitor of HIV-1 integrase. This guanine-rich DNA sequence adopts an unusually stable dimeric quadruplex architecture in K+ solution. Within each 16-nt monomer subunit, which contains one A.(G.G.G.G) pentad sandwiched between two G.G.G.G tetrads, all G-stretches are parallel, and all guanines are anti with the exception of G1, which is syn. Dimer formation is achieved through mutual pairing of G1 of one monomer, with G2, G6, and G13 of the other monomer, to complete G.G.G.G tetrad formation. There are three single-nucleotide double-chain-reversal loops within each monomer fold, such that the first (T5) and third (A12) loops bridge three G-tetrad layers, whereas the second (A9) loop bridges two G-tetrad layers and participates in A.(G.G.G.G) pentad formation. Results of NMR and of integrase inhibition assays on loop-modified sequences allowed us to propose a strategy toward the potential design of improved HIV-1 integrase inhibitors. Finally, we propose a model, based on molecular docking approaches, for positioning the 93del dimeric DNA quadruplex within a basic channel/canyon formed between subunits of a dimer of dimers of HIV-1 integrase.

-	~~{{STRUCTURE_1y8d\| PDB=1y8d \| SCENE= }}~~	+	An interlocked dimeric parallel-stranded DNA quadruplex: a potent inhibitor of HIV-1 integrase.,Phan AT, Kuryavyi V, Ma JB, Faure A, Andreola ML, Patel DJ Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):634-9. Epub 2005 Jan 6. PMID:15637158<ref>PMID:15637158</ref>

-	~~===Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface~~, ~~single-residue chain reversal loops and GAG triad in~~ the ~~context of A(GGGG) pentad===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15637158}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1y8d]] is a 2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1Y8D OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015637158<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Andreola, M L.]]		[[Category: Andreola, M L.]]
	[[Category: Faure, A.]]		[[Category: Faure, A.]]

OCA: Protected "1y8d" [edit=sysop:move=sysop]

2012-08-14T14:34:09Z

Protected "1y8d" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:34, 14 August 2012

OCA at 14:34, 14 August 2012

2012-08-14T14:34:08Z

←Older revision		Revision as of 14:34, 14 August 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1y8d.png\|left\|200px]]		[[Image:1y8d.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1y8d", creates the "Structure Box" on the page.
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	{{STRUCTURE_1y8d\| PDB=1y8d \| SCENE= }}		{{STRUCTURE_1y8d\| PDB=1y8d \| SCENE= }}

	===Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad===		===Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15637158}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15637158 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_15637158}}		{{ABSTRACT_PUBMED_15637158}}

	==About this Structure==		==About this Structure==
-	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA].	+	[[1y8d]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA].

	==Reference==		==Reference==
-	An interlocked dimeric parallel-stranded DNA quadruplex: a potent inhibitor of HIV-1 integrase., Phan AT, Kuryavyi V, Ma JB, Faure A, Andreola ML, Patel DJ, Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):634-9. Epub 2005 Jan 6. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~15637158 15637158]~~	+	<ref group="xtra">PMID:015637158</ref><references group="xtra"/>
	[[Category: Andreola, M L.]]		[[Category: Andreola, M L.]]
	[[Category: Faure, A.]]		[[Category: Faure, A.]]
Line 32:		Line 20:
	[[Category: 3+1 g-tetrad]]		[[Category: 3+1 g-tetrad]]
	[[Category: Dimeric parallel-stranded quadruplex]]		[[Category: Dimeric parallel-stranded quadruplex]]
-	[[Category: Dna aptamer~~;hiv-1 integrase inhibitor design~~]]	+	[[Category: Dna]]
		+	[[Category: Dna aptamer]]
	[[Category: Gag triad]]		[[Category: Gag triad]]
		+	[[Category: Hiv-1 integrase inhibitor design]]
	[[Category: Single nucleotide chain reversal loop]]		[[Category: Single nucleotide chain reversal loop]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:27:13 2008''

OCA at 10:27, 28 July 2008

2008-07-28T10:27:16Z

←Older revision		Revision as of 10:27, 28 July 2008
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-	[[Image:1y8d.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1y8d.png\|left\|200px]]

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	{{STRUCTURE_1y8d\| PDB=1y8d \| SCENE= }}		{{STRUCTURE_1y8d\| PDB=1y8d \| SCENE= }}

-	~~'''~~Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad~~'''~~	+	===Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad===


-	~~==Overview==~~	+	<!--
-	~~We report on the NMR~~-~~based solution structure of the 93del d(GGGGTGGGAGGAGGGT) aptamer, a potent nanomolar inhibitor of HIV~~-~~1 integrase. This guanine-rich DNA sequence adopts an unusually stable dimeric quadruplex architecture in K+ solution. Within each 16-nt monomer subunit~~, ~~which contains one A.(G.G.G.G) pentad sandwiched between two G.G.G.G tetrads, all G-stretches are parallel~~, ~~and all guanines are anti with~~ the ~~exception of G1, which is syn. Dimer formation is achieved through mutual pairing of G1 of one monomer, with G2, G6, and G13 of~~ the ~~other monomer, to complete G~~.G.~~G.G tetrad formation. There are three single-nucleotide double-chain-reversal loops within each monomer fold, such that the first (T5~~) ~~and third (A12) loops bridge three G-tetrad layers~~, ~~whereas~~ the ~~second (A9) loop bridges two G-tetrad layers and participates in A~~.~~(G.G.G.G) pentad formation. Results of NMR and of integrase inhibition assays on loop~~-~~modified sequences allowed us to propose a strategy toward the potential design of improved HIV~~-1 integrase inhibitors. Finally, we propose a model, based on molecular docking approaches, for positioning the 93del dimeric DNA quadruplex within a basic channel/canyon formed between subunits of a dimer of dimers of HIV-1 integrase.	+	The line below this paragraph, {{ABSTRACT_PUBMED_15637158}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 15637158 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_15637158}}

	==About this Structure==		==About this Structure==
-	Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA].	+	Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y8D OCA].

	==Reference==		==Reference==
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	[[Category: Gag triad]]		[[Category: Gag triad]]
	[[Category: Single nucleotide chain reversal loop]]		[[Category: Single nucleotide chain reversal loop]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 16~~:00:07 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 13:27:13 2008''