2oey - Revision history

OCA at 12:53, 20 December 2023

OCA — Wed, 20 Dec 2023 12:53:05 GMT

←Older revision		Revision as of 12:53, 20 December 2023
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	==Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA==		==Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA==
-	<StructureSection load='2oey' size='340' side='right'caption='[[2oey~~]], [[NMR_Ensembles_of_Models \| 8 NMR models~~]]' scene=''>	+	<StructureSection load='2oey' size='340' side='right'caption='[[2oey]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2oey]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OEY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2oey]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OEY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=S2A:(1R,3AS,10S,10AR)-7-METHOXY-2-OXO-10,10A-DIHYDRO-2H,3AH-SPIRO[NAPHTHALENE-1,3-PENTALENO[1,2-B]NAPHTHALEN]-10-YL+2,6-DIDEOXY-2-(METHYLAMINO)-ALPHA-D-GALACTOPYRANOSIDE'>S2A</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=S2A:(1R,3AS,10S,10AR)-7-METHOXY-2-OXO-10,10A-DIHYDRO-2H,3AH-SPIRO[NAPHTHALENE-1,3-PENTALENO[1,2-B]NAPHTHALEN]-10-YL+2,6-DIDEOXY-2-(METHYLAMINO)-ALPHA-D-GALACTOPYRANOSIDE'>S2A</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=2oey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oey OCA], [https://pdbe.org/2oey PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oey RCSB], [https://www.ebi.ac.uk/pdbsum/2oey PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oey 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=2oey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oey OCA], [https://pdbe.org/2oey PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oey RCSB], [https://www.ebi.ac.uk/pdbsum/2oey PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oey ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Goldberg~~, I H~~]]	+	[[Category: Goldberg IH]]
-	[[Category: Jones~~, G B~~]]	+	[[Category: Jones GB]]
-	[[Category: Lin, Y]]	+	[[Category: Lin Y]]
-	[[Category: Xiao, Z]]	+	[[Category: Xiao Z]]
-	[[Category: Zhang, N]]	+	[[Category: Zhang N]]
-	~~[[Category: Designed spirocyclic helical ligand-bulged dna complex]]~~	+
-	~~[[Category: Dna~~]]	+

OCA at 07:51, 2 March 2022

OCA — Wed, 02 Mar 2022 07:51:07 GMT

←Older revision		Revision as of 07:51, 2 March 2022
Line 3:		Line 3:
	<StructureSection load='2oey' size='340' side='right'caption='[[2oey]], [[NMR_Ensembles_of_Models \| 8 NMR models]]' scene=''>		<StructureSection load='2oey' size='340' side='right'caption='[[2oey]], [[NMR_Ensembles_of_Models \| 8 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oey]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2OEY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oey]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OEY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=S2A:(1R,3AS,10S,10AR)-7-METHOXY-2-OXO-10,10A-DIHYDRO-2H,3AH-SPIRO[NAPHTHALENE-1,3-PENTALENO[1,2-B]NAPHTHALEN]-10-YL+2,6-DIDEOXY-2-(METHYLAMINO)-ALPHA-D-GALACTOPYRANOSIDE'>S2A</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=S2A:(1R,3AS,10S,10AR)-7-METHOXY-2-OXO-10,10A-DIHYDRO-2H,3AH-SPIRO[NAPHTHALENE-1,3-PENTALENO[1,2-B]NAPHTHALEN]-10-YL+2,6-DIDEOXY-2-(METHYLAMINO)-ALPHA-D-GALACTOPYRANOSIDE'>S2A</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=2oey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oey OCA], [~~http~~://pdbe.org/2oey PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2oey RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2oey PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2oey 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=2oey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oey OCA], [https://pdbe.org/2oey PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oey RCSB], [https://www.ebi.ac.uk/pdbsum/2oey PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oey ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:00, 27 May 2020

OCA — Wed, 27 May 2020 08:00:15 GMT

←Older revision		Revision as of 08:00, 27 May 2020
Line 1:		Line 1:

	==Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA==		==Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA==
-	<StructureSection load='2oey' size='340' side='right' caption='[[2oey]], [[NMR_Ensembles_of_Models \| 8 NMR models]]' scene=''>	+	<StructureSection load='2oey' size='340' side='right'caption='[[2oey]], [[NMR_Ensembles_of_Models \| 8 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oey]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2OEY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oey]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2OEY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=S2A:(1R,3AS,10S,10AR)-7-METHOXY-2-OXO-10,10A-DIHYDRO-2H,3AH-SPIRO[NAPHTHALENE-1,3-PENTALENO[1,2-B]NAPHTHALEN]-10-YL+2,6-DIDEOXY-2-(METHYLAMINO)-ALPHA-D-GALACTOPYRANOSIDE'>S2A</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=S2A:(1R,3AS,10S,10AR)-7-METHOXY-2-OXO-10,10A-DIHYDRO-2H,3AH-SPIRO[NAPHTHALENE-1,3-PENTALENO[1,2-B]NAPHTHALEN]-10-YL+2,6-DIDEOXY-2-(METHYLAMINO)-ALPHA-D-GALACTOPYRANOSIDE'>S2A</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=2oey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oey OCA], [http://pdbe.org/2oey PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oey RCSB], [http://www.ebi.ac.uk/pdbsum/2oey PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2oey ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2oey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oey OCA], [http://pdbe.org/2oey PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oey RCSB], [http://www.ebi.ac.uk/pdbsum/2oey PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2oey ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Goldberg, I H]]		[[Category: Goldberg, I H]]
	[[Category: Jones, G B]]		[[Category: Jones, G B]]

OCA at 07:24, 22 August 2018

OCA — Wed, 22 Aug 2018 07:24:34 GMT

←Older revision		Revision as of 07:24, 22 August 2018
Line 1:		Line 1:
		+
	==Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA==		==Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA==
	<StructureSection load='2oey' size='340' side='right' caption='[[2oey]], [[NMR_Ensembles_of_Models \| 8 NMR models]]' scene=''>		<StructureSection load='2oey' size='340' side='right' caption='[[2oey]], [[NMR_Ensembles_of_Models \| 8 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2oey]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OEY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2oey]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OEY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=S2A:(1R,3AS,10S,10AR)-7-METHOXY-2-OXO-10,10A-DIHYDRO-2H,3AH-SPIRO[NAPHTHALENE-1,3-PENTALENO[1,2-B]NAPHTHALEN]-10-YL+2,6-DIDEOXY-2-(METHYLAMINO)-ALPHA-D-GALACTOPYRANOSIDE'>S2A</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=S2A:(1R,3AS,10S,10AR)-7-METHOXY-2-OXO-10,10A-DIHYDRO-2H,3AH-SPIRO[NAPHTHALENE-1,3-PENTALENO[1,2-B]NAPHTHALEN]-10-YL+2,6-DIDEOXY-2-(METHYLAMINO)-ALPHA-D-GALACTOPYRANOSIDE'>S2A</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=2oey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oey OCA], [http://pdbe.org/2oey PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oey RCSB], [http://www.ebi.ac.uk/pdbsum/2oey 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=2oey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oey OCA], [http://pdbe.org/2oey PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oey RCSB], [http://www.ebi.ac.uk/pdbsum/2oey PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2oey ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:06, 10 September 2015

OCA — Thu, 10 Sep 2015 18:06:55 GMT

←Older revision		Revision as of 18:06, 10 September 2015
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[2oey]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OEY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2oey]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OEY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=S2A:(1R,3AS,10S,10AR)-7-METHOXY-2-OXO-10,10A-DIHYDRO-2H,3AH-SPIRO[NAPHTHALENE-1,3-PENTALENO[1,2-B]NAPHTHALEN]-10-YL+2,6-DIDEOXY-2-(METHYLAMINO)-ALPHA-D-GALACTOPYRANOSIDE'>S2A</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=S2A:(1R,3AS,10S,10AR)-7-METHOXY-2-OXO-10,10A-DIHYDRO-2H,3AH-SPIRO[NAPHTHALENE-1,3-PENTALENO[1,2-B]NAPHTHALEN]-10-YL+2,6-DIDEOXY-2-(METHYLAMINO)-ALPHA-D-GALACTOPYRANOSIDE'>S2A</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=2oey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oey OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oey RCSB], [http://www.ebi.ac.uk/pdbsum/2oey 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=2oey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oey OCA], [http://pdbe.org/2oey PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oey RCSB], [http://www.ebi.ac.uk/pdbsum/2oey 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 2oey" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:40, 25 January 2015

OCA — Sun, 25 Jan 2015 10:40:35 GMT

←Older revision		Revision as of 10:40, 25 January 2015
Line 18:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Goldberg, I H.]]	+	[[Category: Goldberg, I H]]
-	[[Category: Jones, G B.]]	+	[[Category: Jones, G B]]
-	[[Category: Lin, Y.]]	+	[[Category: Lin, Y]]
-	[[Category: Xiao, Z.]]	+	[[Category: Xiao, Z]]
-	[[Category: Zhang, N.]]	+	[[Category: Zhang, N]]
	[[Category: Designed spirocyclic helical ligand-bulged dna complex]]		[[Category: Designed spirocyclic helical ligand-bulged dna complex]]
	[[Category: Dna]]		[[Category: Dna]]

OCA at 09:27, 5 November 2014

OCA — Wed, 05 Nov 2014 09:27:18 GMT

←Older revision		Revision as of 09:27, 5 November 2014
Line 1:		Line 1:
-	[[~~Image:~~2oey.~~png~~\|~~left\|200px~~]]	+	==Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA==
		+	<StructureSection load='2oey' size='340' side='right' caption='[[2oey]], [[NMR_Ensembles_of_Models \| 8 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2oey]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OEY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OEY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=S2A:(1R,3AS,10S,10AR)-7-METHOXY-2-OXO-10,10A-DIHYDRO-2H,3AH-SPIRO[NAPHTHALENE-1,3-PENTALENO[1,2-B]NAPHTHALEN]-10-YL+2,6-DIDEOXY-2-(METHYLAMINO)-ALPHA-D-GALACTOPYRANOSIDE'>S2A</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=2oey FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oey OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oey RCSB], [http://www.ebi.ac.uk/pdbsum/2oey PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The solution structure of the complex formed between an oligodeoxynucleotide containing a two-base bulge (5'-CCATCGTCTACCTTTGGTAGGATGG) and SCA-alpha2, a designed spirocyclic helical molecule, has been elucidated. SCA-alpha2, a close mimic of the metabolite, NCSi-gb, of the DNA bulge-specific enediyne antibiotic neocarzinostatin, differs in possessing a more stable spirocyclic ring system and in lacking certain bulky groupings that compromise bulged DNA binding. This study provides a detailed comparison of the binding modes of the two complexes and provides new insights into the importance of shape and space, as opposed to simple nucleotide sequence, in complex formation at the bulge site. The two rigidly held aromatic rings of SCA-alpha2 form a right-handed helical molecular wedge that specifically penetrates the bulge-binding pocket and immobilizes the two bulge residues (GT), which point toward the minor groove, rather than the major groove as in the NCSi-gb.bulged DNA complex. The ligand aromatic ring systems stack on the DNA bulge-flanking base pairs that define the long sides of the triangular prism binding pocket. Like NCSi-gb, SCA-alpha2 possesses the natural N-methylfuranose moiety, alpha-linked to the benzindanol (BI) moiety. The amino sugar anchors in the major groove of the DNA and points toward the 3'-bulge-flanking base pair. Lacking the bulky cyclocarbonate of NCSi-gb, the SCA-alpha2.bulged DNA complex has a much less twisted and buckled 3'-bulge-flanking base pair (dG20.dC8), and the G20 residue stacks directly above the BI ring platform. Also, the absence of the methyl group and the free rotation of the methoxy group on the dihydronaphthanone (NA) moiety of SCA-alpha2 allow better stacking geometry of the NA ring above the 5'-bulge-flanking dG21.dC5 base pair. These and other considerations help to explain why NCSi-gb binds very poorly to bulged RNA and are consistent with the recent observation of good binding with SCA-alpha2. Thus, although the two complexes resemble each other closely, they differ in important local environmental details. SCA-alpha2 has a better hand-in-glove fit at the bulge site, making it an ideal platform for the placement of moieties that can react covalently with the DNA and for generating congeners specific for bulges in RNA.

-	~~{{STRUCTURE_2oey\| PDB=2oey \| SCENE= }}~~	+	Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA.,Zhang N, Lin Y, Xiao Z, Jones GB, Goldberg IH Biochemistry. 2007 Apr 24;46(16):4793-803. Epub 2007 Mar 28. PMID:17388570<ref>PMID:17388570</ref>

-	~~===Solution Structure~~ of ~~a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17388570}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2oey]] is a 1 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=2OEY OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017388570<~~/~~ref~~><~~ref group="xtra">PMID:008658168</ref><references group="xtra"~~/>	+
	[[Category: Goldberg, I H.]]		[[Category: Goldberg, I H.]]
	[[Category: Jones, G B.]]		[[Category: Jones, G B.]]

OCA at 13:12, 30 January 2013

OCA — Wed, 30 Jan 2013 13:12:05 GMT

←Older revision		Revision as of 13:12, 30 January 2013
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	[[Image:2oey.png\|left\|200px]]		[[Image:2oey.png\|left\|200px]]

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	{{STRUCTURE_2oey\| PDB=2oey \| SCENE= }}		{{STRUCTURE_2oey\| PDB=2oey \| SCENE= }}

	===Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA===		===Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA===

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	{{ABSTRACT_PUBMED_17388570}}		{{ABSTRACT_PUBMED_17388570}}

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	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17388570~~</ref><ref group="xtra">PMID:~~8658168</ref><ref group="xtra">PMID:11955061~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017388570</ref><ref group="xtra">PMID:008658168</ref><references group="xtra"/>
	[[Category: Goldberg, I H.]]		[[Category: Goldberg, I H.]]
	[[Category: Jones, G B.]]		[[Category: Jones, G B.]]
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	[[Category: Zhang, N.]]		[[Category: Zhang, N.]]
	[[Category: Designed spirocyclic helical ligand-bulged dna complex]]		[[Category: Designed spirocyclic helical ligand-bulged dna complex]]
		+	[[Category: Dna]]

OCA: Protected "2oey" [edit=sysop:move=sysop]

OCA — Mon, 14 Mar 2011 22:40:18 GMT

Protected "2oey" [edit=sysop:move=sysop]

←Older revision

Revision as of 22:40, 14 March 2011

OCA at 22:40, 14 March 2011

OCA — Mon, 14 Mar 2011 22:40:16 GMT

←Older revision		Revision as of 22:40, 14 March 2011
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-	{{Seed}}
	[[Image:2oey.png\|left\|200px]]		[[Image:2oey.png\|left\|200px]]

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

	==Reference==		==Reference==
-	Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA., Zhang N, Lin Y, Xiao Z, Jones GB, Goldberg IH, Biochemistry. 2007 Apr 24;46(16):4793-803. Epub 2007 Mar 28. PMID:~~[http:~~/~~/www.ncbi.nlm.nih.gov/pubmed/17388570 17388570]~~	+	<ref group="xtra">PMID:17388570</ref><ref group="xtra">PMID:8658168</ref><ref group="xtra">PMID:11955061</ref><references group="xtra"/>
-		+
-	~~Solution structure of a two-base DNA bulge complexed with an enediyne cleaving analog., Stassinopoulos A, Ji J, Gao X, Goldberg IH, Science. 1996 Jun 28;272(5270):1943-6.~~ PMID:~~[http:~~/~~/www.ncbi.nlm.nih.gov/pubmed/8658168 8658168]~~	+
-		+
-	Induced formation of a DNA bulge structure by a molecular wedge ligand-postactivated neocarzinostatin chromophore., Gao X, Stassinopoulos A, Ji J, Kwon Y, Bare S, Goldberg IH, Biochemistry. 2002 Apr 23;41(16):5131-43. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/11955061 11955061]~~	+
	[[Category: Goldberg, I H.]]		[[Category: Goldberg, I H.]]
	[[Category: Jones, G B.]]		[[Category: Jones, G B.]]
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	[[Category: Zhang, N.]]		[[Category: Zhang, N.]]
	[[Category: Designed spirocyclic helical ligand-bulged dna complex]]		[[Category: Designed spirocyclic helical ligand-bulged dna complex]]
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-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 09:32:16 2008''