5tgg - Revision history

OCA at 10:24, 14 June 2023

OCA — Wed, 14 Jun 2023 10:24:48 GMT

←Older revision		Revision as of 10:24, 14 June 2023
Line 1:		Line 1:

	==Solution structure of parallel stranded adenosine duplex==		==Solution structure of parallel stranded adenosine duplex==
-	<StructureSection load='5tgg' size='340' side='right'caption='[[5tgg~~]], [[NMR_Ensembles_of_Models \| 11 NMR models~~]]' scene=''>	+	<StructureSection load='5tgg' size='340' side='right'caption='[[5tgg]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tgg]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TGG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TGG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tgg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TGG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TGG FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jrd\|4jrd]]~~</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=5tgg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tgg OCA], [https://pdbe.org/5tgg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tgg RCSB], [https://www.ebi.ac.uk/pdbsum/5tgg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tgg ProSAT]</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=5tgg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tgg OCA], [~~http~~://pdbe.org/5tgg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tgg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tgg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tgg ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Denisov, A]]	+	[[Category: Synthetic construct]]
-	[[Category: Gehring, K]]	+	[[Category: Denisov A]]
-	[[Category: Noronha, A]]	+	[[Category: Gehring K]]
-	[[Category: Wilds, C]]	+	[[Category: Noronha A]]
-	~~[[Category: Dna]]~~	+	[[Category: Wilds C]]
-	~~[[Category: Parallel stranded duplex]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 08:17, 8 January 2020

OCA — Wed, 08 Jan 2020 08:17:35 GMT

←Older revision		Revision as of 08:17, 8 January 2020
Line 1:		Line 1:

	==Solution structure of parallel stranded adenosine duplex==		==Solution structure of parallel stranded adenosine duplex==
-	<StructureSection load='5tgg' size='340' side='right' caption='[[5tgg]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>	+	<StructureSection load='5tgg' size='340' side='right'caption='[[5tgg]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tgg]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TGG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TGG FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tgg]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TGG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TGG FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Denisov, A]]		[[Category: Denisov, A]]
	[[Category: Gehring, K]]		[[Category: Gehring, K]]

OCA at 06:54, 11 October 2017

OCA — Wed, 11 Oct 2017 06:54:13 GMT

←Older revision		Revision as of 06:54, 11 October 2017
Line 8:		Line 8:
	<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=5tgg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tgg OCA], [http://pdbe.org/5tgg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tgg RCSB], [http://www.ebi.ac.uk/pdbsum/5tgg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tgg ProSAT]</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=5tgg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tgg OCA], [http://pdbe.org/5tgg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tgg RCSB], [http://www.ebi.ac.uk/pdbsum/5tgg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tgg ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2'-deoxyribose, 2'-O-methyl-ribose, 2'-deoxy-2'-fluoro-ribose, arabinose and 2'-deoxy-2'-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2' modifications gave a variety of effects. Arabinose and 2'-deoxy-2'-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2'-O-methyl and 2'-deoxy-2'-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability.
		+
		+	Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.,Copp W, Denisov AY, Xie J, Noronha AM, Liczner C, Safaee N, Wilds CJ, Gehring K Nucleic Acids Res. 2017 Sep 29;45(17):10321-10331. doi: 10.1093/nar/gkx713. PMID:28973475<ref>PMID:28973475</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5tgg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:52, 7 October 2017

OCA — Sat, 07 Oct 2017 10:52:31 GMT

←Older revision		Revision as of 10:52, 7 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5tgg ~~is ON HOLD until Paper Publication~~	+	==Solution structure of parallel stranded adenosine duplex==
-		+	<StructureSection load='5tgg' size='340' side='right' caption='[[5tgg]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
-	~~Authors~~: ~~Denisov, A~~.~~, Noronha, A~~.~~, Gehring, K~~.~~, Wilds, C~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5tgg]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TGG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TGG FirstGlance]. <br>
-	~~Description~~: ~~Solution structure of parallel stranded adenosine duplex r(AAAA)~~-dA-r(~~AAA~~)	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jrd\|4jrd]]</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=5tgg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tgg OCA], [http://pdbe.org/5tgg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tgg RCSB], [http://www.ebi.ac.uk/pdbsum/5tgg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tgg ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Denisov, A]]		[[Category: Denisov, A]]
		+	[[Category: Gehring, K]]
		+	[[Category: Noronha, A]]
	[[Category: Wilds, C]]		[[Category: Wilds, C]]
-	[[Category: ~~Noronha, A~~]]	+	[[Category: Dna]]
-	[[Category: ~~Gehring, K~~]]	+	[[Category: Parallel stranded duplex]]
		+	[[Category: Rna]]

OCA at 17:29, 9 December 2016

OCA — Fri, 09 Dec 2016 17:29:24 GMT

←Older revision		Revision as of 17:29, 9 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5tgg is ON HOLD	+	The entry 5tgg is ON HOLD until Paper Publication

	Authors: Denisov, A., Noronha, A., Gehring, K., Wilds, C.		Authors: Denisov, A., Noronha, A., Gehring, K., Wilds, C.

OCA: Protected "5tgg" [edit=sysop:move=sysop]

OCA — Wed, 05 Oct 2016 20:03:26 GMT

Protected "5tgg" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:03, 5 October 2016

OCA: New page: '''Unreleased structure''' The entry 5tgg is ON HOLD Authors: Denisov, A., Noronha, A., Gehring, K., Wilds, C. Description: Solution structure of parallel stranded adenosine duplex r(A...

OCA — Wed, 05 Oct 2016 20:03:25 GMT

New page: '''Unreleased structure''' The entry 5tgg is ON HOLD Authors: Denisov, A., Noronha, A., Gehring, K., Wilds, C. Description: Solution structure of parallel stranded adenosine duplex r(A...

New page

'''Unreleased structure'''

The entry 5tgg is ON HOLD

Authors: Denisov, A., Noronha, A., Gehring, K., Wilds, C.

Description: Solution structure of parallel stranded adenosine duplex r(AAAA)-dA-r(AAA)
[[Category: Unreleased Structures]]
[[Category: Denisov, A]]
[[Category: Wilds, C]]
[[Category: Noronha, A]]
[[Category: Gehring, K]]