4rip - Revision history

OCA at 12:53, 1 March 2024

OCA — Fri, 01 Mar 2024 12:53:04 GMT

←Older revision		Revision as of 12:53, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rip]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RIP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rip]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RIP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</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=4rip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rip OCA], [https://pdbe.org/4rip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rip RCSB], [https://www.ebi.ac.uk/pdbsum/4rip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rip 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=4rip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rip OCA], [https://pdbe.org/4rip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rip RCSB], [https://www.ebi.ac.uk/pdbsum/4rip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rip ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson-Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A-A base pairs between adjacent G-G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H-1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.
-
-	An intercalation-locked parallel-stranded DNA tetraplex.,Tripathi S, Zhang D, Paukstelis PJ Nucleic Acids Res. 2015 Jan 27. pii: gkv033. PMID:25628357<ref>PMID:25628357</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4rip" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:58, 2 March 2023

OCA — Thu, 02 Mar 2023 06:58:38 GMT

←Older revision		Revision as of 06:58, 2 March 2023
Line 3:		Line 3:
	<StructureSection load='4rip' size='340' side='right'caption='[[4rip]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4rip' size='340' side='right'caption='[[4rip]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4rip]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RIP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RIP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4rip]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RIP FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rim\|4rim]]~~</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=4rip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rip OCA], [https://pdbe.org/4rip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rip RCSB], [https://www.ebi.ac.uk/pdbsum/4rip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rip 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=4rip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rip OCA], [~~http~~://pdbe.org/4rip PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rip RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rip PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rip ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Paukstelis, P~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Tripathi, S K~~]]	+	[[Category: Paukstelis P]]
-	[[Category: ~~Zhang, D~~]]	+	[[Category: Tripathi SK]]
-	[[Category: ~~Bromouracil]]~~	+	[[Category: Zhang D]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Homoduplex]]~~	+
-	~~[[Category: Intercalation-locked dna tetraplex~~]]	+

OCA at 10:39, 1 May 2019

OCA — Wed, 01 May 2019 10:39:14 GMT

←Older revision		Revision as of 10:39, 1 May 2019
Line 1:		Line 1:

	==BromoUracil substituted structure of intercalation-locked DNA tetraplex==		==BromoUracil substituted structure of intercalation-locked DNA tetraplex==
-	<StructureSection load='4rip' size='340' side='right' caption='[[4rip]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='4rip' size='340' side='right'caption='[[4rip]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rip]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RIP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RIP FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rip]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RIP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RIP FirstGlance]. <br>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Paukstelis, P]]		[[Category: Paukstelis, P]]
	[[Category: Tripathi, S K]]		[[Category: Tripathi, S K]]

OCA at 17:33, 18 January 2017

OCA — Wed, 18 Jan 2017 17:33:42 GMT

←Older revision		Revision as of 17:33, 18 January 2017
Line 1:		Line 1:
		+
	==BromoUracil substituted structure of intercalation-locked DNA tetraplex==		==BromoUracil substituted structure of intercalation-locked DNA tetraplex==
	<StructureSection load='4rip' size='340' side='right' caption='[[4rip]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4rip' size='340' side='right' caption='[[4rip]], [[Resolution\|resolution]] 2.10Å' 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=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</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=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rim\|4rim]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rim\|4rim]]</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=4rip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rip OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rip RCSB], [http://www.ebi.ac.uk/pdbsum/4rip 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=4rip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rip OCA], [http://pdbe.org/4rip PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rip RCSB], [http://www.ebi.ac.uk/pdbsum/4rip PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rip ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4rip" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:53, 12 February 2015

OCA — Thu, 12 Feb 2015 11:53:56 GMT

←Older revision		Revision as of 11:53, 12 February 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==BromoUracil substituted structure of intercalation-locked DNA tetraplex==
		+	<StructureSection load='4rip' size='340' side='right' caption='[[4rip]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4rip]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RIP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RIP FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4rim\|4rim]]</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=4rip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rip OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rip RCSB], [http://www.ebi.ac.uk/pdbsum/4rip PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson-Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A-A base pairs between adjacent G-G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H-1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.

-	~~The entry 4rip is ON HOLD until Feb 11 2016~~	+	An intercalation-locked parallel-stranded DNA tetraplex.,Tripathi S, Zhang D, Paukstelis PJ Nucleic Acids Res. 2015 Jan 27. pii: gkv033. PMID:25628357<ref>PMID:25628357</ref>

-	~~Authors: Tripathi~~, S.~~K., Zhang, D., Paukstelis, P~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: BromoUracil substituted structure of intercalation-locked DNA tetraplex~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Paukstelis, P]]		[[Category: Paukstelis, P]]
-	[[Category: Tripathi, S.K]]	+	[[Category: Tripathi, S K]]
	[[Category: Zhang, D]]		[[Category: Zhang, D]]
		+	[[Category: Bromouracil]]
		+	[[Category: Dna]]
		+	[[Category: Homoduplex]]
		+	[[Category: Intercalation-locked dna tetraplex]]

OCA at 13:12, 28 January 2015

OCA — Wed, 28 Jan 2015 13:12:59 GMT

←Older revision		Revision as of 13:12, 28 January 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4rip is ON HOLD until ~~Paper Publication~~	+	The entry 4rip is ON HOLD until Feb 11 2016

	Authors: Tripathi, S.K., Zhang, D., Paukstelis, P.		Authors: Tripathi, S.K., Zhang, D., Paukstelis, P.

OCA at 16:56, 24 December 2014

OCA — Wed, 24 Dec 2014 16:56:13 GMT

←Older revision		Revision as of 16:56, 24 December 2014
Line 6:		Line 6:

	Description: BromoUracil substituted structure of intercalation-locked DNA tetraplex		Description: BromoUracil substituted structure of intercalation-locked DNA tetraplex
		+	[[Category: Unreleased Structures]]
		+	[[Category: Paukstelis, P]]
		+	[[Category: Tripathi, S.K]]
		+	[[Category: Zhang, D]]

OCA at 06:42, 26 November 2014

OCA — Wed, 26 Nov 2014 06:42:45 GMT

←Older revision		Revision as of 06:42, 26 November 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4rip is ON HOLD	+	The entry 4rip is ON HOLD until Paper Publication

	Authors: Tripathi, S.K., Zhang, D., Paukstelis, P.		Authors: Tripathi, S.K., Zhang, D., Paukstelis, P.

	Description: BromoUracil substituted structure of intercalation-locked DNA tetraplex		Description: BromoUracil substituted structure of intercalation-locked DNA tetraplex

OCA: Protected "4rip" [edit=sysop:move=sysop]

OCA — Mon, 20 Oct 2014 09:30:24 GMT

Protected "4rip" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:30, 20 October 2014

OCA: New page: '''Unreleased structure''' The entry 4rip is ON HOLD Authors: Tripathi, S.K., Zhang, D., Paukstelis, P. Description: BromoUracil substituted structure of intercalation-locked DNA tetra...

OCA — Mon, 20 Oct 2014 09:30:22 GMT

New page: '''Unreleased structure''' The entry 4rip is ON HOLD Authors: Tripathi, S.K., Zhang, D., Paukstelis, P. Description: BromoUracil substituted structure of intercalation-locked DNA tetra...

New page

'''Unreleased structure'''

The entry 4rip is ON HOLD

Authors: Tripathi, S.K., Zhang, D., Paukstelis, P.

Description: BromoUracil substituted structure of intercalation-locked DNA tetraplex