5vy7 - Revision history

OCA at 14:12, 13 March 2024

2024-03-13T14:12:56Z

←Older revision		Revision as of 14:12, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='5vy7' size='340' side='right'caption='[[5vy7]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='5vy7' size='340' side='right'caption='[[5vy7]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vy7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VY7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5VY7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vy7]] is a 4 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=5VY7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VY7 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=0DA:2-DEOXY-L-RIBO-FURANOSYL+ADENOSINE-5-MONOPHOSPHATE'>0DA</scene>, <scene name='pdbligand=0DC:2-DEOXY-L-RIBO-FURANOSYL+CYTOSINE-5-MONOPHOSPHATE'>0DC</scene>, <scene name='pdbligand=0DG:2-DEOXY-L-RIBO-FURANOSYL+GUANINE-5-MONOPHOSPHATE'>0DG</scene>, <scene name='pdbligand=0DT:2-DEOXY-L-RIBO-FURANOSYL+THYMIDINE-5-MONOPHOSPHATE'>0DT</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]] 3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vy6\|5vy6]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0DA:2-DEOXY-L-RIBO-FURANOSYL+ADENOSINE-5-MONOPHOSPHATE'>0DA</scene>, <scene name='pdbligand=0DC:2-DEOXY-L-RIBO-FURANOSYL+CYTOSINE-5-MONOPHOSPHATE'>0DC</scene>, <scene name='pdbligand=0DG:2-DEOXY-L-RIBO-FURANOSYL+GUANINE-5-MONOPHOSPHATE'>0DG</scene>, <scene name='pdbligand=0DT:2-DEOXY-L-RIBO-FURANOSYL+THYMIDINE-5-MONOPHOSPHATE'>0DT</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=5vy7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vy7 OCA], [~~http~~://pdbe.org/5vy7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vy7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vy7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vy7 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=5vy7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vy7 OCA], [https://pdbe.org/5vy7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vy7 RCSB], [https://www.ebi.ac.uk/pdbsum/5vy7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vy7 ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The foundational goal of structural DNA nanotechnology-the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems-was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 x 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 x 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 A resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest-DNA conjugates with a specified crystalline hand.
-
-	Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals.,Simmons CR, Zhang F, MacCulloch T, Fahmi N, Stephanopoulos N, Liu Y, Seeman NC, Yan H J Am Chem Soc. 2017 Aug 2. doi: 10.1021/jacs.7b06485. PMID:28731332<ref>PMID:28731332</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5vy7" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Simmons, C R~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Yan, H~~]]	+	[[Category: Simmons CR]]
-	[[Category: ~~Dna]]~~	+	[[Category: Yan H]]
-	~~[[Category: Dna nanotechnology]]~~	+
-	~~[[Category: Dna structure]]~~	+
-	~~[[Category: Self-assembly~~]]	+

OCA at 08:45, 30 September 2020

2020-09-30T08:45:30Z

←Older revision		Revision as of 08:45, 30 September 2020
Line 1:		Line 1:

	==A self-assembling L-form DNA crystal lattice==		==A self-assembling L-form DNA crystal lattice==
-	<StructureSection load='5vy7' size='340' side='right' caption='[[5vy7]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='5vy7' size='340' side='right'caption='[[5vy7]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vy7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VY7 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VY7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vy7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VY7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VY7 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=0DA:2-DEOXY-L-RIBO-FURANOSYL+ADENOSINE-5-MONOPHOSPHATE'>0DA</scene>, <scene name='pdbligand=0DC:2-DEOXY-L-RIBO-FURANOSYL+CYTOSINE-5-MONOPHOSPHATE'>0DC</scene>, <scene name='pdbligand=0DG:2-DEOXY-L-RIBO-FURANOSYL+GUANINE-5-MONOPHOSPHATE'>0DG</scene>, <scene name='pdbligand=0DT:2-DEOXY-L-RIBO-FURANOSYL+THYMIDINE-5-MONOPHOSPHATE'>0DT</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=0DA:2-DEOXY-L-RIBO-FURANOSYL+ADENOSINE-5-MONOPHOSPHATE'>0DA</scene>, <scene name='pdbligand=0DC:2-DEOXY-L-RIBO-FURANOSYL+CYTOSINE-5-MONOPHOSPHATE'>0DC</scene>, <scene name='pdbligand=0DG:2-DEOXY-L-RIBO-FURANOSYL+GUANINE-5-MONOPHOSPHATE'>0DG</scene>, <scene name='pdbligand=0DT:2-DEOXY-L-RIBO-FURANOSYL+THYMIDINE-5-MONOPHOSPHATE'>0DT</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vy6\|5vy6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vy6\|5vy6]]</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=5vy7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vy7 OCA], [http://pdbe.org/5vy7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vy7 RCSB], [http://www.ebi.ac.uk/pdbsum/5vy7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vy7 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=5vy7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vy7 OCA], [http://pdbe.org/5vy7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vy7 RCSB], [http://www.ebi.ac.uk/pdbsum/5vy7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vy7 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Simmons, C R]]		[[Category: Simmons, C R]]
	[[Category: Yan, H]]		[[Category: Yan, H]]

OCA: Protected "5vy7" [edit=sysop:move=sysop]

2017-08-09T09:03:24Z

Protected "5vy7" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:03, 9 August 2017

OCA: New page: ==A self-assembling L-form DNA crystal lattice== == Structural hi...

2017-08-09T09:03:22Z

New page: ==A self-assembling L-form DNA crystal lattice== <StructureSection load='5vy7' size='340' side='right' caption='5vy7, resolution 3.00Å' scene=''> == Structural hi...

New page

==A self-assembling L-form DNA crystal lattice==
<StructureSection load='5vy7' size='340' side='right' caption='[[5vy7]], [[Resolution|resolution]] 3.00Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5vy7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VY7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VY7 FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=0DA:2-DEOXY-L-RIBO-FURANOSYL+ADENOSINE-5-MONOPHOSPHATE'>0DA</scene>, <scene name='pdbligand=0DC:2-DEOXY-L-RIBO-FURANOSYL+CYTOSINE-5-MONOPHOSPHATE'>0DC</scene>, <scene name='pdbligand=0DG:2-DEOXY-L-RIBO-FURANOSYL+GUANINE-5-MONOPHOSPHATE'>0DG</scene>, <scene name='pdbligand=0DT:2-DEOXY-L-RIBO-FURANOSYL+THYMIDINE-5-MONOPHOSPHATE'>0DT</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5vy6|5vy6]]</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=5vy7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vy7 OCA], [http://pdbe.org/5vy7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vy7 RCSB], [http://www.ebi.ac.uk/pdbsum/5vy7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vy7 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The foundational goal of structural DNA nanotechnology-the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems-was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 x 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 x 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 A resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest-DNA conjugates with a specified crystalline hand.

Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals.,Simmons CR, Zhang F, MacCulloch T, Fahmi N, Stephanopoulos N, Liu Y, Seeman NC, Yan H J Am Chem Soc. 2017 Aug 2. doi: 10.1021/jacs.7b06485. PMID:28731332<ref>PMID:28731332</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5vy7" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Simmons, C R]]
[[Category: Yan, H]]
[[Category: Dna]]
[[Category: Dna nanotechnology]]
[[Category: Dna structure]]
[[Category: Self-assembly]]