4rhd: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4rhd]] is a 8 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=4RHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RHD FirstGlance]. <br>
<table><tr><td colspan='2'>[[4rhd]] is a 8 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=4RHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RHD FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1W5:(1R)-1-(6-AMINO-2-HYDROXY-5-NITROPYRIDIN-3-YL)-1,4-ANHYDRO-2-DEOXY-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>1W5</scene>, <scene name='pdbligand=1WA:2-AMINO-8-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-4-HYDROXY-1H-IMIDAZO[1,2-A][1,3,5]TRIAZINE-5,8-DIIUM'>1WA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=T5S:2-deoxy-5-(methylselanyl)uridine+5-phosphate'>T5S</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]] 1.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1W5:(1R)-1-(6-AMINO-2-HYDROXY-5-NITROPYRIDIN-3-YL)-1,4-ANHYDRO-2-DEOXY-5-O-PHOSPHONO-D-ERYTHRO-PENTITOL'>1W5</scene>, <scene name='pdbligand=1WA:2-AMINO-8-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-4-HYDROXY-1H-IMIDAZO[1,2-A][1,3,5]TRIAZINE-5,8-DIIUM'>1WA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=T5S:2-deoxy-5-(methylselanyl)uridine+5-phosphate'>T5S</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=4rhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rhd OCA], [https://pdbe.org/4rhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rhd RCSB], [https://www.ebi.ac.uk/pdbsum/4rhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rhd 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=4rhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rhd OCA], [https://pdbe.org/4rhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rhd RCSB], [https://www.ebi.ac.uk/pdbsum/4rhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rhd ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Axiomatically, the density of information stored in DNA, with just four nucleotides (GACT), is higher than in a binary code, but less than it might be if synthetic biologists succeed in adding independently replicating nucleotides to genetic systems. Such addition could also add functional groups not found in natural DNA, but useful for molecular performance. Here, we consider two new nucleotides (Z and P, 6-amino-5-nitro-3-(1'-beta-d-2'-deoxyribo-furanosyl)-2(1H)-pyridone and 2-amino-8-(1'-beta-d-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-on e). These are designed to pair via complete Watson-Crick geometry. These were added to a library of oligonucleotides used in a laboratory in vitro evolution (LIVE) experiment; the GACTZP library was challenged to deliver molecules that bind selectively to liver cancer cells, but not to untransformed liver cells. Unlike in classical in vitro selection, low levels of mutation allow this system to evolve to create binding molecules not necessarily present in the original library. Over a dozen binding species were recovered. The best had Z and/or P in their sequences. Several had multiple, nearby, and adjacent Zs and Ps. Only the weaker binders contained no Z or P at all. This suggests that this system explored much of the sequence space available to this genetic system and that GACTZP libraries are richer reservoirs of functionality than standard libraries.
Evolution of functional six-nucleotide DNA.,Zhang L, Yang Z, Sefah K, Bradley KM, Hoshika S, Kim MJ, Kim HJ, Zhu G, Jimenez E, Cansiz S, Teng IT, Champanhac C, McLendon C, Liu C, Zhang W, Gerloff DL, Huang Z, Tan W, Benner SA J Am Chem Soc. 2015 Jun 3;137(21):6734-7. doi: 10.1021/jacs.5b02251. Epub 2015, May 20. PMID:25966323<ref>PMID:25966323</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4rhd" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
</StructureSection>

Latest revision as of 12:52, 1 March 2024

DNA Duplex with Novel ZP Base Pair

4rhd, resolution 1.70Å

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