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7xkm
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[7xkm]] 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=7XKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XKM FirstGlance]. <br> | <table><tr><td colspan='2'>[[7xkm]] 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=7XKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XKM FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG:SILVER+ION'>AG</scene>, <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]] 2.79Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG:SILVER+ION'>AG</scene>, <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=7xkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xkm OCA], [https://pdbe.org/7xkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xkm RCSB], [https://www.ebi.ac.uk/pdbsum/7xkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xkm 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=7xkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xkm OCA], [https://pdbe.org/7xkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xkm RCSB], [https://www.ebi.ac.uk/pdbsum/7xkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xkm ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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DNA/RNA duplexes containing metal-ion-mediated base pairs (metallo-base pairs) have potential applications in developing nucleic acid-based nanodevices and genetic code expansion. Many metallo-base pairs are formed within duplexes stabilized by Watson-Crick base pairs. Recently, the crystal structure of an Ag(I) -DNA nanowire with an uninterrupted one-dimensional silver array was determined. Here, we present a new DNA helical wire, the "Ag(I) -DNA rod", containing an uninterrupted array of 11 Ag(I) ions. The Ag(I) -DNA rod consisted of only C-Ag(I) -C, G-Ag(I) -G, G-Ag(I) -5-bromouracil ((Br) U), and (Br) U-Ag(I) -(Br) U metallo base pairs, with no Watson-Crick pairs. The Ag(I) -DNA rods were connected by non-canonical G-G pairs in crystals. Notably, data from our absorbance, circular dichroism, nuclear magnetic resonance, and mass spectrometry analyses suggested that the Ag(I) -DNA rods formed in solution, as well as within crystals. | DNA/RNA duplexes containing metal-ion-mediated base pairs (metallo-base pairs) have potential applications in developing nucleic acid-based nanodevices and genetic code expansion. Many metallo-base pairs are formed within duplexes stabilized by Watson-Crick base pairs. Recently, the crystal structure of an Ag(I) -DNA nanowire with an uninterrupted one-dimensional silver array was determined. Here, we present a new DNA helical wire, the "Ag(I) -DNA rod", containing an uninterrupted array of 11 Ag(I) ions. The Ag(I) -DNA rod consisted of only C-Ag(I) -C, G-Ag(I) -G, G-Ag(I) -5-bromouracil ((Br) U), and (Br) U-Ag(I) -(Br) U metallo base pairs, with no Watson-Crick pairs. The Ag(I) -DNA rods were connected by non-canonical G-G pairs in crystals. Notably, data from our absorbance, circular dichroism, nuclear magnetic resonance, and mass spectrometry analyses suggested that the Ag(I) -DNA rods formed in solution, as well as within crystals. | ||
| - | A Novel Ag(I) -DNA Rod Comprising a One-Dimensional Array of 11 Silver Ions within a Double Helical Structure.,Atsugi T, Ono A, Tasaka M, Eguchi N, Fujiwara S, Kondo J Angew Chem Int Ed Engl. 2022 | + | A Novel Ag(I) -DNA Rod Comprising a One-Dimensional Array of 11 Silver Ions within a Double Helical Structure.,Atsugi T, Ono A, Tasaka M, Eguchi N, Fujiwara S, Kondo J Angew Chem Int Ed Engl. 2022 Aug 1;61(31):e202204798. doi: , 10.1002/anie.202204798. Epub 2022 Jun 21. PMID:35641885<ref>PMID:35641885</ref> |
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> | ||
Current revision
Crystal structure of DNA-Ag(I) rod comprising a one-dimensional array of 11 silver ions
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