5ki4: Difference between revisions

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==Structural impact of single ribonucleotides in DNA==
==Structural impact of single ribonucleotides in DNA==
<StructureSection load='5ki4' size='340' side='right' caption='[[5ki4]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''>
<StructureSection load='5ki4' size='340' side='right'caption='[[5ki4]]' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5ki4]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KI4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KI4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5ki4]] 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=5KI4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KI4 FirstGlance]. <br>
</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=5ki4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ki4 OCA], [http://pdbe.org/5ki4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ki4 RCSB], [http://www.ebi.ac.uk/pdbsum/5ki4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ki4 ProSAT]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=5ki4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ki4 OCA], [https://pdbe.org/5ki4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ki4 RCSB], [https://www.ebi.ac.uk/pdbsum/5ki4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ki4 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Single ribonucleotide intrusions represent the most common non-standard nucleotide in genomic DNA, yet little is known of their structural impact. This lesion incurs genomic instability in addition to affecting the physical properties of the DNA.To probe for structural and dynamic effects of single ribonucleotides in various sequence contexts, AxC, CxG and GxC, where x=rG or dG, we report the structures of three single ribonucleotide containing DNA duplexes and the corresponding DNA controls. This lesion subtly and locally perturbs the structure asymmetrically 3' of the lesion on both the riboguanosine-containing and complementary strand of the duplex. The perturbations are mainly restricted to the sugar and phosphodiester backbone. The ribose and 3' downstream deoxyriboses are predominately in N-type conformation, while backbone torsion angles epsilon and/or zeta of the ribonucleotide or upstream deoxyribonucleotide are affected. Depending on the flanking sequences, the C2'-OH group forms hydrogen bonds with the backbone, 3'- neighboring base and/or sugar. Interestingly, even in a similar purine-rG-pyrimidine environment (A-rG-C and G-rG-C), a riboguanosine affects DNA in a distinct manner and manifests different hydrogen bonds, which makes generalizations difficult.
Structural impact of single ribonucleotides in DNA.,Evich M, Spring-Connell AM, Storici F, Germann MW Chembiochem. 2016 Aug 9. doi: 10.1002/cbic.201600385. PMID:27504600<ref>PMID:27504600</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5ki4" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Evich, M]]
[[Category: Large Structures]]
[[Category: Spring-Connell, A M]]
[[Category: Synthetic construct]]
[[Category: Storici, F]]
[[Category: Evich M]]
[[Category: Dna]]
[[Category: Spring-Connell AM]]
[[Category: Storici F]]

Latest revision as of 10:24, 1 May 2024

Structural impact of single ribonucleotides in DNAStructural impact of single ribonucleotides in DNA

Structural highlights

5ki4 is a 2 chain structure with sequence from Synthetic construct. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT
Drag the structure with the mouse to rotate

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