2kp3: Difference between revisions
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New page: '''Unreleased structure''' The entry 2kp3 is ON HOLD Authors: Gonzalez, C., Martn-Pintado, N., Watts, J., Gomez-Pinto, I., Dhama, M., Orozco, M., Schwartzentruber, J., Portella, G. Des... |
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==Structure of ANA-RNA hybrid duplex== | |||
<StructureSection load='2kp3' size='340' side='right'caption='[[2kp3]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2kp3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KP3 FirstGlance]. <br> | |||
</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A5O:ADENINE+ARABINOSE-5-PHOSPHATE'>A5O</scene>, <scene name='pdbligand=CAR:CYTOSINE+ARABINOSE-5-PHOSPHATE'>CAR</scene>, <scene name='pdbligand=GAO:GUANINE+ARABINOSE-5-PHOSPHATE'>GAO</scene>, <scene name='pdbligand=UAR:URACIL+ARABINOSE-5-PHOSPHATE'>UAR</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=2kp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kp3 OCA], [https://pdbe.org/2kp3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kp3 RCSB], [https://www.ebi.ac.uk/pdbsum/2kp3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kp3 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Hybrids of RNA with arabinonucleic acids 2'F-ANA and ANA have very similar structures but strikingly different thermal stabilities. We now present a thorough study combining NMR and other biophysical methods together with state-of-the-art theoretical calculations on a fully modified 10-mer hybrid duplex. Comparison between the solution structure of 2'F-ANA*RNA and ANA*RNA hybrids indicates that the increased binding affinity of 2'F-ANA is related to several subtle differences, most importantly a favorable pseudohydrogen bond (2'F-purine H8) which contrasts with unfavorable 2'-OH-nucleobase steric interactions in the case of ANA. While both 2'F-ANA and ANA strands maintained conformations in the southern/eastern sugar pucker range, the 2'F-ANA strand's structure was more compatible with the A-like structure of a hybrid duplex. No dramatic differences are found in terms of relative hydration for the two hybrids, but the ANA*RNA duplex showed lower uptake of counterions than its 2'F-ANA*RNA counterpart. Finally, while the two hybrid duplexes are of similar rigidities, 2'F-ANA single strands may be more suitably preorganized for duplex formation. Thus the dramatically increased stability of 2'F-ANA*RNA and ANA*RNA duplexes is caused by differences in at least four areas, of which structure and pseudohydrogen bonding are the most important. | |||
Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility.,Watts JK, Martin-Pintado N, Gomez-Pinto I, Schwartzentruber J, Portella G, Orozco M, Gonzalez C, Damha MJ Nucleic Acids Res. 2010 Apr;38(7):2498-511. Epub 2010 Jan 13. PMID:20071751<ref>PMID:20071751</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2kp3" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Dhama M]] | |||
[[Category: Gomez-Pinto I]] | |||
[[Category: Gonzalez C]] | |||
[[Category: Martn-Pintado N]] | |||
[[Category: Orozco M]] | |||
[[Category: Portella G]] | |||
[[Category: Schwartzentruber J]] | |||
[[Category: Watts J]] | |||
Latest revision as of 12:51, 20 December 2023
Structure of ANA-RNA hybrid duplex
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