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2kp3

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[[Image:2kp3.png|left|200px]]
 
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==Structure of ANA-RNA hybrid duplex==
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<StructureSection load='2kp3' size='340' side='right'caption='[[2kp3]]' scene=''>
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<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>
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{{STRUCTURE_2kp3| PDB=2kp3 | SCENE= }}
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<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>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Structure of ANA-RNA hybrid duplex===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2kp3" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 20071751 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_20071751}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2KP3 is a 2 chains structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KP3 OCA].
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[[Category: Dhama M]]
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[[Category: Gomez-Pinto I]]
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==Reference==
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[[Category: Gonzalez C]]
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<ref group="xtra">PMID:20071751</ref><references group="xtra"/>
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[[Category: Martn-Pintado N]]
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[[Category: Dhama, M.]]
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[[Category: Orozco M]]
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[[Category: Gomez-Pinto, I.]]
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[[Category: Portella G]]
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[[Category: Gonzalez, C.]]
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[[Category: Schwartzentruber J]]
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[[Category: Martn-Pintado, N.]]
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[[Category: Watts J]]
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[[Category: Orozco, M.]]
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[[Category: Portella, G.]]
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[[Category: Schwartzentruber, J.]]
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[[Category: Watts, J.]]
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[[Category: Ana]]
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[[Category: Arabinonucleic acid]]
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[[Category: Hybrid duplex]]
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[[Category: Nmr/md/ti]]
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[[Category: Nucleic acid structure]]
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[[Category: Rna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 28 11:14:04 2010''
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Current revision

Structure of ANA-RNA hybrid duplex

PDB ID 2kp3

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