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| | ==Structure of ANA-RNA hybrid duplex== | | ==Structure of ANA-RNA hybrid duplex== |
| - | <StructureSection load='2kp3' size='340' side='right' caption='[[2kp3]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | + | <StructureSection load='2kp3' size='340' side='right'caption='[[2kp3]]' scene=''> |
| | == Structural highlights == | | == 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KP3 FirstGlance]. <br> | + | <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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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> | + | </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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2kp3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kp3 OCA], [http://pdbe.org/2kp3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kp3 RCSB], [http://www.ebi.ac.uk/pdbsum/2kp3 PDBsum]</span></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> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Dhama, M]] | + | [[Category: Large Structures]] |
| - | [[Category: Gomez-Pinto, I]] | + | [[Category: Dhama M]] |
| - | [[Category: Gonzalez, C]] | + | [[Category: Gomez-Pinto I]] |
| - | [[Category: Martn-Pintado, N]] | + | [[Category: Gonzalez C]] |
| - | [[Category: Orozco, M]] | + | [[Category: Martn-Pintado N]] |
| - | [[Category: Portella, G]] | + | [[Category: Orozco M]] |
| - | [[Category: Schwartzentruber, J]] | + | [[Category: Portella G]] |
| - | [[Category: Watts, J]] | + | [[Category: Schwartzentruber J]] |
| - | [[Category: Ana]]
| + | [[Category: Watts J]] |
| - | [[Category: Arabinonucleic acid]]
| + | |
| - | [[Category: Hybrid duplex]]
| + | |
| - | [[Category: Nmr/md/ti]]
| + | |
| - | [[Category: Nucleic acid structure]]
| + | |
| - | [[Category: Rna]]
| + | |
| Structural highlights
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Watts JK, Martin-Pintado N, Gomez-Pinto I, Schwartzentruber J, Portella G, Orozco M, Gonzalez C, Damha MJ. Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility. Nucleic Acids Res. 2010 Apr;38(7):2498-511. Epub 2010 Jan 13. PMID:20071751 doi:10.1093/nar/gkp1225
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