2kp4: Difference between revisions

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{{Seed}}
[[Image:2kp4.png|left|200px]]


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==Structure of 2'F-ANA/RNA hybrid duplex==
The line below this paragraph, containing "STRUCTURE_2kp4", creates the "Structure Box" on the page.
<StructureSection load='2kp4' size='340' side='right'caption='[[2kp4]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2kp4]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KP4 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</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=A5L:9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-9H-PURIN-6-AMINE'>A5L</scene>, <scene name='pdbligand=CFL:4-AMINO-1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)PYRIMIDIN-2(1H)-ONE'>CFL</scene>, <scene name='pdbligand=GFL:2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>GFL</scene>, <scene name='pdbligand=TAF:2-DEOXY-2-FLUORO-ARABINO-FURANOSYL+THYMINE-5-PHOSPHATE'>TAF</scene></td></tr>
{{STRUCTURE_2kp4|  PDB=2kp4  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2kp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kp4 OCA], [https://pdbe.org/2kp4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kp4 RCSB], [https://www.ebi.ac.uk/pdbsum/2kp4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kp4 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.


===Structure of 2'F-ANA/RNA hybrid duplex===
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_20071751}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2kp4" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 20071751 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_20071751}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2KP4 is a 2 chains structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KP4 OCA].
[[Category: Dhama M]]
 
[[Category: Gomez-Pinto I]]
==Reference==
[[Category: Gonzalez C]]
<ref group="xtra">PMID:20071751</ref><references group="xtra"/>
[[Category: Martin-Pintado N]]
[[Category: Dhama, M.]]
[[Category: Orozco M]]
[[Category: Gomez-Pinto, I.]]
[[Category: Portella G]]
[[Category: Gonzalez, C.]]
[[Category: Schwartzentruber J]]
[[Category: Martin-Pintado, N.]]
[[Category: Watts J]]
[[Category: Orozco, M.]]
[[Category: Portella, G.]]
[[Category: Schwartzentruber, J.]]
[[Category: Watts, J.]]
[[Category: 2-deoxy-2-fluoro-d-arabinose]]
[[Category: Dna-rna complex]]
[[Category: Fana]]
[[Category: Hybrid duplex]]
[[Category: Nmr/md/ti]]
[[Category: Nucleic acid structure]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 28 11:14:07 2010''

Latest revision as of 12:51, 20 December 2023

Structure of 2'F-ANA/RNA hybrid duplex

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