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PDBsum entry 2kp4
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References listed in PDB file
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Key reference
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Title
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Differential stability of 2'F-AnaRna and anaRna hybrid duplexes: roles of structure, Pseudohydrogen bonding, Hydration, Ion uptake and flexibility.
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Authors
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J.K.Watts,
N.Martín-Pintado,
I.Gómez-Pinto,
J.Schwartzentruber,
G.Portella,
M.Orozco,
C.González,
M.J.Damha.
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Ref.
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Nucleic Acids Res, 2010,
38,
2498-2511.
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PubMed id
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Abstract
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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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Headers
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