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Nucleic Acids Research
Article . 2010 . Peer-reviewed
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Nucleic Acids Research
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Thermodynamics of RNA duplexes modified with unlocked nucleic acid nucleotides

Authors: Pasternak, Anna; Wengel, Jesper;

Thermodynamics of RNA duplexes modified with unlocked nucleic acid nucleotides

Abstract

Thermodynamics provides insights into the influence of modified nucleotide residues on stability of nucleic acids and is crucial for designing duplexes with given properties. In this article, we introduce detailed thermodynamic analysis of RNA duplexes modified with unlocked nucleic acid (UNA) nucleotide residues. We investigate UNA single substitutions as well as model mismatch and dangling end effects. UNA residues placed in a central position makes RNA duplex structure less favourable by 4.0-6.6 kcal/mol. Slight destabilization, by ∼0.5-1.5 kcal/mol, is observed for 5'- or 3'-terminal UNA residues. Furthermore, thermodynamic effects caused by UNA residues are extremely additive with ΔG°(37) conformity up to 98%. Direct mismatches involving UNA residues decrease the thermodynamic stability less than unmodified mismatches in RNA duplexes. Additionally, the presence of UNA residues adjacent to unpaired RNA residues reduces mismatch discrimination. Thermodynamic analysis of UNA 5'- and 3'-dangling ends revealed that stacking interactions of UNA residues are always less favourable than that of RNA residues. Finally, circular dichroism spectra imply no changes in overall A-form structure of UNA-RNA/RNA duplexes relative to the unmodified RNA duplexes.

Country
Denmark
Related Organizations
Keywords

Base Pair Mismatch, Nucleotides, Circular Dichroism, RNA, Thermodynamics, RNA, Double-Stranded

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
54
Top 10%
Top 10%
Top 10%
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gold