Allele-selective inhibition of expression of huntingtin and ataxin-3 by RNA duplexes containing unlocked nucleic acid substitutions

Yuichiro Aiba, Jiaxin Hu, Jing Liu, Qin Xiang, Carlos Martinez, David R. Corey

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Unlocked nucleic acid (UNA) is an acyclic analogue of RNA that can be introduced into RNA or DNA oligonucleotides. The increased flexibility conferred by the acyclic structure fundamentally affects the strength of base pairing, creating opportunities for improved applications and new insights into molecular recognition. Here we test how UNA substitutions affect allele-selective inhibition of expression of trinucleotide repeat genes Huntingtin (HTT) and Ataxin-3 (ATX-3). We find that the either the combination of mismatched bases and UNA substitutions or UNA substitutions alone can improve potency and selectivity. Inhibition is potent, and selectivities of >40-fold for inhibiting mutant versus wild-type expression can be achieved. Surprisingly, even though UNA preserves the potential for complete base pairing, the introduction of UNA substitutions at central positions within fully complementary duplexes leads to >19-fold selectivity. Like mismatched bases, the introduction of central UNA bases disrupts the potential for cleavage of substrate by argonaute 2 (AGO2) during gene silencing. UNA-substituted duplexes are as effective as other strategies for allele-selective silencing of trinucleotide repeat disease genes. Modulation of AGO2 activity by the introduction of UNA substitutions demonstrates that backbone flexibility is as important as base pairing for catalysis of fully complementary duplex substrates. UNA can be used to tailor RNA silencing for optimal properties and allele-selective action.

Original languageEnglish (US)
Pages (from-to)9329-9338
Number of pages10
JournalBiochemistry
Volume52
Issue number51
DOIs
StatePublished - Dec 23 2013

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Nucleic Acids
Substitution reactions
Alleles
RNA
Base Pairing
Trinucleotide Repeats
Genes
Ataxin-3
Molecular recognition
Gene Silencing
Substrates
RNA Interference
Catalysis
Oligonucleotides
Modulation
DNA

ASJC Scopus subject areas

  • Biochemistry

Cite this

Allele-selective inhibition of expression of huntingtin and ataxin-3 by RNA duplexes containing unlocked nucleic acid substitutions. / Aiba, Yuichiro; Hu, Jiaxin; Liu, Jing; Xiang, Qin; Martinez, Carlos; Corey, David R.

In: Biochemistry, Vol. 52, No. 51, 23.12.2013, p. 9329-9338.

Research output: Contribution to journalArticle

Aiba, Yuichiro ; Hu, Jiaxin ; Liu, Jing ; Xiang, Qin ; Martinez, Carlos ; Corey, David R. / Allele-selective inhibition of expression of huntingtin and ataxin-3 by RNA duplexes containing unlocked nucleic acid substitutions. In: Biochemistry. 2013 ; Vol. 52, No. 51. pp. 9329-9338.
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