Terminal Duplex Stability and Nucleotide Identity Differentially Control siRNA Loading and Activity in RNA Interference

Phillip A. Angart, Rebecca J. Carlson, Kwasi Adu-Berchie, S. Patrick Walton

Research output: Contribution to journalArticle

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Abstract

Efficient short interfering RNA (siRNA)-mediated gene silencing requires selection of a sequence that is complementary to the intended target and possesses sequence and structural features that encourage favorable functional interactions with the RNA interference (RNAi) pathway proteins. In this study, we investigated how terminal sequence and structural characteristics of siRNAs contribute to siRNA strand loading and silencing activity and how these characteristics ultimately result in a functionally asymmetric duplex in cultured HeLa cells. Our results reiterate that the most important characteristic in determining siRNA activity is the 5′ terminal nucleotide identity. Our findings further suggest that siRNA loading is controlled principally by the hybridization stability of the 5′ terminus (Nucleotides: 1-2) of each siRNA strand, independent of the opposing terminus. Postloading, RNA-induced silencing complex (RISC)-specific activity was found to be improved by lower hybridization stability in the 5′ terminus (Nucleotides: 3-4) of the loaded siRNA strand and greater hybridization stability toward the 3′ terminus (Nucleotides: 17-18). Concomitantly, specific recognition of the 5′ terminal nucleotide sequence by human Argonaute 2 (Ago2) improves RISC half-life. These findings indicate that careful selection of siRNA sequences can maximize both the loading and the specific activity of the intended guide strand.

LanguageEnglish (US)
Pages309-317
Number of pages9
JournalNucleic Acid Therapeutics
Volume26
Issue number5
DOIs
StatePublished - Oct 1 2016

Profile

RNA Interference
Small Interfering RNA
Nucleotides
RNA
RNA-Induced Silencing Complex
Gene Silencing
HeLa Cells
Half-Life
Cultured Cells
Genes
Proteins

Keywords

  • Ago2
  • duplex thermodynamics
  • functional asymmetry
  • RNAi
  • siRNA
  • terminal nucleotide

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Genetics
  • Drug Discovery

Cite this

Terminal Duplex Stability and Nucleotide Identity Differentially Control siRNA Loading and Activity in RNA Interference. / Angart, Phillip A.; Carlson, Rebecca J.; Adu-Berchie, Kwasi; Walton, S. Patrick.

In: Nucleic Acid Therapeutics, Vol. 26, No. 5, 01.10.2016, p. 309-317.

Research output: Contribution to journalArticle

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