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Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants

The canonical exogenous trigger of RNA interference (RNAi) in mammals is small interfering RNA (siRNA). One promising application of RNAi is siRNA-based therapeutics, and therefore the optimization of siRNA efficacy is an important consideration. To reduce unfavorable properties of canonical 21mer s...

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Autores principales: Snead, Nicholas M., Wu, Xiwei, Li, Arthur, Cui, Qi, Sakurai, Kumi, Burnett, John C., Rossi, John J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695504/
https://www.ncbi.nlm.nih.gov/pubmed/23620279
http://dx.doi.org/10.1093/nar/gkt200
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author Snead, Nicholas M.
Wu, Xiwei
Li, Arthur
Cui, Qi
Sakurai, Kumi
Burnett, John C.
Rossi, John J.
author_facet Snead, Nicholas M.
Wu, Xiwei
Li, Arthur
Cui, Qi
Sakurai, Kumi
Burnett, John C.
Rossi, John J.
author_sort Snead, Nicholas M.
collection PubMed
description The canonical exogenous trigger of RNA interference (RNAi) in mammals is small interfering RNA (siRNA). One promising application of RNAi is siRNA-based therapeutics, and therefore the optimization of siRNA efficacy is an important consideration. To reduce unfavorable properties of canonical 21mer siRNAs, structural and chemical variations to canonical siRNA have been reported. Several of these siRNA variants demonstrate increased potency in downstream readout-based assays, but the molecular mechanism underlying the increased potency is not clear. Here, we tested the performance of canonical siRNAs and several sequence-matched variants in parallel in gene silencing, RNA-induced silencing complex (RISC) assembly, stability and Argonaute (Ago) loading assays. The commonly used 19mer with two deoxythymidine overhangs (19merTT) variant performed similarly to canonical 21mer siRNA. A shorter 16mer variant (16merTT) did not perform comparably in our assays. Dicer substrate interfering RNA (dsiRNA) demonstrated better gene silencing by the guide strand (target complementary strand), better RISC assembly, persistence of the guide strand and relatively more loading of the guide strand into Ago. Hence, we demonstrate the advantageous properties of dsiRNAs at upstream, intermediate and downstream molecular steps of the RNAi pathway.
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spelling pubmed-36955042013-06-28 Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants Snead, Nicholas M. Wu, Xiwei Li, Arthur Cui, Qi Sakurai, Kumi Burnett, John C. Rossi, John J. Nucleic Acids Res RNA The canonical exogenous trigger of RNA interference (RNAi) in mammals is small interfering RNA (siRNA). One promising application of RNAi is siRNA-based therapeutics, and therefore the optimization of siRNA efficacy is an important consideration. To reduce unfavorable properties of canonical 21mer siRNAs, structural and chemical variations to canonical siRNA have been reported. Several of these siRNA variants demonstrate increased potency in downstream readout-based assays, but the molecular mechanism underlying the increased potency is not clear. Here, we tested the performance of canonical siRNAs and several sequence-matched variants in parallel in gene silencing, RNA-induced silencing complex (RISC) assembly, stability and Argonaute (Ago) loading assays. The commonly used 19mer with two deoxythymidine overhangs (19merTT) variant performed similarly to canonical 21mer siRNA. A shorter 16mer variant (16merTT) did not perform comparably in our assays. Dicer substrate interfering RNA (dsiRNA) demonstrated better gene silencing by the guide strand (target complementary strand), better RISC assembly, persistence of the guide strand and relatively more loading of the guide strand into Ago. Hence, we demonstrate the advantageous properties of dsiRNAs at upstream, intermediate and downstream molecular steps of the RNAi pathway. Oxford University Press 2013-07 2013-04-24 /pmc/articles/PMC3695504/ /pubmed/23620279 http://dx.doi.org/10.1093/nar/gkt200 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA
Snead, Nicholas M.
Wu, Xiwei
Li, Arthur
Cui, Qi
Sakurai, Kumi
Burnett, John C.
Rossi, John J.
Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants
title Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants
title_full Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants
title_fullStr Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants
title_full_unstemmed Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants
title_short Molecular basis for improved gene silencing by Dicer substrate interfering RNA compared with other siRNA variants
title_sort molecular basis for improved gene silencing by dicer substrate interfering rna compared with other sirna variants
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695504/
https://www.ncbi.nlm.nih.gov/pubmed/23620279
http://dx.doi.org/10.1093/nar/gkt200
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