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siRNA Design Software for a Target Gene-Specific RNA Interference

RNA interference (RNAi) is a mechanism through which small interfering RNA (siRNA) induces sequence-specific posttranscriptional gene silencing. RNAi is commonly recognized as a powerful tool not only for functional genomics but also for therapeutic applications. Twenty-one-nucleotide-long siRNA sup...

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Detalles Bibliográficos
Autores principales: Naito, Yuki, Ui-Tei, Kumiko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Research Foundation 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371628/
https://www.ncbi.nlm.nih.gov/pubmed/22701467
http://dx.doi.org/10.3389/fgene.2012.00102
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author Naito, Yuki
Ui-Tei, Kumiko
author_facet Naito, Yuki
Ui-Tei, Kumiko
author_sort Naito, Yuki
collection PubMed
description RNA interference (RNAi) is a mechanism through which small interfering RNA (siRNA) induces sequence-specific posttranscriptional gene silencing. RNAi is commonly recognized as a powerful tool not only for functional genomics but also for therapeutic applications. Twenty-one-nucleotide-long siRNA suppresses the expression of the intended gene whose transcript possesses perfect complementarity to the siRNA guide strand. Hence, its silencing effect has been assumed to be extremely specific. However, accumulated evidences revealed that siRNA could downregulate unintended genes with partial complementarities mainly to the seven-nucleotide seed region of siRNA. This phenomenon is referred to as off-target effect. We have revealed that the capability to induce off-target effect is strongly correlated to the thermodynamic stability in siRNA seed-target duplex. For understanding accurate target gene function and successful therapeutic application, it may be critical to select a target gene-specific siRNA with minimized off-target effect. Here we present our siRNA design software for a target-specific RNAi. In addition, we also introduce the software programs open to the public for designing functional siRNAs.
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spelling pubmed-33716282012-06-14 siRNA Design Software for a Target Gene-Specific RNA Interference Naito, Yuki Ui-Tei, Kumiko Front Genet Genetics RNA interference (RNAi) is a mechanism through which small interfering RNA (siRNA) induces sequence-specific posttranscriptional gene silencing. RNAi is commonly recognized as a powerful tool not only for functional genomics but also for therapeutic applications. Twenty-one-nucleotide-long siRNA suppresses the expression of the intended gene whose transcript possesses perfect complementarity to the siRNA guide strand. Hence, its silencing effect has been assumed to be extremely specific. However, accumulated evidences revealed that siRNA could downregulate unintended genes with partial complementarities mainly to the seven-nucleotide seed region of siRNA. This phenomenon is referred to as off-target effect. We have revealed that the capability to induce off-target effect is strongly correlated to the thermodynamic stability in siRNA seed-target duplex. For understanding accurate target gene function and successful therapeutic application, it may be critical to select a target gene-specific siRNA with minimized off-target effect. Here we present our siRNA design software for a target-specific RNAi. In addition, we also introduce the software programs open to the public for designing functional siRNAs. Frontiers Research Foundation 2012-06-11 /pmc/articles/PMC3371628/ /pubmed/22701467 http://dx.doi.org/10.3389/fgene.2012.00102 Text en Copyright © 2012 Naito and Ui-Tei. http://www.frontiersin.org/licenseagreement This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.
spellingShingle Genetics
Naito, Yuki
Ui-Tei, Kumiko
siRNA Design Software for a Target Gene-Specific RNA Interference
title siRNA Design Software for a Target Gene-Specific RNA Interference
title_full siRNA Design Software for a Target Gene-Specific RNA Interference
title_fullStr siRNA Design Software for a Target Gene-Specific RNA Interference
title_full_unstemmed siRNA Design Software for a Target Gene-Specific RNA Interference
title_short siRNA Design Software for a Target Gene-Specific RNA Interference
title_sort sirna design software for a target gene-specific rna interference
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371628/
https://www.ncbi.nlm.nih.gov/pubmed/22701467
http://dx.doi.org/10.3389/fgene.2012.00102
work_keys_str_mv AT naitoyuki sirnadesignsoftwareforatargetgenespecificrnainterference
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