Exploring PAZ/3′-overhang interaction to improve siRNA specificity. A combined experimental and modeling study
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10316/107535 https://doi.org/10.1039/C8SC00010G |
Resumo: | The understanding of the dynamical and mechanistic aspects that lie behind siRNA-based gene regulation is a requisite to boost the performance of siRNA therapeutics. A systematic experimental and computational study on the 30-overhang structural requirements for the design of more specific and potent siRNA molecules was carried out using nucleotide analogues differing in structural parameters, such as sugar constraint, lack of nucleobase, distance between the phosphodiester backbone and nucleobase, enantioselectivity, and steric hindrance. The results established a set of rules governing the siRNAmediated silencing, indicating that the thermodynamic stability of the 50-end is a crucial determinant for antisense-mediated silencing but is not sufficient to avoid sense-mediated silencing. Both theoretical and experimental approaches consistently evidence the existence of a direct connection between the PAZ/30-overhang binding affinity and siRNA’s potency and specificity. An overall description of the systems is thus achieved by atomistic simulations and free energy calculations that allow us to propose a robust and self-contained procedure for studying the factors implied in PAZ/30-overhang siRNA interactions. A higher RNAi activity is associated with a moderate-to-strong PAZ/30-overhang binding. Contrarily, lower binding energies compromise siRNA potency, increase specificity, and favor siRNA downregulation by Ago2-independent mechanisms. This work provides in-depth details for the design of powerful and safe synthetic nucleotide analogues for substitution at the 30-overhang, enabling some of the intrinsic siRNA disadvantages to be overcome. |
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Exploring PAZ/3′-overhang interaction to improve siRNA specificity. A combined experimental and modeling studyThe understanding of the dynamical and mechanistic aspects that lie behind siRNA-based gene regulation is a requisite to boost the performance of siRNA therapeutics. A systematic experimental and computational study on the 30-overhang structural requirements for the design of more specific and potent siRNA molecules was carried out using nucleotide analogues differing in structural parameters, such as sugar constraint, lack of nucleobase, distance between the phosphodiester backbone and nucleobase, enantioselectivity, and steric hindrance. The results established a set of rules governing the siRNAmediated silencing, indicating that the thermodynamic stability of the 50-end is a crucial determinant for antisense-mediated silencing but is not sufficient to avoid sense-mediated silencing. Both theoretical and experimental approaches consistently evidence the existence of a direct connection between the PAZ/30-overhang binding affinity and siRNA’s potency and specificity. An overall description of the systems is thus achieved by atomistic simulations and free energy calculations that allow us to propose a robust and self-contained procedure for studying the factors implied in PAZ/30-overhang siRNA interactions. A higher RNAi activity is associated with a moderate-to-strong PAZ/30-overhang binding. Contrarily, lower binding energies compromise siRNA potency, increase specificity, and favor siRNA downregulation by Ago2-independent mechanisms. This work provides in-depth details for the design of powerful and safe synthetic nucleotide analogues for substitution at the 30-overhang, enabling some of the intrinsic siRNA disadvantages to be overcome.Royal Society of Chemistry2018info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://hdl.handle.net/10316/107535http://hdl.handle.net/10316/107535https://doi.org/10.1039/C8SC00010Geng2041-65202041-6539Alagia, AdeleJorge, Andreia F.Aviñó, AnnaCova, Tânia F. G. G.Crehuet, RamonGrijalvo, SantiagoPais, AlbertoEritja, Ramoninfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-19T09:10:53Zoai:estudogeral.uc.pt:10316/107535Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T21:23:52.902962Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Exploring PAZ/3′-overhang interaction to improve siRNA specificity. A combined experimental and modeling study |
title |
Exploring PAZ/3′-overhang interaction to improve siRNA specificity. A combined experimental and modeling study |
spellingShingle |
Exploring PAZ/3′-overhang interaction to improve siRNA specificity. A combined experimental and modeling study Alagia, Adele |
title_short |
Exploring PAZ/3′-overhang interaction to improve siRNA specificity. A combined experimental and modeling study |
title_full |
Exploring PAZ/3′-overhang interaction to improve siRNA specificity. A combined experimental and modeling study |
title_fullStr |
Exploring PAZ/3′-overhang interaction to improve siRNA specificity. A combined experimental and modeling study |
title_full_unstemmed |
Exploring PAZ/3′-overhang interaction to improve siRNA specificity. A combined experimental and modeling study |
title_sort |
Exploring PAZ/3′-overhang interaction to improve siRNA specificity. A combined experimental and modeling study |
author |
Alagia, Adele |
author_facet |
Alagia, Adele Jorge, Andreia F. Aviñó, Anna Cova, Tânia F. G. G. Crehuet, Ramon Grijalvo, Santiago Pais, Alberto Eritja, Ramon |
author_role |
author |
author2 |
Jorge, Andreia F. Aviñó, Anna Cova, Tânia F. G. G. Crehuet, Ramon Grijalvo, Santiago Pais, Alberto Eritja, Ramon |
author2_role |
author author author author author author author |
dc.contributor.author.fl_str_mv |
Alagia, Adele Jorge, Andreia F. Aviñó, Anna Cova, Tânia F. G. G. Crehuet, Ramon Grijalvo, Santiago Pais, Alberto Eritja, Ramon |
description |
The understanding of the dynamical and mechanistic aspects that lie behind siRNA-based gene regulation is a requisite to boost the performance of siRNA therapeutics. A systematic experimental and computational study on the 30-overhang structural requirements for the design of more specific and potent siRNA molecules was carried out using nucleotide analogues differing in structural parameters, such as sugar constraint, lack of nucleobase, distance between the phosphodiester backbone and nucleobase, enantioselectivity, and steric hindrance. The results established a set of rules governing the siRNAmediated silencing, indicating that the thermodynamic stability of the 50-end is a crucial determinant for antisense-mediated silencing but is not sufficient to avoid sense-mediated silencing. Both theoretical and experimental approaches consistently evidence the existence of a direct connection between the PAZ/30-overhang binding affinity and siRNA’s potency and specificity. An overall description of the systems is thus achieved by atomistic simulations and free energy calculations that allow us to propose a robust and self-contained procedure for studying the factors implied in PAZ/30-overhang siRNA interactions. A higher RNAi activity is associated with a moderate-to-strong PAZ/30-overhang binding. Contrarily, lower binding energies compromise siRNA potency, increase specificity, and favor siRNA downregulation by Ago2-independent mechanisms. This work provides in-depth details for the design of powerful and safe synthetic nucleotide analogues for substitution at the 30-overhang, enabling some of the intrinsic siRNA disadvantages to be overcome. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10316/107535 http://hdl.handle.net/10316/107535 https://doi.org/10.1039/C8SC00010G |
url |
http://hdl.handle.net/10316/107535 https://doi.org/10.1039/C8SC00010G |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
2041-6520 2041-6539 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Royal Society of Chemistry |
publisher.none.fl_str_mv |
Royal Society of Chemistry |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
|
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1799134125087522816 |