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SNP Discrimination by Tolane-Modified Peptide Nucleic Acids: Application for the Detection of Drug Resistance in Pathogens

During the treatment of viral or bacterial infections, it is important to evaluate any resistance to the therapeutic agents used. An amino acid substitution arising from a single base mutation in a particular gene often causes drug resistance in pathogens. Therefore, molecular tools that discriminat...

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Autores principales: Takagi, Kenji, Hayashi, Tenko, Sawada, Shinjiro, Okazaki, Miku, Hori, Sakiko, Ogata, Katsuya, Kato, Nobuo, Ebara, Yasuhito, Kaihatsu, Kunihiro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7070780/
https://www.ncbi.nlm.nih.gov/pubmed/32053960
http://dx.doi.org/10.3390/molecules25040769
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author Takagi, Kenji
Hayashi, Tenko
Sawada, Shinjiro
Okazaki, Miku
Hori, Sakiko
Ogata, Katsuya
Kato, Nobuo
Ebara, Yasuhito
Kaihatsu, Kunihiro
author_facet Takagi, Kenji
Hayashi, Tenko
Sawada, Shinjiro
Okazaki, Miku
Hori, Sakiko
Ogata, Katsuya
Kato, Nobuo
Ebara, Yasuhito
Kaihatsu, Kunihiro
author_sort Takagi, Kenji
collection PubMed
description During the treatment of viral or bacterial infections, it is important to evaluate any resistance to the therapeutic agents used. An amino acid substitution arising from a single base mutation in a particular gene often causes drug resistance in pathogens. Therefore, molecular tools that discriminate a single base mismatch in the target sequence are required for achieving therapeutic success. Here, we synthesized peptide nucleic acids (PNAs) derivatized with tolane via an amide linkage at the N-terminus and succeeded in improving the sequence specificity, even with a mismatched base pair located near the terminal region of the duplex. We assessed the sequence specificities of the tolane-PNAs for single-strand DNA and RNA by UV-melting temperature analysis, thermodynamic analysis, an in silico conformational search, and a gel mobility shift assay. As a result, all of the PNA-tolane derivatives stabilized duplex formation to the matched target sequence without inducing mismatch target binding. Among the different PNA-tolane derivatives, PNA that was modified with a naphthyl-type tolane could efficiently discriminate a mismatched base pair and be utilized for the detection of resistance to neuraminidase inhibitors of the influenza A/H1N1 virus. Therefore, our molecular tool can be used to discriminate single nucleotide polymorphisms that are related to drug resistance in pathogens.
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spelling pubmed-70707802020-03-19 SNP Discrimination by Tolane-Modified Peptide Nucleic Acids: Application for the Detection of Drug Resistance in Pathogens Takagi, Kenji Hayashi, Tenko Sawada, Shinjiro Okazaki, Miku Hori, Sakiko Ogata, Katsuya Kato, Nobuo Ebara, Yasuhito Kaihatsu, Kunihiro Molecules Article During the treatment of viral or bacterial infections, it is important to evaluate any resistance to the therapeutic agents used. An amino acid substitution arising from a single base mutation in a particular gene often causes drug resistance in pathogens. Therefore, molecular tools that discriminate a single base mismatch in the target sequence are required for achieving therapeutic success. Here, we synthesized peptide nucleic acids (PNAs) derivatized with tolane via an amide linkage at the N-terminus and succeeded in improving the sequence specificity, even with a mismatched base pair located near the terminal region of the duplex. We assessed the sequence specificities of the tolane-PNAs for single-strand DNA and RNA by UV-melting temperature analysis, thermodynamic analysis, an in silico conformational search, and a gel mobility shift assay. As a result, all of the PNA-tolane derivatives stabilized duplex formation to the matched target sequence without inducing mismatch target binding. Among the different PNA-tolane derivatives, PNA that was modified with a naphthyl-type tolane could efficiently discriminate a mismatched base pair and be utilized for the detection of resistance to neuraminidase inhibitors of the influenza A/H1N1 virus. Therefore, our molecular tool can be used to discriminate single nucleotide polymorphisms that are related to drug resistance in pathogens. MDPI 2020-02-11 /pmc/articles/PMC7070780/ /pubmed/32053960 http://dx.doi.org/10.3390/molecules25040769 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Takagi, Kenji
Hayashi, Tenko
Sawada, Shinjiro
Okazaki, Miku
Hori, Sakiko
Ogata, Katsuya
Kato, Nobuo
Ebara, Yasuhito
Kaihatsu, Kunihiro
SNP Discrimination by Tolane-Modified Peptide Nucleic Acids: Application for the Detection of Drug Resistance in Pathogens
title SNP Discrimination by Tolane-Modified Peptide Nucleic Acids: Application for the Detection of Drug Resistance in Pathogens
title_full SNP Discrimination by Tolane-Modified Peptide Nucleic Acids: Application for the Detection of Drug Resistance in Pathogens
title_fullStr SNP Discrimination by Tolane-Modified Peptide Nucleic Acids: Application for the Detection of Drug Resistance in Pathogens
title_full_unstemmed SNP Discrimination by Tolane-Modified Peptide Nucleic Acids: Application for the Detection of Drug Resistance in Pathogens
title_short SNP Discrimination by Tolane-Modified Peptide Nucleic Acids: Application for the Detection of Drug Resistance in Pathogens
title_sort snp discrimination by tolane-modified peptide nucleic acids: application for the detection of drug resistance in pathogens
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7070780/
https://www.ncbi.nlm.nih.gov/pubmed/32053960
http://dx.doi.org/10.3390/molecules25040769
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