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

• Published in: Molecules (Basel, Switzerland) Vol. 25; no. 4; p. 769
• Main Authors: Takagi, Kenji, Hayashi, Tenko, Sawada, Shinjiro, Okazaki, Miku, Hori, Sakiko, Ogata, Katsuya, Kato, Nobuo, Ebara, Yasuhito, Kaihatsu, Kunihiro
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI 11.02.2020; MDPI AG
• Subjects: drug resistance; influenza virus; peptide nucleic acid; single nucleotide polymorphism; tolane; influenza virus; drug resistance; single nucleotide polymorphism; tolane; peptide nucleic acid
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules25040769

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.