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

Abstract

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.

A Biotinylated cpFIT-PNA Platform for the Facile Detection of Drug Resistance to Artemisinin in Plasmodium falciparum

“…PNA-based RNA/DNA sensors have been developed by various chemical approaches, − among them, FIT-PNAs (forced intercalation-peptide nucleic acids). − …”

Peptide Nucleic Acids: Applications in Biomedical Sciences

“…Chemical modifications to PNA may be also introduced at either the C or N termini. The Kaihatsu lab [ 19 ] report in this Special Issue a panel of Tolane-modified PNAs (introduced at the N-terminus) that present good mismatch discrimination between single point mutated vs. wild type DNA or RNA. One such analog (a naphtyl derivative) was shown as a practical PNA probe for SNP detection of the influenza A virus neuraminidase gene that is associated with drug resistance.…”