Interactions of pyrrolidinyl peptide nucleic acid with oligodeoxyguanosine and biosensing applications

Abstract

Pyrrolidinyl peptide nucleic acid is a DNA mimic consisting of proline-2-aminocyclopentane carboxylic acid (acpcPNA) as a core structure. It binds to DNA to form a more stable hybrid while showing greater selectivity and affinity than the conventional DNA and PNA probes. In this study, we aim to develop novel DNA sensing systems based on the acpcPNA probe. In the first part, graphene oxide (GO) was used as an external quencher which could effectively quench the fluorescein-labeled PNA probe. A remarkable fluorescence restoration was achieved after the addition of a complementary DNA target. This acpcPNA-GO combination was successfully used to monitor the strand-invasion of the duplex DNA by acpcPNA, and to detect two DNA targets in a multiplex, multicolor detection. In the second part, we demonstrated the effective quenching of fluorescently labeled acpcPNA by using oligodeoxyguanosine as an external quencher. The electrostatic interaction between the positively-charged modification on the PNA probe and the phosphate backbone of the oligodeoxyguanosine (dGX) resulted in a strong association, resulting in an effective quenching of the fluorescence by photoinduced electron transfer. The addition of the complementary DNA strand rapidly and completely restored the fluorescence without detaching the dGX from the PNA probe. This sensing system could detect the complementary DNA target with single-base mismatch specificity and could be applied to detect various other DNA sequences. The acpcPNA-dGX platform has been used in the multiplex detection of two DNA sequences and to detect Hg²⁺ ion as well as to monitor the PNA ligation. In the last part, a new DNA sensing system based on the combination of acpcPNA-dGX in the context of DNAzyme was explored. Preliminary studies revealed a promising result from the colorimetric DNA detection employing a strand displacement probe strategy. In short, binding of the dGX-modified DNA strand to PNA diminished its peroxidase activity, which could be restored when the DNA target was added to displace the DNAzyme.