Label-free potentiometry for detecting DNA hybridization using peptide nucleic acid and DNA probes.

Tatsuro Goda,Ankit Balram Singi,Akira Matsumoto,Masaki Torimura,Yasuhiro Maeda,Hiroshi Aoki,Yuji Miyahara

doi:10.3390/s130202267

Abstract

Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry.

Highlights

The development of biosensors with high sensitivity and selectivity is of paramount importance for clinical diagnostics, genomics, and drug discovery
We focused on using a high input impedance electrometer for label-free detection of the DNA hybridization by the direct electrical readout of captured DNA charges [22]
We compared the performance of Peptide nucleic acid (PNA) probes with DNA ones on the sensitivity and specificity to DNA target at the solution/electrode interface using the electrometer-based potentiometric biosensor

Summary

Introduction

The development of biosensors with high sensitivity and selectivity is of paramount importance for clinical diagnostics, genomics, and drug discovery. Electrochemical techniques have been developed for nucleic acids biosensing with high sensitivity and selectivity to DNA target [3]. The signal generation is mainly based on the modulation of electron transfer activity of labeled or free redox indicators upon hybridization or strand displacement by target recognition. Another promising platform for unlabeled sensing is nanomaterials-based field-effect transistors (FETs) [4,5,6,7,8]. The binding of the specific ligand or complementary DNA modifies the electric field surrounding the device, enabling direct electronic detection as low as femtomolar in a salt free solution and picomolar in solutions at physiological ionic strength. Nanowire/nanotube devices suffer from alignment and reproducibility issues

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