Potentiometric sensing of nucleic acids using chemically modified nanopores

Abstract

Unlike the overwhelming majority of nanopore sensors that are based on the measurement of a transpore ionic current, here we introduce a potentiometric sensing scheme and demonstrate its application for the selective detection of nucleic acids. The sensing concept uses the charge inversion that occurs in the sensing zone of a nanopore upon binding of negatively charged microRNA strands to positively charged peptide-nucleic acid (PNA) modified nanopores. The initial anionic permselectivity of PNA-modified nanopores is thus gradually changed to cationic permselectivity, which can be detected simply by measuring the nanoporous membrane potential. A quantitative theoretical treatment of the potentiometric microRNA response is provided based on the Nernst-Planck/Poisson model for the nanopore system assuming first order kinetics for the nucleic acid hybridization. An excellent correlation between the theoretical and experimental results was observed, which revealed that the binding process is focused at the nanopore entrance with contributions from both in pore and out of pore sections of the nanoporous membrane. The theoretical treatment is able to give clear guidelines for further optimization of potentiometric nanopore-based nucleic acid sensors by predicting the effect of the most important experimental parameters on the potential response.

Multiplexed assessment of the surface density of DNA probes on DNA microarrays by surface plasmon resonance imaging

“…The study revealed that DNA probes microspotted in both single stranded and prehybridized form can ultimately provide the same hybridization efficiency. For high spot density DNA microarrays the prehybridization with a complementary strand may not be practical due to higher cost, but it contours as the most robust approach for (i) kinetic measurements, (ii) small spot density DNA microarrays and (iii) in case of surface morphologies or nanoscale confinements where reproducible hybridization efficiencies are otherwise difficult to achieve, e.g., nanopores [35]. Arrays with microspotted ssDNA strands require more elaborate optimization in terms of hybridization efficiency, however allows for fine tuning of the surface coverage for a better discrimination of single mismatch targets.…”

PNA-Based MicroRNA Detection Methodologies

“…In presence of the target miR, DNA displacement occurs accompanied by the release of the AuNPs, thus affording a measurable variation of system impedance. Based on the obtained results, the same group later reported on a new, optimized, nanopore array for potentiometric detection of the same miR, exploiting a different approach [69]. In this device, gold nanopores were decorated with positively charged PNAs to ensure anionic permselectivity, thus avoiding the passage of cations through the pore.…”

PT2 - Solid-state nanopores for sensing

“…Furthermore, the potentiometric transduction mechanism could be also extended for the selective detection of nucleic acids with peptide nucleic acid functionalized nanopores. [14]…”