Quantum-NanoElectroPore Platform for Single-Molecule Conductance and Raman Detection of Biomolecules

The great advancement in nanopore technology has enabled real-time sequencing without the need for sample amplification with long read length. However, the ionic-current-based readout has limitations in the specificity and resolution, leading to higher error rate. The growing interest in analyzing other biomolecules such as proteins using nanopore configurations also demands integration of additional readout mechanisms such as recognition tunneling and metal-gap enhanced Raman. However so far there is very little success in the integration of single-molecule delivery, and multi-mode detection of the same molecule. We recently developed a new strategy to fabricate a single-molecule sensing microchip platform, Quantum Tunneling NanoElectroPore (Q-NEP), which integrates inside a nanofluidic channel a pair of tunneling electrodes self-aligned with a nanopore, by combining standard top-down lithography on standard semiconductor substrates with <i>in situ</i> reversible electrochemical deposition with feedback control. We have demonstrated simultaneous detection of DNA translocation events from coincidental ionic and tunneling current signals, and successfully obtained quantized conductance from short thiolated oligonucleotides bridging the tunneling gap as they were delivered through the nanopore. In addition, metal-gap enhanced Raman signals are also obtained from L-cysteine molecules through the device. These results provide the first step for the integration of ionic, tunneling current and Raman multi-mode analysis of individual molecules on the Q-NEP platform, and reveal the promising potential for a unified microchip platform for multi-omics analysis with high resolution and specificity.