Integrated Nano-Opto-Fluidic System on Sapphire towards Single-Molecule Protein Sequencing - PROJECT SUMMARY/ ABSTRACT
Enabled by the development of high-throughput, low-cost nucleic acids sequencing technologies, there have
been accelerated development in genomics and transcriptomics in the past two decades, profoundly reshaping
our knowledge in biology and medicine. However, similar technologies have yet to emerge for rapid identification
and quantification of proteins. This is attributed to more complex structures of proteins, lack of polymerase chain
reaction-like amplification methods, cellular heterogeneity, etc. Conventional protein sequencing methods, such
as Edman degradation and mass spectrometry, are slow, expensive, and not suitable for detecting low-
abundance proteins. Such ensemble measurements also can mask our fundamental understandings on how
cells of a particular genotype function and respond to therapeutics. Single-molecule protein sequencing (SMPS)
is an emerging research direction that directly reads amino acids sequence from individual protein or peptide
molecules. Yet, a promising strategy using fluorosequencing still relies on long Edman degradation cycles and
bulky fluorescent microscopes, not ideal for fast and low-cost readout. Electronic SMPS technologies using
tunneling or nanopore sensors are emerging methods for development of portable and inexpensive sequencing
systems. However, they still face challenges in precise nanofabrication, structural instability, high electronic
noise, and inability in detection of all amino acids. To address the multi-faceted challenges in next-generation
SMPS, we will design an on-chip integrated, electronic system that incorporates nano-opto-fluidic structures to
transduce protein fingerprints into electronic signals at a high speed, a low cost and a small system foot-print.
Our platform features an all-sapphire nanopore (AlSaPore) fluidic device that has a small capacitance and a
greatly improved structural stability, and accordingly suited for high-speed, low-noise, high-throughput, electronic
detection. Further, an ultrathin nitride-based metasurface-integrated circuit (MIC) structure is created on the
AlSaPore to optically interrogate the fluorescently tagged single amino acids passing through the nanopore
without conventional fluorescent microscopy. Subsequently, the fluorescent tag signals are transmitted through
the waveguide and collected by on-chip integrated photodetectors. The optoelectronic channel (IA for amino acids
tags) and ionic current channel (IP for protein primary structure) will be synchronously recorded, classified by
deep learning algorithms, and used in combination to improve the protein sequencing accuracy. Supported by
well-established nitride-on-sapphire device design and manufacturing technology, our MIC-AlSaPore is a
scalable and compact platform that achieves single-molecule sensitivity with a potential to read out all 20 amino
acids. The development of MIC-AlSaPore platform will have far-reaching impact in biomedicine beyond protein
sequencing. It may be used for studying DNA-protein interactions at single-molecule levels, classification of
specific genes, genome mapping and de novo assembly. Additionally, it may inspire future multi-omic (genomic,
transcriptomic, and proteomic) diagnostic solutions with potential clinical applications.