High-Throughput Block Optical DNA Sequence Identification

The goal of developing a label-free optical DNA sequencing technique will require nanoscale focusing of light to single molecules and high-throughput, multiplexed analysis. We use surface-enhanced Raman spectroscopy to demonstrate label-free identification of DNA nucleobases from multiplexed three-dimensional plasmonic nanofocusing and characterization of molecular vibrations within the fingerprinting region of ~400-1400 cm^-1. While nanometer-scale mode volumes prevent resolution of single nucleobases, our block optical technique can identify relative A, T, G, and C content in DNA k-mers (where k ~10 nucleotides for a volume of ~100 nm³). We show that the content of k-mer blocks can be used as a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single letter sequencing. Additionally, we show that coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization [1]. The results pave the way for a novel, high-throughput block optical sequencing (BOS) method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition.
[1] Korshoj, Sagar, Hanson, Chowdhury, Otoupal, Chatterjee, Nagpal, Small 2017, In Press