title: Two color DNA barcode detection in photoluminescence suppressed silicon nitride nanopores.
abstract: Optical sensing of solid-state nanopores is a relatively new approach that can enable high-throughput, multicolor readout from a collection of nanopores. It is therefore highly attractive for applications such as nanopore-based DNA sequencing and genotyping using DNA barcodes. However, to date optical readout has been plagued by the need to achieve sufficiently high signal-to-noise ratio (SNR) for single fluorophore sensing, while still maintaining millisecond resolution. One of the main factors degrading the optical SNR in solid-state nanopores is the high photoluminescence (PL) background emanating from the silicon nitride (SiNx) membrane in which pores are commonly fabricated. Focusing on the optical properties of SiNx nanopores we show that the local membrane PL intensity is substantially reduced, and its spectrum is shifted toward shorter wavelengths with increasing e-beam dose. This phenomenon, which is correlated with a marked photocurrent enhancement in these nanopores, is utilized to perform for the first time single molecule fluorescence detection using both green and red laser excitations. Specifically, the reduction in PL and the concurrent measurement of the nanopore photocurrent enhancement allow us to maximize the background suppression and to detect a dual color, five-unit DNA barcode with high SNR levels.
authors.affiliation: Department of Biomedical Engineering, Boston University , Boston, Massachusetts 02215 United States.
authors.forename: Ossama N
authors.initials: ON
authors.lastname: Assad
authors.forename: Nicolas
authors.initials: N
authors.lastname: Di Fiori
authors.forename: Allison H
authors.initials: AH
authors.lastname: Squires
authors.forename: Amit
authors.initials: A
authors.lastname: Meller
mesh_terms: D004247:DNA / Q000737:chemistry*; D008163:Luminescent Measurements; D008567:Membranes, Artificial; D058608:Nanopores; D059629:Signal-To-Noise Ratio
chemical_list: D008567:Membranes, Artificial; D004247:DNA
keywords: Solid-state nanopore; electron-beam; optical detection; photoluminescence; silicon nitride; single-molecule