title: High-throughput optical sensing of nucleic acids in a nanopore array.
abstract: Protein nanopores such as α-haemolysin and Mycobacterium smegmatis porin A (MspA) can be used to sequence long strands of DNA at low cost. To provide high-speed sequencing, large arrays of nanopores are required, but current nanopore sequencing methods rely on ionic current measurements from individually addressed pores and such methods are likely to prove difficult to scale up. Here we show that, by optically encoding the ionic flux through protein nanopores, the discrimination of nucleic acid sequences and the detection of sequence-specific nucleic acid hybridization events can be parallelized. We make optical recordings at a density of ∼10(4) nanopores per mm(2) in a single droplet interface bilayer. Nanopore blockades can discriminate between DNAs with sub-picoampere equivalent resolution, and specific miRNA sequences can be identified by differences in unzipping kinetics. By creating an array of 2,500 bilayers with a micropatterned hydrogel chip, we are also able to load different samples into specific bilayers suitable for high-throughput nanopore recording.
authors: Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.|School of Chemistry and Chemical Engineering, Nanjing University 210093, China.
authors: Shuo
authors: S
authors: Huang
authors: Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.
authors: Mercedes
authors: M
authors: Romero-Ruiz
authors: Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.|School of Pharmacy and Pharmaceutical Sciences, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF10 3NB, UK.
authors: Oliver K
authors: OK
authors: Castell
authors: Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.
authors: Hagan
authors: H
authors: Bayley
authors: Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.
authors: Mark I
authors: http://orcid.org/0000-0002-5692-8313
authors: MI
authors: Wallace
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D001483:Base Sequence; D004247:DNA / Q000032:analysis*; D005453:Fluorescence; D006460:Hemolysin Proteins / Q000737:chemistry; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000032:analysis*; D020102:Mycobacterium smegmatis / Q000737:chemistry; D058608:Nanopores / Q000648:ultrastructure; D009696:Nucleic Acids / Q000032:analysis; D018272:Porins / Q000737:chemistry; D017422:Sequence Analysis, DNA / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D001426:Bacterial Proteins; D006460:Hemolysin Proteins; D035683:MicroRNAs; D009696:Nucleic Acids; D018272:Porins; D004247:DNA