title: Nanopore arrays in a silicon membrane for parallel single-molecule detection: DNA translocation.
abstract: Optical nanopore sensing offers great potential in single-molecule detection, genotyping, or DNA sequencing for high-throughput applications. However, one of the bottle-necks for fluorophore-based biomolecule sensing is the lack of an optically optimized membrane with a large array of nanopores, which has large pore-to-pore distance, small variation in pore size and low background photoluminescence (PL). Here, we demonstrate parallel detection of single-fluorophore-labeled DNA strands (450 bps) translocating through an array of silicon nanopores that fulfills the above-mentioned requirements for optical sensing. The nanopore array was fabricated using electron beam lithography and anisotropic etching followed by electrochemical etching resulting in pore diameters down to ∼7 nm. The DNA translocation measurements were performed in a conventional wide-field microscope tailored for effective background PL control. The individual nanopore diameter was found to have a substantial effect on the translocation velocity, where smaller openings slow the translocation enough for the event to be clearly detectable in the fluorescence. Our results demonstrate that a uniform silicon nanopore array combined with wide-field optical detection is a promising alternative with which to realize massively-parallel single-molecule detection.
authors.affiliation: Materials and Nano Physics, School of Information and Communication Technology, KTH Royal Institute of Technology, Electrum 229, SE-16440 Kista-Stockholm, Sweden.
authors.forename: Miao
authors.initials: M
authors.lastname: Zhang
authors.forename: Torsten
authors.initials: T
authors.lastname: Schmidt
authors.forename: Anders
authors.initials: A
authors.lastname: Jemt
authors.forename: Pelin
authors.initials: P
authors.lastname: Sahlén
authors.forename: Ilya
authors.initials: I
authors.lastname: Sychugov
authors.forename: Joakim
authors.initials: J
authors.lastname: Lundeberg
authors.forename: Jan
authors.initials: J
authors.lastname: Linnros
mesh_terms: D015374:Biosensing Techniques / Q000295:instrumentation* / Q000379:methods*; D004247:DNA / Q000032:analysis / Q000737:chemistry*; D055664:Electrochemical Techniques; D008163:Luminescent Measurements; D008567:Membranes, Artificial; D058608:Nanopores / Q000648:ultrastructure; D012825:Silicon
chemical_list: D008567:Membranes, Artificial; D004247:DNA; D012825:Silicon