Design and fabrication of three-dimensionally structured, gold membranes containing hexagonally close-packed microcavities with nanopores in the base, are described. Our aim is to create a nanoporous structure with localized enhancement of the fluorescence or Raman scattering at, and in the nanopore when excited with light of approximately 600 nm, with a view to provide sensitive detection of b...

BACKGROUND Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from small genomes in a matter of seconds. The Oxford Nanopore technology is truly disruptive; it has the potential to revolutionize genomic applications due to its portability, low cost, and ease o...

The introduction of the MinION sequencing device by Oxford Background: Nanopore Technologies may greatly accelerate whole genome sequencing. It has been shown that the nanopore sequence data, in combination with other sequencing technologies, is highly useful for accurate annotation of all genes in the genome. However, it also offers great potential for assembly of de novo complex genomes wi...

Enzymes that move directionally on single-stranded nucleic acids are at the core of emerging nanopore sequencing technology. Of a particular use are DNA helicases, molecular motors that bind single-stranded DNA (ssDNA) independently of its sequence and use ATP to fuel their directional motion along the DNA (1). In nanopore-based sequencing, a pore formed by a protein channel embedded into a lip...

SP1 protein as a new type of biological nanopore is described and is utilized to distinguish single-stranded DNA at the single-molecule level. Using the SP1 nanopore to investigate single molecule detection broadens the existing research areas of pore-forming biomaterials from unsymmetrical biological nanopores to symmetrical biological nanopores. This novel nanopore could provide a good candid...

Nanopore sequencing [1-4], a promising single-molecule DNA sequencing technology, exhibits many attractive qualities and, in time, could potentially surpass current sequencing technologies. Nanopore sequencing promises higher throughput, lower cost, and increased read length, and it does not require a prior amplification step. Nanopore sequencers rely solely on the electrochemical structure of ...

Many efforts are being made in translating the nanopore into an ultrasensitive single-molecule platform for various genetic and epigenetic detections. However, compared with current approaches including PCR, the low throughput limits the nanopore applications in biological research and clinical settings, which usually requires simultaneous detection of multiple biomarkers for accurate disease d...

Despite advances in sequencing, structural variants (SVs) remain difficult to reliably detect due to the short read length (<300 bp) of 2nd generation sequencing. Not only do the reads (or paired-end reads) need to straddle a breakpoint, but repetitive elements often lead to ambiguities in the alignment of short reads. We propose to use the long-reads (up to 20 kb) possible with 3rd generation ...

MOTIVATION Recent emergence of nanopore sequencing technology set a challenge for established assembly methods. In this work, we assessed how existing hybrid and non-hybrid de novo assembly methods perform on long and error prone nanopore reads. RESULTS We benchmarked five non-hybrid (in terms of both error correction and scaffolding) assembly pipelines as well as two hybrid assemblers which ...

Nanopore-based technologies have attracted much attention recently for their promising use in low-cost and high-throughput genome sequencing. To achieve single-base resolution of DNA sequencing, it is critical to slow and control the translocation of DNA, which has been achieved in a protein nanopore but not yet in a solid-state nanopore. Using all-atom molecular dynamics simulations, we invest...