Abstract: Disclosed are compositions, devices, and methods for loading molecules of interest onto a substrate by contacting beads having molecules of interest attached to them with the substrate, for example by providing a field that brings the beads into proximity or contact with the substrate and moves the beads with respect to the substrate. Such molecules of interest can be deposited onto substrates for single-molecule analysis.

Abstract: Optics collection and detection systems are provided for measuring optical signals from an array of optical sources over time. Methods of using the optics collection and detection systems are also described.

Abstract: An analytical device including an optically opaque cladding, a sequencing layer including a substrate disposed below the cladding, and a waveguide assembly for receiving optical illumination and introducing illumination into the device. The illumination may be received from a top, a side edge, and a bottom of the device. The waveguide assembly may include a nanoscale aperture disposed in the substrate and extending through the cladding. The aperture defines a reaction cell for receiving a set of reactants. In various aspects, the device includes a sensor element and the illumination pathway is through the sensor element. Waveguides and illumination devices, such as plasmonic illumination devices, are also disclosed. Methods for forming and operating the devices are also disclosed.

Abstract: The invention relates to devices and methods for nanopore sequencing. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS. In some cases, the arrays of nanopores comprise resistive openings for isolating the electronic signals for improved sequencing. Methods for controlling translocation of through the nanopore are disclosed.

Abstract: Provided are compositions that include an at least partially single-stranded nucleic acid, at least one first molecular beacon, and an enzyme comprising a helicase activity, which enzyme is capable of removing the first molecular beacon from the single-stranded nucleic acid wherein the first molecular beacon is hybridized to a first complementary subsequence of the nucleic acid. Also provided are methods of determining the sequence of a template nucleic acid that include removing molecular beacons that are hybridized to the template from the template in a sequential manner using an enzyme that exhibits a helicase activity, detecting a sequence of fluorescent signals that is produced by the removal of a molecular beacons, and converting the sequence of fluorescent signals into nucleotide sequence information. Sequencing systems in which compositions and methods of the invention can be used are also provided.

Abstract: Methods, compositions and arrays for non-random loading of single analyte molecules into array structures are provided.