Methods and apparatus for long read, label-free, optical nanopore long chain molecule sequencing. In general, the present disclosure describes a novel sequencing technology based on the integration of nanochannels to deliver single long-chain molecules with widely spaced (>wavelength), ˜1-nm aperture “tortuous” nanopores that slow translocation sufficiently to provide massively parallel, single base resolution using optical techniques. A novel, directed self-assembly nanofabrication scheme using simple colloidal nanoparticles is used to form the nanopore arrays atop nanochannels that unfold the long chain molecules. At the surface of the nanoparticle array, strongly localized electromagnetic fields in engineered plasmonic/polaritonic structures allow for single base resolution using optical techniques.

Methods and apparatus for long read, label-free, optical nanopore long chain molecule sequencing. In general, the present disclosure describes a novel sequencing technology based on the integration of nanochannels to deliver single long-chain molecules with widely spaced (>wavelength), ˜1-nm aperture “tortuous” nanopores that slow translocation sufficiently to provide massively parallel, single base resolution using optical techniques. A novel, directed self-assembly nanofabrication scheme using simple colloidal nanoparticles is used to form the nanopore arrays atop nanochannels that unfold the long chain molecules. At the surface of the nanoparticle array, strongly localized electromagnetic fields in engineered plasmonic/polaritonic structures allow for single base resolution using optical techniques.

Methods and systems are disclosed for encoding and decoding data from genetic traits. In one embodiment, the invention provides a method of encoding data from genetic traits. The method comprises encoding genetic traits information, including using quantum dot wavelengths to identify distinct genetic traits, and using numbers of the quantum dots to represent probabilities associated with the traits. In an embodiment, the invention provides a genetic characteristics decoding system for decoding genetic information encoded using quantum dots in a carrier. The decoding system comprises a light source for charging the quantum dots in the carrier; a scanner for scanning the carrier to retrieve information from the charged quantum dots; and a processing system for processing the retrieved information to determine quantum dot wavelengths to identify distinct genetic traits, and to determine numbers of the quantum dots to identify probabilities associated with the genetic traits.

Methods and systems are disclosed for encoding and decoding data from genetic traits. In one embodiment, the invention provides a method of encoding data from genetic traits. The method comprises encoding genetic traits information, including using quantum dot wavelengths to identify distinct genetic traits, and using numbers of the quantum dots to represent probabilities associated with the traits. In an embodiment, the invention provides a genetic characteristics decoding system for decoding genetic information encoded using quantum dots in a carrier. The decoding system comprises a light source for charging the quantum dots in the carrier; a scanner for scanning the carrier to retrieve information from the charged quantum dots; and a processing system for processing the retrieved information to determine quantum dot wavelengths to identify distinct genetic traits, and to determine numbers of the quantum dots to identify probabilities associated with the genetic traits.

The present disclosure provides multiplexed methods, and constructs made to be used in said methods, for characterizing microbes from a biological sample to both rapidly identify the microbe and characterize drug susceptibility or resistance and perform microbial taxa identification and nucleic acid target detection at high multiplexity. The methods can also be used to predict future microbe drug susceptibility or resistance.

The present disclosure provides multiplexed methods, and constructs made to be used in said methods, for characterizing microbes from a biological sample to both rapidly identify the microbe and characterize drug susceptibility or resistance and perform microbial taxa identification and nucleic acid target detection at high multiplexity. The methods can also be used to predict future microbe drug susceptibility or resistance.

A carrier molecule for the detection of a target analyte comprises a molecular frame which defines a central void, and a binding moiety which is specific for the target analyte. The binding moiety is bound to the frame and positioned such that the target analyte, when bound to the binding moiety, is located in the central void. The carrier molecule finds use in the detection and/or quantification of target analytes in a sample.

A carrier molecule for the detection of a target analyte comprises a molecular frame which defines a central void, and a binding moiety which is specific for the target analyte. The binding moiety is bound to the frame and positioned such that the target analyte, when bound to the binding moiety, is located in the central void. The carrier molecule finds use in the detection and/or quantification of target analytes in a sample.

Methods for construction of DNA origami nanostructures, as well as for binding, isolation, linking, and deep sequencing information, such as both of TCR alpha and beta CDR3 mRNA, from individual cells within a mixed population of cells without the need for single cell sorting (FIG. 1).

Methods for construction of DNA origami nanostructures, as well as for binding, isolation, linking, and deep sequencing information, such as both of TCR alpha and beta CDR3 mRNA, from individual cells within a mixed population of cells without the need for single cell sorting (FIG. 1).