The present invention provides a new and improved multiplexed oligonucleotide detection method based on the nanopore technology with one or more probes containing a sequence with complementarity to the target oligonucleotide, a terminal extension at the probe's 3′ terminus, 5′ terminus, or both termini and a label attached to the terminus. The improved probes and probe sets enable sensitive, selective, and direct multiplex detection, differentiation and quantification of distinct target oligonucleotides such as miRNAs. The inventive detection method may also be employed as a non-invasive and cost-effective diagnostic method based on miRNA levels in the patient's tissue sample.

The present invention provides a new and improved multiplexed oligonucleotide detection method based on the nanopore technology with one or more probes containing a sequence with complementarity to the target oligonucleotide, a terminal extension at the probe's 3′ terminus, 5′ terminus, or both termini and a label attached to the terminus. The improved probes and probe sets enable sensitive, selective, and direct multiplex detection, differentiation and quantification of distinct target oligonucleotides such as miRNAs. The inventive detection method may also be employed as a non-invasive and cost-effective diagnostic method based on miRNA levels in the patient's tissue sample.

Provided herein are nanostructure-based sequencing methods and systems.

Provided herein are nanostructure-based sequencing methods and systems.

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.

Disclosed are methods for generating physical maps from feature density profiles of a nucleic acid using a constriction device, and associated methods of analyzing said genomic profiles. In addition, disclosed are devices and methods for analyzing secondary, tertiary and quaternary structures on nucleic acids in spatial and temporal context of the 3-D organization of the genome in a constriction or sensor device.

Disclosed are methods for generating physical maps from feature density profiles of a nucleic acid using a constriction device, and associated methods of analyzing said genomic profiles. In addition, disclosed are devices and methods for analyzing secondary, tertiary and quaternary structures on nucleic acids in spatial and temporal context of the 3-D organization of the genome in a constriction or sensor device.

A method of operating a pore field-effect transistor (FET) sensor for detecting particles, wherein the pore FET sensor comprises a FET wherein a gate is controlled by a pore filled by a fluid, comprises: controlling a first voltage (V.sub.cis) to set the FET in a subthreshold region; controlling a second voltage (V.sub.trans) to set a voltage difference between the first and second voltages (V.sub.trans) such that an effective difference in gate voltage experienced between a minimum and a maximum effective gate voltage during movement of a particle in the fluid is at least kT/q; and detecting a drain-source current in the FET, wherein the particle passing through the pore modulates the drain-source current for detecting presence of the particle.

A method of operating a pore field-effect transistor (FET) sensor for detecting particles, wherein the pore FET sensor comprises a FET wherein a gate is controlled by a pore filled by a fluid, comprises: controlling a first voltage (V.sub.cis) to set the FET in a subthreshold region; controlling a second voltage (V.sub.trans) to set a voltage difference between the first and second voltages (V.sub.trans) such that an effective difference in gate voltage experienced between a minimum and a maximum effective gate voltage during movement of a particle in the fluid is at least kT/q; and detecting a drain-source current in the FET, wherein the particle passing through the pore modulates the drain-source current for detecting presence of the particle.