This invention provides methods and systems for measuring the concentration of multiple nucleic acid sequences in a sample. The nucleic acid sequences in the sample are simultaneously amplified, for example, using polymerase chain reaction (PCR) in the presence of an array of nucleic acid probes. The amount of amplicon corresponding to the multiple nucleic acid sequences can be measured in real-time during or after each cycle using a real-time microarray. The measured amount of amplicon produced can be used to determine the original amount of the nucleic acid sequences in the sample. Also provided herein are biosensor arrays, systems and methods for affinity based assays that are able to simultaneously obtain high quality measurements of the binding characteristics of multiple analytes, and that are able to determine the amounts of those analytes in solution. The invention also provides a fully integrated bioarray for detecting real-time characteristics of affinity based assays.

Disclosed herein are compositions for detecting the presence of one or more target(s) of interest, wherein the composition comprises a first hairpin initiator molecule and a second initiator molecule. Also disclosed herein are methods of using the same.

Disclosed herein are compositions for detecting the presence of one or more target(s) of interest, wherein the composition comprises a first hairpin initiator molecule and a second initiator molecule. Also disclosed herein are methods of using the same.

The present invention provides an oligonucleotide probe for single nucleotide polymorphism detection to be used for a target nucleic acid where a single nucleotide polymorphism is present, the oligonucleotide probe comprising a reporter region, an anchor region, and a linker region. The reporter region comprises: an oligonucleotide consisting of a sequence perfectly matching when a nucleotide of the single nucleotide polymorphism is a first nucleotide, and mismatching when the nucleotide of the single nucleotide polymorphism is a nucleotide other than the first nucleotide; and a fluorescent dye quenching when the reporter region hybridize to the target nucleic acid.

The present invention provides an oligonucleotide probe for single nucleotide polymorphism detection to be used for a target nucleic acid where a single nucleotide polymorphism is present, the oligonucleotide probe comprising a reporter region, an anchor region, and a linker region. The reporter region comprises: an oligonucleotide consisting of a sequence perfectly matching when a nucleotide of the single nucleotide polymorphism is a first nucleotide, and mismatching when the nucleotide of the single nucleotide polymorphism is a nucleotide other than the first nucleotide; and a fluorescent dye quenching when the reporter region hybridize to the target nucleic acid.

Described herein are systems and methods for multiplexed analysis of two or more targets in a test sample including a first set of particles including a first set of target-specific reagents and a first optically detectable identifier capable of emitting a first wavelength indicative of a first target, and at least one second set of particles including a second set of target-specific reagents and a second optically detectable identifier capable of emitting a second wavelength indicative of a second target; and at least one optically detectable reporter probe capable of constitutively emitting a third wavelength in response to reaction of the first set of target-specific reagents with the first target in the test sample and/or reaction of the second set of target-specific reagents with the second target in the test sample, wherein the first wavelength, the second wavelength, and the third wavelength are optically discernable from one another.

Described herein are systems and methods for multiplexed analysis of two or more targets in a test sample including a first set of particles including a first set of target-specific reagents and a first optically detectable identifier capable of emitting a first wavelength indicative of a first target, and at least one second set of particles including a second set of target-specific reagents and a second optically detectable identifier capable of emitting a second wavelength indicative of a second target; and at least one optically detectable reporter probe capable of constitutively emitting a third wavelength in response to reaction of the first set of target-specific reagents with the first target in the test sample and/or reaction of the second set of target-specific reagents with the second target in the test sample, wherein the first wavelength, the second wavelength, and the third wavelength are optically discernable from one another.

The invention relates to methods of detecting and/or quantifying analytes in a sample, as well as methods of detecting mutations and/or polymorphisms in nucleic acid molecules. The methods include: providing at least one carrier nucleic acid molecule comprising at least one single-stranded region; providing at least one detection element comprising: at least one fluorophore, at least one fluorescence quencher that quenches spectroscopic detection of the fluorophore; at least one analyte-binding moiety; and at least one nucleic acid moiety that binds to a single stranded region on the carrier nucleic acid molecule; wherein the detection element is configured such that in the absence of the analyte the fluorophore is quenched by the fluorescence quencher and upon analyte binding to the analyte-binding moiety fluorescence is restored; binding these with an analyte to form a complex; translocating the complex through a nanopore via voltage-driven translocation and monitoring time-dependent current response; irradiating the nanopore with radiation that excites the fluorophore and monitoring radiation emissions of the fluorophore over time; and comparing the signals from time-dependent current response and emission over time.

The invention relates to methods of detecting and/or quantifying analytes in a sample, as well as methods of detecting mutations and/or polymorphisms in nucleic acid molecules. The methods include: providing at least one carrier nucleic acid molecule comprising at least one single-stranded region; providing at least one detection element comprising: at least one fluorophore, at least one fluorescence quencher that quenches spectroscopic detection of the fluorophore; at least one analyte-binding moiety; and at least one nucleic acid moiety that binds to a single stranded region on the carrier nucleic acid molecule; wherein the detection element is configured such that in the absence of the analyte the fluorophore is quenched by the fluorescence quencher and upon analyte binding to the analyte-binding moiety fluorescence is restored; binding these with an analyte to form a complex; translocating the complex through a nanopore via voltage-driven translocation and monitoring time-dependent current response; irradiating the nanopore with radiation that excites the fluorophore and monitoring radiation emissions of the fluorophore over time; and comparing the signals from time-dependent current response and emission over time.

The present disclosure provides methods and systems for sequencing nucleic acid molecules in a manner that enables higher sequencing accuracy. Methods and systems provided herein may enable sequences that may have low-accuracy reads, such as homopolymer sequences or other repeating sequences, to be determined at a higher accuracy and efficiency.