A CRISPR electrochemical biosensing system (E-CRISPR) for detection of analytes includes a disposable, micro-fabricated three-electrode sensor that includes a working electrode, a counter electrode, a reference electrode, and a nonspecific ssDNA reporter with an electrochemical tag for signal transduction tethered to a surface of the working electrode; and a Cas12a-crRNA duplex that is designed to specifically recognize and cleave target nucleic acid strand based on the protospacer adjacent motif (PAM) sequence of the target and crRNA sequence, wherein the PAM recognition depends on specific 5′ TTTN nucleic acid sequence located at an opposite strand of a recognition strand, and wherein only upon the recognition of the PAM sequence by the Cas protein, the Cas protein, acting as a DNA helicase, unwinds the target DNA.

A CRISPR electrochemical biosensing system (E-CRISPR) for detection of analytes includes a disposable, micro-fabricated three-electrode sensor that includes a working electrode, a counter electrode, a reference electrode, and a nonspecific ssDNA reporter with an electrochemical tag for signal transduction tethered to a surface of the working electrode; and a Cas12a-crRNA duplex that is designed to specifically recognize and cleave target nucleic acid strand based on the protospacer adjacent motif (PAM) sequence of the target and crRNA sequence, wherein the PAM recognition depends on specific 5′ TTTN nucleic acid sequence located at an opposite strand of a recognition strand, and wherein only upon the recognition of the PAM sequence by the Cas protein, the Cas protein, acting as a DNA helicase, unwinds the target DNA.

Provided herein is a method for enriching a sample for polynucleotides comprising a breakpoint of a fusion gene, comprising: a) contacting a probe set comprising a plurality of polynucleotide probes, each probe configured to specifically hybridize to a fusion gene, wherein the set comprises one or more high affinity polynucleotide probes (e.g., a polynucleotide comprising one or more locked nucleic acid nucleotides), with a mixture of polynucleotides under hybridization conditions to produce probe-captured polynucleotides; and b) isolating the probe-captured polynucleotides from the mixture, to produce a sample enriched with polynucleotides comprising breakpoint fragments of the fusion gene.

Provided herein is a method for enriching a sample for polynucleotides comprising a breakpoint of a fusion gene, comprising: a) contacting a probe set comprising a plurality of polynucleotide probes, each probe configured to specifically hybridize to a fusion gene, wherein the set comprises one or more high affinity polynucleotide probes (e.g., a polynucleotide comprising one or more locked nucleic acid nucleotides), with a mixture of polynucleotides under hybridization conditions to produce probe-captured polynucleotides; and b) isolating the probe-captured polynucleotides from the mixture, to produce a sample enriched with polynucleotides comprising breakpoint fragments of the fusion gene.

The present invention relates to a method for enrichment of target DNA with high GC content based on target sequence capture and multiple displacement amplification, as well as a kit suitable for this method. The present invention also relates to a method for constructing a sequencing library of target DNA with high GC content based on the enrichment method of the present invention.

The present invention relates to a method for enrichment of target DNA with high GC content based on target sequence capture and multiple displacement amplification, as well as a kit suitable for this method. The present invention also relates to a method for constructing a sequencing library of target DNA with high GC content based on the enrichment method of the present invention.

Disclosed herein are methods and systems for correcting errors in sample amplification, including the errors occurred in determining the number of targets in samples. In some embodiments, the method comprises: stochastically barcoding a plurality of targets in the samples using oligonucleotides comprising stochastic barcodes to generate stochastically barcoded targets; contacting one or more defined barcoded primers with each of the one or more samples; and determining an amplification noise.

Disclosed herein are methods and systems for correcting errors in sample amplification, including the errors occurred in determining the number of targets in samples. In some embodiments, the method comprises: stochastically barcoding a plurality of targets in the samples using oligonucleotides comprising stochastic barcodes to generate stochastically barcoded targets; contacting one or more defined barcoded primers with each of the one or more samples; and determining an amplification noise.

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.

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.