The invention provides barcode libraries and methods of making and using them including obtaining a plurality of nucleic acid constructs in which each construct comprises a unique N-mer and a functional N-mer and segregating the constructs into a fluid compartments such that each compartment contains one or more copies of a unique construct. The invention further provides methods for digital PCR and for use of barcode libraries in digital PCR.

CRISPR-based diagnostic methods and compositions are provided. One embodiment provides the use of DNA-barcoded antibodies or peptide-MHC (pMHC) tetramers (e.g., Kb-OVA.sub.257-264, Db-GP100.sub.25-33, Db-GP.sub.33-41) and CRISPR-Cas protein, and a guided DNA endonuclease, to achieve ultrasensitive detection of soluble and cell surface proteins. The disclosed embodiments can use type V: Cas12a; type VI: Cas13a, or Cas13b. Combining DNA encoding with CRISPR-Cas protein recognition is a sensitive system because barcodes can be isothermally amplified and Cas, for example Cas12a, enzymatically cleaves DNA reporters upon barcode detection, providing two rounds of amplification and enabling measurement of protein concentration by sample fluorescence or using by paper-based assays. This platform enables monitoring of protein and cellular biomarkers and further expands the toolbox of CRISPR/Cas-based technologies

CRISPR-based diagnostic methods and compositions are provided. One embodiment provides the use of DNA-barcoded antibodies or peptide-MHC (pMHC) tetramers (e.g., Kb-OVA.sub.257-264, Db-GP100.sub.25-33, Db-GP.sub.33-41) and CRISPR-Cas protein, and a guided DNA endonuclease, to achieve ultrasensitive detection of soluble and cell surface proteins. The disclosed embodiments can use type V: Cas12a; type VI: Cas13a, or Cas13b. Combining DNA encoding with CRISPR-Cas protein recognition is a sensitive system because barcodes can be isothermally amplified and Cas, for example Cas12a, enzymatically cleaves DNA reporters upon barcode detection, providing two rounds of amplification and enabling measurement of protein concentration by sample fluorescence or using by paper-based assays. This platform enables monitoring of protein and cellular biomarkers and further expands the toolbox of CRISPR/Cas-based technologies

The present invention provides a use of a Cas protein, and a method and a kit for detecting target nucleic acid molecules. The method for detecting target nucleic acid molecules comprises adding a guide RNA, a Cas12a, and a nucleic acid probe into a reaction system containing target nucleic acid molecules to be detected, and detecting it after the reaction is completed.

The present invention provides a use of a Cas protein, and a method and a kit for detecting target nucleic acid molecules. The method for detecting target nucleic acid molecules comprises adding a guide RNA, a Cas12a, and a nucleic acid probe into a reaction system containing target nucleic acid molecules to be detected, and detecting it after the reaction is completed.

Provided herein are methods and systems for sequencing a nucleic acid molecule utilizing a polymerase enzyme, a template nucleic acid, and a polymerase reagent solution.

Provided herein are methods and systems for sequencing a nucleic acid molecule utilizing a polymerase enzyme, a template nucleic acid, and a polymerase reagent solution.

Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.

Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.

The invention relates to a method of performing in situ hybridization such as fluorescence in situ hybridization (FISH) using liposomal spherical nucleic acids (L-SNAs) nanoparticles labeled with dye molecules. The nanoparticles contain one or more nucleic acids that recognize a target of interest in a sample.