The present invention relates to compositions and methods for the detection of target molecules, and the amplification of detectable signals generated by detection assays. More specifically, the present invention relates to methods utilizing catalytic nucleic acid enzymes to generate and/or amplify a signal indicative of the presence of target molecules (e.g. nucleic acids and proteins), and compositions for use in the methods.

Methods are provided for characterizing a sample comprising polynucleotide sequences. The methods can comprise labeling nucleic acid molecules of the sample, translocating the plurality of labeled sample nucleic acid molecules though one or more fluidic nanochannels, detecting physical counts of signals from the labeled sample nucleic acid molecule, and determining a copy number of a genome or a fragment or fragments thereof in the sample.

Methods are provided for characterizing a sample comprising polynucleotide sequences. The methods can comprise labeling nucleic acid molecules of the sample, translocating the plurality of labeled sample nucleic acid molecules though one or more fluidic nanochannels, detecting physical counts of signals from the labeled sample nucleic acid molecule, and determining a copy number of a genome or a fragment or fragments thereof in the sample.

The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.

The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.

Methods are provided for detecting and quantitating molecules using fluidics. In preferred embodiments, the methods comprise analyzing blood to detect the presence of circulating DNA or cells from a fetus or tumor.

Methods are provided for detecting and quantitating molecules using fluidics. In preferred embodiments, the methods comprise analyzing blood to detect the presence of circulating DNA or cells from a fetus or tumor.

Single cell analysis from tumor tissue comprising tumor cells and immune competent cells and from peripheral white blood cells are used to obtain an immunome signature, and to gain information about the TCR repertoire. Such information is then employed to generate recombinant and patient specific therapeutic cells, including T cells (including T effector memory, T memory stem, naïve T, T central memory, CD8+ T, and CD4+ T cells), NK cells (cord-blood derived or PBMC derived or NK92), NKT cells, and dendritic cells.

Single cell analysis from tumor tissue comprising tumor cells and immune competent cells and from peripheral white blood cells are used to obtain an immunome signature, and to gain information about the TCR repertoire. Such information is then employed to generate recombinant and patient specific therapeutic cells, including T cells (including T effector memory, T memory stem, naïve T, T central memory, CD8+ T, and CD4+ T cells), NK cells (cord-blood derived or PBMC derived or NK92), NKT cells, and dendritic cells.

The present disclosure relates to compositions that comprise a fluorescent and/or MS-active nucleic acid probe that comprises (a) a nucleic-acid-based moiety and (b) a fluorescent moiety comprising a fluorophore, an MS-active moiety, or both a fluorescent moiety and an MS-active moiety, linked to the nucleic-acid-based moiety, among other aspects.