Provided herein are methods and compositions for performing highly sensitive in vitro assays to define substrate preferences and off-target sites of nucleic-acid binding, modifying, and cleaving agents.

The present invention relates to the field of cancer. More specifically, the present invention provides methods and compositions useful for assessing prostate cancer. In a specific embodiment, present inventors have developed and applied a new technology and associated computation methods enabling simultaneous genome-scale analysis of genetic (copy number) and epigenetic (total methylation (TM) and allele-specific methylation (ASM) alternation, This method, called MBD-SNP, features affinity enrichment or methylated genomic DNA fragments using a methyl-binding domain polypeptide.

The present invention relates to the field of cancer. More specifically, the present invention provides methods and compositions useful for assessing prostate cancer. In a specific embodiment, present inventors have developed and applied a new technology and associated computation methods enabling simultaneous genome-scale analysis of genetic (copy number) and epigenetic (total methylation (TM) and allele-specific methylation (ASM) alternation, This method, called MBD-SNP, features affinity enrichment or methylated genomic DNA fragments using a methyl-binding domain polypeptide.

Provided herein is a method of analyzing DNA comprising a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA; sequence-specifically degrading target sequences in the DNA; and detecting target sequences that are not degraded. Also provided is a combination comprising a population of DNA and a sequence-specific nuclease, wherein the population comprises or was derived from DNA with a cytosine modification, and wherein the population comprises a first, converted nucleobase and a second nucleobase without altered base pairing specificity; wherein the form of the first nucleobase originally present in the DNA prior to alteration of base pairing specificity and the second nucleobase have the same base pairing specificity.

Provided herein is a method of analyzing DNA comprising a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA; sequence-specifically degrading target sequences in the DNA; and detecting target sequences that are not degraded. Also provided is a combination comprising a population of DNA and a sequence-specific nuclease, wherein the population comprises or was derived from DNA with a cytosine modification, and wherein the population comprises a first, converted nucleobase and a second nucleobase without altered base pairing specificity; wherein the form of the first nucleobase originally present in the DNA prior to alteration of base pairing specificity and the second nucleobase have the same base pairing specificity.

Provided herein are compositions and methods for sequencing using metal-coated polymers. In some examples, a bridge spans a space between first and second electrodes and includes a polymer chain having a first metal-coated region contacting the first electrode, a second metal-coated region contacting the second electrode, and an exposed region located between the first and second regions. The composition includes first and second polynucleotides; a plurality of nucleotides, each nucleotide coupled to a corresponding label; and a polymerase to add nucleotides of the plurality of nucleotides to the first polynucleotide using at least a sequence of the second polynucleotide. The composition includes detection circuitry to detect a sequence in which the polymerase adds the nucleotides to the first polynucleotide using at least changes in an electrical signal through the bridge, the changes being responsive to contact between the labels corresponding to those nucleotides and the exposed region.

Provided herein are compositions and methods for sequencing using metal-coated polymers. In some examples, a bridge spans a space between first and second electrodes and includes a polymer chain having a first metal-coated region contacting the first electrode, a second metal-coated region contacting the second electrode, and an exposed region located between the first and second regions. The composition includes first and second polynucleotides; a plurality of nucleotides, each nucleotide coupled to a corresponding label; and a polymerase to add nucleotides of the plurality of nucleotides to the first polynucleotide using at least a sequence of the second polynucleotide. The composition includes detection circuitry to detect a sequence in which the polymerase adds the nucleotides to the first polynucleotide using at least changes in an electrical signal through the bridge, the changes being responsive to contact between the labels corresponding to those nucleotides and the exposed region.

Methods and compositions for performing highly sensitive in vitro assays to define substrate preferences and off-target sites of nucleic-acid binding, modifying, and cleaving agents.

Methods and compositions for performing highly sensitive in vitro assays to define substrate preferences and off-target sites of nucleic-acid binding, modifying, and cleaving agents.

Provided herein is a method and system for analyzing a sample. In some embodiments the method makes use of a plurality of capture agents that are each linked to a different oligonucleotide and a corresponding plurality of labeled nucleic acid probes, wherein each of the labeled nucleic acid probes specifically hybridizes with only one of the oligonucleotides. The sample is labeled with the capture agents en masse, and sub-sets of the capture agents are detected using iterative cycles using corresponding subsets of the labeled nucleic acid probes.