In various aspects, the present disclosure provides methods, compositions, reactions mixtures, kits, and systems for sequencing both RNA and DNA from a single source sample. In some embodiments, RNA is treated so as to differentiate RNA sequences from DNA sequences derived from the same sample. In some embodiments, the RNA and DNA are cell-free polynucleotides.

In various aspects, the present disclosure provides methods, compositions, reactions mixtures, kits, and systems for sequencing both RNA and DNA from a single source sample. In some embodiments, RNA is treated so as to differentiate RNA sequences from DNA sequences derived from the same sample. In some embodiments, the RNA and DNA are cell-free polynucleotides.

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.

Kits and methods of using the kits for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding are disclosed. The sample analysis kits employ nucleic acid encoding and/or nucleic acid recording of a molecular interaction and/or reaction, such as recognition events (e.g., between an antigen and an antibody, between a modified terminal amino acid residue, or between a small molecule or peptide therapeutic and a target, etc.). Additional barcoding reagents, such as those for cycle-specific barcoding (e.g., “clocking”), compartment barcoding, combinatorial barcoding, spatial barcoding, or any combination thereof, may be included in the kits. The sample may comprise macromolecules, including peptides, polypeptides, and proteins, and the recording may generate molecular interaction and/or reaction information, and/or polypeptide sequence information. The kits may be used in high-throughput, multiplexed, and/or automated analysis, and are suitable for analysis of a proteome or subset thereof.

This disclosure provides for methods and reagents for rapid multiplex RPA reactions and improved methods for detection of multiplex RPA reaction products. In addition, the disclosure provides new methods for eliminating carryover contamination between RPA processes.

This disclosure provides for methods and reagents for rapid multiplex RPA reactions and improved methods for detection of multiplex RPA reaction products. In addition, the disclosure provides new methods for eliminating carryover contamination between RPA processes.

Provided herein are methods for enhanced specificity of multiplexed measurements. Methods provided herein include immunoassay reactions and/or measuring protein-protein interactions with direct sequencing readouts of DNA barcodes.

Provided herein are methods for enhanced specificity of multiplexed measurements. Methods provided herein include immunoassay reactions and/or measuring protein-protein interactions with direct sequencing readouts of DNA barcodes.

In the present invention, it has been confirmed that, when an RNA interference-inducing nucleic acid including at least one 8-oxoguanine (o.sup.8G) in 1st to 9th nucleotides from the 5′-end of at least one single strand of a double strand of a nucleic acid, and a modified nucleic acid that specifically binds to microRNA and in which at least one guanine (G) from among the 1st to 9th nucleotides from the 5′-end are modified with 8-oxoguanine (o.sup.8G), are produced and administered to cells or mice, various pathophysiological phenomena are induced.

In addition, the positions where G>T modifications occur have been identified in cDNA produced through the reverse transcription of microRNA in which guanine (G) is oxidatively modified with 8-oxoguanine (o.sup.8G) by oxidative stress in a seed region of microRNA, to confirm the positions where oxidative modification to 8-oxoguanine has occurred.

In the present invention, it has been confirmed that, when an RNA interference-inducing nucleic acid including at least one 8-oxoguanine (o.sup.8G) in 1st to 9th nucleotides from the 5′-end of at least one single strand of a double strand of a nucleic acid, and a modified nucleic acid that specifically binds to microRNA and in which at least one guanine (G) from among the 1st to 9th nucleotides from the 5′-end are modified with 8-oxoguanine (o.sup.8G), are produced and administered to cells or mice, various pathophysiological phenomena are induced.

In addition, the positions where G>T modifications occur have been identified in cDNA produced through the reverse transcription of microRNA in which guanine (G) is oxidatively modified with 8-oxoguanine (o.sup.8G) by oxidative stress in a seed region of microRNA, to confirm the positions where oxidative modification to 8-oxoguanine has occurred.