The disclosure is directed to conjugates, e.g. PNA conjugates, as well as methods of employing the conjugates for detecting one or more targets in a biological sample, e.g. a tissue sample.

The disclosure is directed to conjugates, e.g. PNA conjugates, as well as methods of employing the conjugates for detecting one or more targets in a biological sample, e.g. a tissue sample.

Provided herein are hybrid capture-based methods to extract single-stranded DNA or RNA directly from non-treated biospecimens. The methods allow for the detection and analysis of unexplored short single-stranded DNA (sssDNA, mean length 50 nt) and ultrashort single-stranded DNA (ussDNA, mean length 15 nt) of human origin present in the biospecimen. The methods allow the discovery of unexplored short single-stranded DNA (sssDNA) in isolated red blood cells, which were believed to be deprived of nucleic acids because of the lack of a nucleus in mature red blood cells. The DNA or RNA extracted using the disclosed methods can be used as disease prognostic biomarkers and treatment predictive biomarkers.

Provided herein are hybrid capture-based methods to extract single-stranded DNA or RNA directly from non-treated biospecimens. The methods allow for the detection and analysis of unexplored short single-stranded DNA (sssDNA, mean length 50 nt) and ultrashort single-stranded DNA (ussDNA, mean length 15 nt) of human origin present in the biospecimen. The methods allow the discovery of unexplored short single-stranded DNA (sssDNA) in isolated red blood cells, which were believed to be deprived of nucleic acids because of the lack of a nucleus in mature red blood cells. The DNA or RNA extracted using the disclosed methods can be used as disease prognostic biomarkers and treatment predictive biomarkers.

Described herein are systems and methods for multiplexed analysis of two or more targets in a test sample including a first set of particles including a first set of target-specific reagents and a first optically detectable identifier capable of emitting a first wavelength indicative of a first target, and at least one second set of particles including a second set of target-specific reagents and a second optically detectable identifier capable of emitting a second wavelength indicative of a second target; and at least one optically detectable reporter probe capable of constitutively emitting a third wavelength in response to reaction of the first set of target-specific reagents with the first target in the test sample and/or reaction of the second set of target-specific reagents with the second target in the test sample, wherein the first wavelength, the second wavelength, and the third wavelength are optically discernable from one another.

Described herein are systems and methods for multiplexed analysis of two or more targets in a test sample including a first set of particles including a first set of target-specific reagents and a first optically detectable identifier capable of emitting a first wavelength indicative of a first target, and at least one second set of particles including a second set of target-specific reagents and a second optically detectable identifier capable of emitting a second wavelength indicative of a second target; and at least one optically detectable reporter probe capable of constitutively emitting a third wavelength in response to reaction of the first set of target-specific reagents with the first target in the test sample and/or reaction of the second set of target-specific reagents with the second target in the test sample, wherein the first wavelength, the second wavelength, and the third wavelength are optically discernable from one another.

RNA editing tools for use in systems designed to measure RNA in vivo and manipulate specific cell types are disclosed herein. An RNA sensor system comprising a) a single-stranded RNA (ssRNA) sensor comprising a stop codon and a payload; optionally wherein the ssRNA sensor further comprises a normalizing gene; and b) an adenosine deaminase acting on RNA (ADAR) deaminase; wherein the sensor is capable of binding to a ssRNA target to form a double-stranded RNA (dsRNA) duplex that becomes a substrate for the ADAR deaminase; wherein the substrate comprises a mispairing within the stop codon; and wherein the mispairing is editable by the ADAR deaminase, which editing can effectively remove the stop codon so as to enable translation and expression of the payload. A method of quantifying ribonucleic acid (RNA) levels using the RNA sensor system is also disclosed.

RNA editing tools for use in systems designed to measure RNA in vivo and manipulate specific cell types are disclosed herein. An RNA sensor system comprising a) a single-stranded RNA (ssRNA) sensor comprising a stop codon and a payload; optionally wherein the ssRNA sensor further comprises a normalizing gene; and b) an adenosine deaminase acting on RNA (ADAR) deaminase; wherein the sensor is capable of binding to a ssRNA target to form a double-stranded RNA (dsRNA) duplex that becomes a substrate for the ADAR deaminase; wherein the substrate comprises a mispairing within the stop codon; and wherein the mispairing is editable by the ADAR deaminase, which editing can effectively remove the stop codon so as to enable translation and expression of the payload. A method of quantifying ribonucleic acid (RNA) levels using the RNA sensor system is also disclosed.

The present disclosure provides compositions comprising nucleic acid molecules coupled to supports and comprising one or more cleavable or excisable moieties. Methods of enriching and sequencing nucleic acid molecules are also provided.

The present disclosure provides compositions comprising nucleic acid molecules coupled to supports and comprising one or more cleavable or excisable moieties. Methods of enriching and sequencing nucleic acid molecules are also provided.