The present invention relates to a set of references nucleic acids for use in a method of detecting methylated CpG-containing nucleic acids by nucleic acid amplification and preferably melting curve analysis of amplification products.

The present disclosure is generally directed to methods for anchoring nucleic acid in a matrix and subsequently imaging nucleic acid targets (e.g. RNA transcript molecules) within tissue samples, for example, formalin-fixed paraffin-embedded (FFPE) tissue sections wherein the nucleic acid may be fragmented. For example, a method of anchoring target nucleic acid within a matrix and clearing non-target cellular components is provided herein, and the method includes contacting a tissue sample with at least two anchoring agents, wherein the first anchoring agent forms a covalent bond with the target nucleic acid and the second anchoring agent contains an oligonucleotide that hybridizes with the target nucleic acid; embedding the sample in a polymer matrix wherein the first and second anchoring agents each form a covalent bond with the polymer matrix; and, clearing the non-target cellular components from the polymer matrix wherein the target nucleic acid remains anchored in the polymer matrix to form a matrix anchored target nucleic acid sample. Additional steps include contacting the anchored target nucleic acid sample with one or more primary oligonucleotide probes that hybridize to the target nucleic acids and a plurality of secondary nucleic acid probes containing a fluorescent label and a recognition sequence that hybridizes to a sequence of the primary nucleic acid probe and imaging the target nucleic acids.

The present disclosure is generally directed to methods for anchoring nucleic acid in a matrix and subsequently imaging nucleic acid targets (e.g. RNA transcript molecules) within tissue samples, for example, formalin-fixed paraffin-embedded (FFPE) tissue sections wherein the nucleic acid may be fragmented. For example, a method of anchoring target nucleic acid within a matrix and clearing non-target cellular components is provided herein, and the method includes contacting a tissue sample with at least two anchoring agents, wherein the first anchoring agent forms a covalent bond with the target nucleic acid and the second anchoring agent contains an oligonucleotide that hybridizes with the target nucleic acid; embedding the sample in a polymer matrix wherein the first and second anchoring agents each form a covalent bond with the polymer matrix; and, clearing the non-target cellular components from the polymer matrix wherein the target nucleic acid remains anchored in the polymer matrix to form a matrix anchored target nucleic acid sample. Additional steps include contacting the anchored target nucleic acid sample with one or more primary oligonucleotide probes that hybridize to the target nucleic acids and a plurality of secondary nucleic acid probes containing a fluorescent label and a recognition sequence that hybridizes to a sequence of the primary nucleic acid probe and imaging the target nucleic acids.

The present disclosure generally relates to the field of ultrasensitive microbial pathogen detection and identification utilizing genomic sequence recognition.

The present disclosure provides methods and systems for detecting nucleic acid sequences in a biological sample having a three-dimensional matrix. The present disclosure also provides methods and systems for processing a biological sample for use in nucleic acid sequence detection.

The present disclosure provides methods and systems for detecting nucleic acid sequences in a biological sample having a three-dimensional matrix. The present disclosure also provides methods and systems for processing a biological sample for use in nucleic acid sequence detection.

Aprotic-protic ionic salt (APS) compositions and methods of using aprotic-protic ionic salt compositions to stabilize nucleic acids at ambient temperatures are provided. Certain aspects provide aprotic-protic ionic salt compositions for long term storage of nucleic acids at ambient temperature in the presence of aqueous solvents.

Methods are provided for the epigenetic analysis of cell-free DNA using organic boranes to convert oxidized 5-methylcytosine residues in the cell-free DNA to dihydrouracil (DHU) residues. Cell-free DNA is contacted with an organic borane selected to successively bring about reduction, deamination, and decarboxylation of oxidized 5-methylcytosine residues such as 5-carboxylcytosine and 5-formylcytosine, resulting in DHU residues in place thereof. Following amplification, the treated cell-free DNA is sequenced, with the DHU residues read as thymine residues. Reaction mixtures, kits and additional methods are also provided, as are related methods for the epigenetic analysis of DNA, including cell-free DNA.

Provided herein is technology relating to amplification of nucleic acids and particularly, but not exclusively, to compositions and methods for doing improving the polymerase chain reaction and providing reagents for polymerase chain reaction with improved stability.

Methods are provided for the epigenetic analysis of cell-free DNA using organic boranes to convert oxidized 5-methylcytosine residues in the cell-free DNA to dihydrouracil (DHU) residues. Cell-free DNA is contacted with an organic borane selected to successively bring about reduction, deamination, and decarboxylation of oxidized 5-methylcytosine residues such as 5-carboxylcytosine and 5-formylcytosine, resulting in DHU residues in place thereof. Following amplification, the treated cell-free DNA is sequenced, with the DHU residues read as thymine residues. Reaction mixtures, kits and additional methods are also provided, as are related methods for the epigenetic analysis of DNA, including cell-free DNA.