Detection of Nucleic Acids
AssigneeAffymetrix, Inc.
InventorsQuan Nguyen, Yunqing Ma, Audrey Lin, Shauna Levinson, Steve Lai
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Abstract
This invention provides compositions, methods, and systems for characterizing, resolving, and quantitating single stranded and double stranded DNA and RNA in-situ. Paired sense and anti-sense probes can signal the presence of double stranded nucleic acids. DNA and RNA can be distinguished in cell and tissue samples by hybridizing with probe sets adapted to highlight differences in these targets in-situ.
Claims31
A composition comprising:
- a first nucleic acid probe comprising a first reporter providing a first signal and comprising a first sequence complementary to a sense strand of a gene;
- and,
- a second nucleic acid probe comprising a second reporter providing a second signal and comprising a second sequence complementary to an anti-sense strand of the gene;
- wherein the first sequence and second sequence are not complementary to each other.
A method of detecting the presence of a double stranded nucleic acid, the method comprising:
- providing a first nucleic acid probe comprising a first reporter providing a first signal, and the first probe comprising a sequence complementary to a sense strand of a gene;
- and,
- providing a second nucleic acid probe comprising a second reporter providing a second signal, and the second probe comprising a sequence complementary to an anti-sense strand of the gene, wherein the first and second probes are not complementary to each other;
- providing a sample comprising a double stranded nucleic acid;
- hybridizing the first and second probes to the double stranded nucleic acid;
- and,
- detecting the first and second signal in the sample;
- wherein the presence of the double stranded nucleic acid is confirmed if both the first signal and second signal are detected.
A composition for simultaneous detection of DNA and RNA by in-situ hybridization, the system comprising:
- a DNA specific probe set comprising a first number of different probes complementary to a DNA gene sequence;
- and,
- an RNA specific probe set comprising a second number of different probes complementary to an RNA sequence;
- wherein the first number is at least 3-fold greater than the second number;
- and,
- wherein the different DNA probes have different probe sequences from each other, and the different RNA probes have different probe sequences from each other.
A method for simultaneous detection of DNA and RNA in-situ in a cell or tissue, the method comprising:
- providing a DNA specific probe set comprising a first number of different probes complementary to a DNA gene sequence, wherein the DNA probes are adapted to provide a first detectable signal;
- providing an RNA specific probe set comprising a second number of different probes complementary to an RNA sequence, wherein the RNA probes are adapted to provide a second detectable signal, wherein the DNA probe set includes at least 3-fold as many different probes than the RNA probe set;
- providing a sample comprising the DNA gene sequence and the RNA sequence;
- simultaneously hybridizing the DNA specific probe set to the DNA gene sequence and the RNA specific probe set to the RNA sequence;
- and,
- detecting the first detectable signal and the second detectable signal in the sample.
Dependencies are inferred from the claim text.