Compositions and methods for analyzing nucleic acids associated with an analyte
AssigneeCdi Laboratories, Inc.
InventorsHeng ZHU, Ignacio PINO
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Abstract
This disclosure provides compositions and methods for analyzing a nucleic acid associated with an analyte.
Claims91
A composition comprising:
- a. a first probe, wherein the first probe comprises a first tag comprising a polynucleotide comprising a region for attaching to a first end of a nucleic acid;
- and
- b. a second probe, wherein the second probe comprises a second tag comprising a polynucleotide comprising a region for attaching to a second end of the nucleic acid,
- wherein the first probe has an affinity to a first binding site on an analyte and the second probe has an affinity to a second binding site on the analyte, wherein the first probe and the second probe are in spatial proximity, and
- i. wherein the first probe is associated with a substrate;
- ii. wherein the second probe is associated with the substrate;
- iii. wherein the first probe is associated with the substrate and wherein the second probe is associated with the substrate;
- iv. wherein the first tag is double stranded where associated with the first probe;
- v. wherein the second tag is double stranded where associated with the second probe;
- vi. wherein the first tag is double stranded where associated with the first probe and wherein the second tag is double stranded where associated with the second probe;
- or
- vii. one of (i), (ii), or (iii) and one of (iv), (v) or (vi).
The composition of any one of the above claims, wherein the solid substrate is magnetic.
The composition of any one of the above claims, wherein the second tag is double stranded.
The composition of any one of the above claims, wherein the first tag comprises a first cleavage site.
The composition of any one of the above claims, wherein the second tag comprises a second cleavage site.
The composition of any one of the above claims, wherein the first tag comprises a first barcode.
The composition of any one of the above claims, wherein the second tag comprises a second barcode.
The composition of any of the above claims, wherein the analyte comprise a first biological molecule.
The composition of any one of the above claims, wherein the analyte further comprises a second protein.
The composition of any one of the above claims, wherein the analyte is associated with a nucleic acid.
The composition of any one of the above claims, wherein the composition is in the form of an array.
A method comprising:
- contacting a sample comprising a nucleic acid associated with an analyte with
- a. a first probe, wherein the first probe comprises a first tag comprising a polynucleotide comprising a region for attaching to a first end of a nucleic acid;
- and
- b. a second probe, wherein the second probe comprises a second tag comprising a polynucleotide comprising a region for attaching to a second end of the nucleic acid,
- wherein the first probe has an affinity to a first binding site on the analyte and the second probe has an affinity to a second binding site on the analyte, wherein the first probe and the second probe are in spatial proximity, and
- i. wherein the first probe is associated with a substrate;
- ii. wherein the second probe is associated with the substrate;
- iii. wherein the first probe is associated with the substrate and wherein the second probe is associated with the substrate;
- iv. wherein the first tag is double stranded where associated with the first probe;
- v. wherein the second tag is double stranded where associated with the second probe;
- vi. wherein the first tag is double stranded where associated with the first probe and wherein the second tag is double stranded where associated with the second probe;
- or
- vii. one of (i), (ii), or (iii) and one of (iv), (v) or (vi).
A method comprising:
- a. extracting an analyte with a nucleic acid associated with the analyte from a sample by contacting the sample with an extraction complex comprising an extraction moiety and an oligonucleotide, wherein the extraction complex binds to the nucleic acid;
- and
- b. contacting the extracted analyte with:
- i. a first probe that has an affinity to a first binding site on the analyte, and
- ii. a second probe that has an affinity to a second binding site on the analyte, wherein the first probe comprises a first tag comprising a first polynucleotide comprising a region for attaching to a first end of the nucleic acid, and the second probe comprises a second tag comprising a second polynucleotide comprising a region for attaching to a second end of the nucleic acid, and wherein the first probe and the second probe are in spatial proximity.
A method comprising:
- a. associating a substrate to a first probe and a second probe, wherein the first probe comprises a first tag comprising a first polynucleotide and the second probe comprises a second tag comprising a second polynucleotide, wherein the first probe has an affinity to a first binding site on an analyte in a sample, and the second probe has an affinity to a second binding site on the analyte, wherein the first tag comprises a region for attaching to a first end of a nucleic acid associated with the analyte, and the second tag comprises a region for attaching to a second end of the nucleic acid associated with the analyte.
Dependencies are inferred from the claim text.