Bio-barcodes based on oligonucleotide-modified nanoparticles
First Claim
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1. A method for detecting for the presence or absence of a target analyte in a sample comprising:
- providing a particle complex probe comprising a particle having oligonucleotides bound thereto, a DNA barcode, and a oligonucleotide having bound thereto a specific binding complement to a target analyte, wherein the DNA barcode has a sequence having at least two portions, at least some of the oligonucleotides attached to the particle have a sequence that is complementary to a first portion of a DNA barcode, the oligonucleotides having bound thereto a specific binding complement have a sequence that is complementary to a second portion of a DNA barcode, and wherein the DNA barcode is hybridized at least to some of the oligonucleotides attached to the particle and to the oligonucleotides having bound thereto the specific binding complement;
contacting the sample with a particle complex probe under conditions effective to allow specific binding interactions between the analyte and the particle complex probe and form an aggregated complex in the presence of the analyte;
isolating the aggregated complex and subjecting the aggregated complex to conditions effective to dehybridize the aggregated complex and to release the DNA barcode;
isolating the DNA barcode; and
detecting for the presence of DNA barcode, wherein the presence of the DNA barcode is indicative of the presence of the target analyte in the sample.
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Abstract
The present invention relates to a screening methods, compositions, and kits for detecting for the presence or absence of one or more target analytes, e.g. proteins such as antibodies, in a sample. In particular, the present invention relates to a method that utilizes reporter oligonucleotides as biochemical barcodes for detecting multiple protein structures or other target analytes in one solution.
286 Citations
22 Claims
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1. A method for detecting for the presence or absence of a target analyte in a sample comprising:
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providing a particle complex probe comprising a particle having oligonucleotides bound thereto, a DNA barcode, and a oligonucleotide having bound thereto a specific binding complement to a target analyte, wherein the DNA barcode has a sequence having at least two portions, at least some of the oligonucleotides attached to the particle have a sequence that is complementary to a first portion of a DNA barcode, the oligonucleotides having bound thereto a specific binding complement have a sequence that is complementary to a second portion of a DNA barcode, and wherein the DNA barcode is hybridized at least to some of the oligonucleotides attached to the particle and to the oligonucleotides having bound thereto the specific binding complement;
contacting the sample with a particle complex probe under conditions effective to allow specific binding interactions between the analyte and the particle complex probe and form an aggregated complex in the presence of the analyte;
isolating the aggregated complex and subjecting the aggregated complex to conditions effective to dehybridize the aggregated complex and to release the DNA barcode;
isolating the DNA barcode; and
detecting for the presence of DNA barcode, wherein the presence of the DNA barcode is indicative of the presence of the target analyte in the sample. - View Dependent Claims (5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22)
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2. A method for detecting for the presence of one or more target analytes in a sample comprising:
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providing one or more types of particle complex probes, each type of complex probe comprising a particle having oligonucleotides bound thereto, a DNA barcode, and a oligonucleotide having bound thereto a specific binding complement to a specific target analyte, wherein (i) the DNA barcode in each type of particle complex probe has a sequence that is different and that serves as an identifier for a particular target analyte;
(ii) the DNA barcode has a sequence having at least two portions;
(iii) at least some of the oligonucleotides attached to the particle have a sequence that is complementary to a first portion of the DNA barcode;
(iv) the oligonucleotides having bound thereto a specific binding complement have a sequence that is complementary to a second portion of the DNA barcode; and
wherein the DNA barcode in each type of particle complex probe is hybridized at least to some of the oligonucleotides attached to the particle and to the oligonucleotides having bound thereto the specific binding complement;
contacting the sample with a particle complex probe under conditions effective to allow specific binding interactions between the analyte and the particle complex probe and to form aggregated complexes in the presence of one or more analytes;
isolating the aggregated complexes and subjecting the aggregated complexes to conditions effective to dehybridize the aggregated complexes and to release the DNA barcodes;
isolating the DNA barcodes; and
detecting for the presence of one or more DNA barcodes having different sequences, wherein the identification of a particular DNA barcode is indicative of the presence of a specific target analyte in the sample.
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3. A method for detecting for the presence of a target analyte in a sample comprising:
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providing particles having oligonucleotides bound thereto, DNA barcodes, and oligonucleotides having bound thereto a specific binding complement to a target analyte, wherein the DNA barcodes have a sequence with at least two portions, at least some of the oligonucleotides attached to the particles have a sequence that is complementary to a first portion of the DNA barcodes, the oligonucleotides having bound thereto a specific binding complement have a sequence that is complementary to a second portion of the DNA barcodes;
contacting the particles having oligonucleotides bound thereto, the DNA barcodes, and the oligonucleotides having bound thereto a specific binding complement to a target analyte under conditions effective to allow the oligonucleotides bound to the particles, the DNA barcodes and the oligonucleotides having bound thereto the specific binding complement to the target analyte to form a particle complex probe;
isolating the particle complex probe;
contacting the sample with a particle complex probe under conditions effective to allow specific binding interactions between the analyte and the particle complex probe and form an aggregated complex in the presence of the analyte;
isolating the aggregated complex and subjecting the aggregated complex to conditions effective to dehybridize the aggregated complex and to release the DNA barcode;
isolating the DNA barcode; and
detecting for the presence of the DNA barcode, wherein the presence the DNA barcode is indicative of the presence of the target analyte in the sample.
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4. A method for detecting for the presence of one or more target analytes in a sample comprising:
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providing one or more types of particles having oligonucleotides bound thereto, one or more types of DNA barcodes, and one or more types of oligonucleotides having bound thereto a specific binding complement to a specific target analyte, wherein (i) the DNA barcode in each type of particle complex probe has a sequence that is different and that serves as an identifier for a particular target analyte;
(ii) each type of DNA barcode has a sequence having at least two portions;
(iii) at least some of the oligonucleotides attached to the particle have a sequence that is complementary to a first portion of one or more types of DNA barcodes;
(iv) each type of oligonucleotides having bound thereto a specific binding complement have a sequence that is complementary to a second portion of a type of DNA barcode; and
(v) each type of DNA barcode serves as an identifier for a particular target analyte and has a sequence that is different from another type of DNA barcode;
contacting the particles having oligonucleotides bound thereto, the DNA barcodes, and the oligonucleotides having bound thereto a specific binding complement to a target analyte under conditions effective to allow the oligonucleotides bound to the particles, the DNA barcodes and the oligonucleotides having bound thereto the specific binding complement to the target analyte to form a particle complex probe;
isolating the particle complex probes;
contacting the sample with a particle complex probe under conditions effective to allow specific binding interactions between the analyte and the particle complex probe and to form aggregated complexes in the presence of one or more analytes;
isolating the aggregated complexes and subjecting the aggregated complexes to conditions effective to dehybridize the aggregated complexes and to release the DNA barcodes;
isolating the DNA barcodes; and
detecting for the presence of one or more DNA barcodes having different sequences, wherein the identification of a particular DNA barcode is indicative of the presence of a specific target analyte.
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Specification