Bio-barcodes based on oligonucleotide-modified nanoparticles

• US 20020192687A1
• Filed: 03/27/2002
• Published: 12/19/2002
• Est. Priority Date: 03/28/2000
• Status: Active Grant

• Current Assignee: Northwestern University
• Original Assignee: Nanosphere Incorporated (DiaSorin S.p.A.)
• Inventors: Mirkin, Chad A., Park, So-Jung, Nam, Jwa-Min
• Granted Patent: US 6,974,669 B2
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: B01J 2219/00274 Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/197 incorporating a spacer/coupling moiety
• CPC Class Codes: C12Q 2563/155 Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2563/185 Nucleic acid dedicated to use as a hidden marker/bar code, e.g. inclusion of nucleic acids to mark art objects or animals
• CPC Class Codes: C40B 40/00 Libraries per se, e.g. arrays, mixtures
• CPC Class Codes: Y10S 977/924 using nanostructure as support of dna analysis

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.

Claims

1. A method for detecting for the presence 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 to form an aggregated complex in the presence of analyte; and

observing whether aggregate formation occurred.

11. The method of any one of claims 1-10 wherein the particles are nanoparticles.

12. The method of any one of claims 1-10 wherein the particles are metal, semiconductor, insulator, or magnetic nanoparticles.

13. The method of any one of claims 1-10 wherein the particles are gold nanoparticles.

15. The method according to claim 14, wherein the substrate having plurality of types of oligonucleotides attached thereto in an array to allow for the detection of multiple portions of a single type of DNA barcode, the detection of multiple different DNA barcodes, or both.

17. The method according to claim 16 wherein the detectable change is the formation of dark areas on the substrate.

18. The method according to claim 16 wherein the detectable change is observed with an optical scanner.

19. The method according to claim 16 wherein the substrate is contacted with silver stain to produce the detectable change.

20. The method according to claim 16 wherein the DNA barcodes are contacted with the substrate so that the DNA barcodes hybridizes with complementary oligonucleotides bound to the substrate and then the DNA barcodes bound to the substrate is contacted with the nanoparticles having oligonucleotides bound thereto so that at least some of the oligonucleotides bound to the nanoparticles hybridize with a portion of the sequence of the DNA barcodes on the substate.

21. The method according to claim 15 wherein the DNA barcodes are contacted with the nanoparticles having oligonucleotides bound thereto so that at least some of the oligonucleotides bound to the nanoparticles hybridize with a portion of the sequence of the DNA barcodes;

and contacting the DNA barcodes bound to the nanoparticles with the substrate so that a portion of the sequence of the DNA barcodes bound to the nanoparticles hybridizes with complementary oligonucleotides bound to the substrate.

27. A kit according to any one of claims 21-26 wherein the particle comprises a nanoparticle.

2. A method for detecting for the presence of one or more target analytes in a sample comprising:

providing one or more types of 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 specific target analyte, wherein (i) the DNA barcode has a sequence having at least two portions, (ii) at least some of the oligonucleotides attached to the particle have a sequence that is complementary to a first portion of a DNA barcode, (iii) the oligonucleotides having bound thereto a specific binding complement have a sequence that is complementary to a second portion of a DNA barcode, and (iv) 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;

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 an aggregated complex in the presence of analyte;

isolating aggregated complexes; and

analyzing the aggregated complexes to determine the presence of one or more DNA barcodes having different sequences.

3. A method for detecting for the presence 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 to form an aggregated complex in the presence of 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.

4. A method for detecting for the presence of one or more target analytes in a sample comprising:

providing one or more types of 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 specific target analyte, wherein (i) the DNA barcode has a sequence having at least two portions, (ii) at least some of the oligonucleotides attached to the particle have a sequence that is complementary to a first portion of a DNA barcode, (iii) the oligonucleotides having bound thereto a specific binding complement have a sequence that is complementary to a second portion of a DNA barcode, and (iv) 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;

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.

5. A method for detecting for the presence of one or more antibodies in a sample comprising:

providing one or more types of particle complex probe comprising a particle having oligonucleotides bound thereto, a DNA barcode, and a oligonucleotide having bound thereto a hapten to a specific target antibody, wherein (i) the DNA barcode has a sequence having at least two portions, (ii) at least some of the oligonucleotides attached to the particle have a sequence that is complementary to a first portion of a DNA barcode, (iii) the oligonucleotides having bound thereto a hapten to a specific target antibody have a sequence that is complementary to a second portion of a DNA barcode, and (iv) 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 antibody;

contacting the sample with a particle complex probe under conditions effective to allow specific binding interactions between the antibody and the particle complex probe and to form aggregated complexes in the presence of one or more target antibodies;

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 antibody.

6. A method for detecting for the presence of a target analyte in a sample comprising:

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 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 barcodes

contacting the sample with a particle complex probe under conditions effective to allow hybridization of the DNA barcode to at least to some of the oligonucleotides attached to the particle and to the oligonucleotides having bound thereto the specific binding complement and to allow specific binding interactions between the analyte and the oligonucleotides having bound thereto a specific binding complement to the analyte, said contacting resulting in the formation of an aggregated complex in the presence of analyte; and

observing whether aggregate formation occurred.

7. A method for detecting for the presence of one or more target analytes in a sample comprising:

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) each type of DNA barcode has a sequence having at least two portions, (ii) 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 barcode, (iii) each type of oligonucleotide having bound thereto a specific binding complement have a sequence that is complementary to a second portion of a type of DNA barcode, and (iv) 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 sample with 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, under conditions effective to allow hybridization of each type of DNA barcodes at least to some of the oligonucleotides attached to the particles and to a type of oligonucleotides having bound thereto the specific binding complement and to allow specific binding interactions between a specific target analyte and a type of oligonucleotides having bound thereto a specific binding complement to the specific target analyte, said contacting resulting in the formation of aggregated complexes in the presence of one or more specific target analytes;

isolating aggregated complexes; and

analyzing the aggregated complexes to determine the presence of one or more DNA barcode, where the presence of a particular DNA barcode is indicative of the presence of a specific target analyte in the sample.

8. A method for detecting for the presence of a target analyte in a sample comprising:

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 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 barcodes;

contacting the sample with a particle complex probe under conditions effective to allow hybridization of the DNA barcode to at least to some of the oligonucleotides attached to the particle and to the oligonucleotides having bound thereto the specific binding complement and to allow specific binding interactions between the analyte and the oligonucleotides having bound thereto a specific binding complement to the analyte, said contacting resulting in the formation of an aggregated complex in the presence of 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.

9. A method for detecting for the presence of one or more target analytes in a sample comprising:

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) each type of DNA barcode has a sequence having at least two portions, (ii) 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 barcode, (iii) each type of oligonucleotide having bound thereto a specific binding complement have a sequence that is complementary to a second portion of a type of DNA barcode, and (iv) 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 sample with 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, under conditions effective to allow hybridization of each type of DNA barcodes at least to some of the oligonucleotides attached to the particles and to a type of oligonucleotides having bound thereto the specific binding complement and to allow specific binding interactions between a specific target analyte and a type of oligonucleotides having bound thereto a specific binding complement to the specific target analyte, said contacting resulting in the formation of aggregated complexes in the presence of one or more specific target 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.

10. A method for detecting for the presence of one or more antibodies in a sample comprising:

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 hapten to a specific antibody, wherein (i) each type of DNA barcode has a sequence having at least two portions, (ii) 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 barcode, (iii) each type of oligonucleotide having bound thereto a hapten to a specific antibody has a sequence that is complementary to a second portion of a type of DNA barcode, and (iv) each type of DNA barcode serves as an identifier for a particular target antibody and has a sequence that is different from another type of DNA barcode;

contacting the sample with 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 hapten to a specific target antibody, under conditions effective to allow hybridization of each type of DNA barcodes at least to some of the oligonucleotides attached to the particles and to a type of oligonucleotides having bound thereto the hapten and to allow specific binding interactions between a specific target antibody and a type of oligonucleotides having bound thereto a hapten to the specific target antibody, said contacting resulting in the formation of aggregated complexes in the presence of one or more specific target antibodies;

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 antibody.

14. The method according to any one of claims 3-5 and 8-10 wherein the DNA barcodes are detected using a substrate having oligonucleotides attached thereto, the oligonucleotides having a sequence complementary to the sequence of a portion of the DNA barcode.

16. The method according to any one of claims 3-5 and 8-10 further comprising

providing a substrate having plurality of types of oligonucleotides attached thereto in an array to allow for the detection of multiple portions of a single type of DNA barcode, the detection of multiple different DNA barcodes, or both;

providing a nanoparticle having oligonucleotides bound thereto, wherein a portion of the oligonucleotides have a sequence that is complementary to a portion of a DNA barcode;

contacting the DNA barcodes with the substrate and the nanoparticles under conditions effective for hybridization of at least a first portion of the DNA barcodes with a complementary oligonucleotide bound to the substrate and the second portion of the DNA barcodes with some of the oligonucleotides bound to the nanoparticles; and

observing a detectable change.

22. A kit for detecting a target analyte in a sample, the kit comprising at least one container including particle complex probes 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 to at least to some of the oligonucleotides attached to the particle and to the oligonucleotides having bound thereto the specific binding complement, and an optional substrate for observing a detectable change.

28. The kit according to claim 27 wherein the particles are metal, semiconductor, insulator, or magnetic nanoparticles.

29. The kit according to claim 27 wherein the particles are gold nanoparticles.

23. A kit for detecting one or more target analytes in a sample, the kit comprising at least one or more containers, container holds a type of 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 specific target analyte, wherein (i) the DNA barcode has a sequence having at least two portions, (ii) at least some of the oligonucleotides attached to the particle have a sequence that is complementary to a first portion of a DNA barcode, (iii) the oligonucleotides having bound thereto a specific binding complement have a sequence that is complementary to a second portion of a DNA barcode, and (iv) 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;

wherein the kit optionally includes a substrate for observing a detectable change.

24. A kit for the detection of a target analyte, the kit includes at least one pair of containers and an optional substrate for observing a detectable change,

the first container of the pair includes particle probe comprising a particle having oligonucleotides bound thereto and a DNA barcode having a sequence of at least two portions, wherein 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 second container of the pair includes an oligonucleotide having a sequence that is complementary to a second portion of the DNA barcode, the oligonucleotide having a moiety that can be used to covalently link a specific binding pair complement of a target analyte.

25. A kit for the detection of multiple target analytes in a sample, the kit includes at least two or more pairs of containers,

the first container of each pair includes particle complex probes having particles having oligonucleotides bound thereto and a DNA barcode having a sequence of at least two portions, wherein at least some of the oligonucleotides bound to the particles have a sequence that is complementary to a first portion of a DNA barcode having at least two portions;

and

the second container of each pair contains a oligonucleotide having a sequence that is complementary to a second portion of the DNA barcode, the oligonucleotide having a moiety that can be used to covalently link a specific binding pair complement of a target analyte,

wherein the DNA barcode for type of particle complex probe has a sequence that is different and that serves as an identifer for a target analyte and wherein the kit optionally include a substrate for observing a detectable change.

26. A kit for the detection of multiple target analytes in a sample, the kit includes a first container and at least two or more pairs of containers,

the first container includes particle complex probes having particles having oligonucleotides bound thereto;

the first container of the pair includes a DNA barcode having a sequence of at least two portions, wherein at least some of the oligonucleotides bound to the particles have a sequence that is complementary to a first portion of the DNA barcode; and

the second container of each pair contains a oligonucleotide having a sequence that is complementary to a second portion of the DNA barcode, the oligonucleotide having a moiety that can be used to covalently link a specific binding pair complement of a target analyte,

wherein the DNA barcode present in the first container of each pair of containers serves as an identifer for a target analyte and has a sequence that is different from a DNA barcode in another pair of containers, and wherein the kite optionally include a substrate for observing a detectable change.

30. A system for detecting one or more target analytes in a sample comprising:

one or more types of particle complex probes, each 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 specific target analyte, wherein (i) the DNA barcode has a sequence having at least two portions, (ii) at least some of the oligonucleotides attached to the particle have a sequence that is complementary to a first portion of a DNA barcode, (iii) the oligonucleotide having bound thereto a specific binding complement have a sequence that is complementary to a second portion of a DNA barcode, and (iv) 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.

31. The system according to claim 30 wherein the particle comprises a nanoparticle.

32. The system according to claim 30 wherein the particles are metal, semiconductor, insulator, or magnetic nanoparticles.

33. The system according to claim 30 wherein the particles are gold nanoparticles.

35. The probe according to claim 34 wherein the particle comprises a nanoparticle.

36. The probe according to claim 34 wherein the particles are metal, semiconductor, insulator, or magnetic nanoparticles.

37. The probe according to claim 34 wherein the particles are gold nanoparticles.

34. 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.

38. An oligonucleotide sequence having bound thereto a specific target complement to a target analyte.

39. A DNA barcode comprising a oligonucleotide sequence that serves as an identifier for the presence of a specific target analyte.

41. The DNA barcodes of claims 39 or 40, wherein the specific target analyte is an antibody.

40. Two or more DNA barcodes comprising an oligonucleotide sequence, each DNA barcode having a different oligonucleotide sequence and serving as an identifier for the presence of a specific target analyte.