Multiplexed analysis by chromatographic separation of molecular tags

• US 20030235832A1
• Filed: 11/08/2002
• Published: 12/25/2003
• Est. Priority Date: 06/21/2000
• Status: Abandoned Application

• Current Assignee: Ahmed Chenna, Herbert Hooper, Sharat Singh, Tracy Matray, Vincent Hernandez
• Original Assignee: Ahmed Chenna, Herbert Hooper, Sharat Singh, Tracy Matray, Vincent Hernandez
• Inventors: Singh, Sharat, Chenna, Ahmed, Hernandez, Vincent, Matray, Tracy, Hooper, Herbert
• Application Number:
  US10/290,613
• Publication Number:
  US 20030235832A1
• Time in Patent Office: Days
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 2565/102 Multiple non-interacting labels
• CPC Class Codes: C12Q 2565/137 Chromatographic separation
• CPC Class Codes: G01N 2030/027 Liquid chromatography
• CPC Class Codes: G01N 33/58 involving labelled substances G01N33/53 takes precedence
• CPC Class Codes: G01N 33/6845 Methods of identifying protein-protein interactions in protein mixtures

Abstract

Methods and kits are disclosed for determining, either in a homogeneous or heterogeneous assay format, one or more target analytes in a sample using binding compositions coupled to molecular tags by cleavable linkages. Generally, an assay mixture is formed comprising a sample and a reagent comprising multiple such binding compositions under conditions that permit stable complexes to form between the binding compositions and analytes. In one aspect of the invention, the interaction between the binding compositions and their respective binding sites brings a cleavage-inducing moiety into close proximity to cleavable linkages or provides a recognizable substrate for a cleavage-inducing moiety. In this way, one or more molecular tags for each of the analytes are released from the complexes. Released molecular tags are chromatographically separated and the presence and/or amount of the target analytes are determined based on the analysis of the released and separated molecular tags.

Claims

1. A method for determining the presence or absence of one or more target compounds in a sample, the method comprising the steps of:

providing a plurality of binding compounds, such that there is at least one binding compound specific for each of the one or more target compounds, each binding compound having one or more molecular tags, each molecular tag being attached by a cleavable linkage, and the molecular tags of each binding compound being distinguishable from those of every other binding compound by one or more physical and/or optical characteristics;

combining with the sample the plurality of binding compounds specific for the one or more target compounds such that in the presence of a target compound a complex is formed between such target compound and a binding compound specific therefor;

cleaving the cleavable linkage of each binding compound forming such complex so that molecular tags are released; and

chromatographically separating and identifying the released molecular tags by the one or more physical characteristics to determine the one or more target compounds in the sample.

2. The method of claim 1 including prior to said step of cleaving, a further step comprising separating said binding compounds forming said complexes from those binding compounds not forming said complexes.

3. The method of claim 2 wherein said step of cleaving includes treating said cleavable linkage with an enzyme to release said molecular tags and wherein said one or more physical characteristics are selected from a group consisting of molecular weight, hydrophobicity, charge, and polarity.

4. The method of claim 2 wherein each of said molecular tags has a fluorescent label or an electrochemical label and wherein said plurality of said target compounds is from 5 to 50.

5. The method of claim 1 wherein said plurality of said target analytes is in a range of from 5 to 50, wherein said one or more physical and/or optical characteristics are selected from a group consisting of molecular weight, hydrophobicity, charge, polarity, and fluorescence, and wherein said binding compound is an antibody binding composition.

6. The method of claim 5 wherein said cleavable linkage is cleaved by oxidation, and wherein said step of cleaving includes providing an active species for oxidizing said cleavable linkage.

7. The method of claim 6 wherein said said step of cleaving further includes providing for each of said plurality of said target analytes a second binding compound specific therefor, the second binding compound having a sensitizer for generating said active species for oxidizing said cleavable linkage.

8. The method according to claim 7 wherein said active species is singlet oxygen, wherein said second binding compound is an antibody binding composition, and wherein said cleavable linkage is an olefin, a thioether, a sulfoxide, or a selenium analog of the thioether or sulfoxide.

9. The method of any one of claims 1 through 8, wherein said plurality is in the range of from 5 to 30 and wherein said step of chromatographically separating includes forcing under pressure a liquid solvent containing said released molecular tags through a column packed with a solid phase particulate adsorbant having a hydrophobic retention ligand bonded thereto such that said released molecular tags form distinct peaks in a chromatogram.

10. The method of any one of claims 1 through 8, wherein said plurality is in the range of from 5 to 30 and wherein said step of chromatographically separating includes electroosmotically flowing a liquid solvent containing said released molecular tags through a column packed with a solid phase particulate adsorbant having a hydrophobic retention ligand bonded thereto such that said released molecular tags form distinct peaks in a chromatogram.

11. A method of detecting the presence or absence of a plurality of polynucleotides in a sample, the method comprising the steps of:

providing for each polynucleotide, a helper probe complementary to a region of the polynucleotide, and a detection probe complementary to the polynucleotide adjacent to said region, each detection probe having a molecular tag attached by a cleavable linkage, and the molecular tag of each detection probe having one or more physical and/or optical characteristics distinct from those of molecular tags attached to other detection probes so that each molecular tag forms a distinguishable peak in a separation profile;

mixing under hybridization conditions a nuclease, the sample, the detection probes, and the helper probes to form an assay mixture, such that the detection probes and the helper probes hybridized to the target polynucleotides to form complexes recognized by the nuclease so that a detection probe in a complex is cleaved at a cleavage site to produce in the assay mixture released molecular tags, uncleaved detection probes, and nonspecific degradation products;

treating the assay mixture to exclude from the separation profile uncleaved detection probes and nonspecific degradation products; and

chromatographically separating and identifying the released molecular tags to determine each of the plurality of polynucleotides.

12. The method of claim 11 wherein each of said released molecular tags has a molecular weight of from 150 to 2500 daltons.

13. The method of claim 12 wherein each of said detection probes has a capture ligand attached to a nucleotide located opposite said cleavage site from said molecular tag and wherein said step of treating further includes reacting the capture ligand with a capture agent.

14. The method of any one of claims 11, 12, or 13, wherein said plurality is in the range of from 5 to 30 and wherein said step of chromatographically separating includes forcing under pressure a liquid solvent containing said released molecular tags through a column packed with a solid phase particulate adsorbant having a hydrophobic retention ligand bonded thereto such that said released molecular tags form distinct peaks in a chromatogram.

15. The method of any one of claims 11, 12, or 13, wherein said plurality is in the range of from 5 to 30 and wherein said step of chromatographically separating includes electroosmotically flowing a liquid solvent containing said released molecular tags through a column packed with a solid phase particulate adsorbant having a hydrophobic retention ligand bonded thereto such that said released molecular tags form distinct peaks in a chromatogram.

16. A method for detecting a plurality of target analyte in a sample, the method comprising the steps of:

providing a binding compound for each of a plurality of target analytes, each binding compound having one or more molecular tags attached thereto by a cleavable linkage, the one or more molecular tags of each binding compound having one or more physical and/or optical characteristics distinct from those of molecular tags attached to other binding compounds so that each molecular tag forms a distinguishable peak in a chromatogram;

providing a second binding compound for each of the plurality of target analytes, each second binding compound having a sensitizer for generating an active species;

combining with the sample a binding compound and a second binding compound for each of the plurality of target analytes such that in the presence of a target analyte a complex is formed between the target analyte and the binding compound and the second binding compound specific therefor, and such that the sensitizer of the second binding compound causes the generation of an active species and the cleavage of one or more cleavable linkages to release one or more molecular tags; and

chromatographically separating and identifying the released molecular tags by the one or more physical characteristics to determine the target analytes in the sample.

17. The method of claim 16 wherein said cleavable linkage is cleaved by oxidation, wherein said one or more physical and/or optical characteristics are selected from a group consisting of molecular weight, hydrophobicity, charge, polarity, and fluorescence, and wherein said binding compound is an antibody binding composition.

18. The method according to claim 17 wherein said active species is singlet oxygen, wherein said second binding compound is an antibody binding composition, and wherein said cleavable linkage is an olefin, a thioether, a sulfoxide, or a selenium analog of the thioether or sulfoxide.

19. The method of any one of claims 16, 17, or 18, wherein said plurality is in the range of from 5 to 30 and wherein said step of chromatographically separating includes forcing under pressure a liquid solvent containing said released molecular tags through a column packed with a solid phase particulate adsorbant having a hydrophobic retention ligand bonded thereto such that said released molecular tags form distinct peaks in a chromatogram.

20. The method of any one of claims 16, 17, or 18, wherein said plurality is in the range of from 5 to 30 and wherein said step of chromatographically separating includes electroosmotically flowing a liquid solvent containing said released molecular tags through a column packed with a solid phase particulate adsorbant having a hydrophobic retention ligand bonded thereto such that said released molecular tags form distinct peaks in a chromatogram.