Methods employing generalized target-binding e-tag probes

• US 6,818,399 B2
• Filed: 04/02/2001
• Issued: 11/16/2004
• Est. Priority Date: 04/30/1999
• Status: Expired due to Term

• Current Assignee: Monogram Biosciences, Inc. (Laboratory Corporation Of America Holdings)
• Original Assignee: Aclara Biosciences, Inc (Laboratory Corporation Of America Holdings)
• Inventors: Salimi-Moosavi, Hossein, Xiao, Vivian, Singh, Sharat
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Tung, Joyce
• Application Number:
  US09/824,984
• Publication Number:
  US 20010049105A1
• Time in Patent Office: 1,324 Days
• Field of Search: 435/6, 536/24.2, 536/24.31, 536/24.33, 536/23.1, 536/25.32, 536/26.6
• US Class Current: 435/6.1
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• 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: C40B 70/00 Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G01N 33/561 Immunoelectrophoresis
• CPC Class Codes: Y10S 435/81 Packaged device or kit

Abstract

Methods for the multiplexed detection of the binding of, or interaction between, one or more ligands and target antiligands are provided. Detection involves the release of identifying tags as a consequence of target recognition. The methods include the use of electrophoretic tag probes or e-tag probes, comprising a detection region and a mobility-defining region called the mobility modifier, both linked to a target-binding moiety. In practicing the methods, target antiligands are contacted with a set of e-tag probes and the contacted antiligands are treated with a selected cleaving agent resulting in a mixture of e-tag reporters and uncleaved and/or partially cleaved e-tag probes. The mixture is exposed to a capture agent effective to bind to uncleaved or partially cleaved e-tag probes, followed by electrophoretic separation. In a multiplexed assay, different released e-tag reporters may be separated and detected providing for target identification.

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 electrophoretic probes specific for the one or more target compounds, each electrophoretic probe having a target-binding moiety and one or more eTag reporters attached by cleavable linkages that are cleaved by oxidation, the one or more eTag reporters of each electrophoretic probe being distinguished from those of other electrophoretic probes by electrophoretic mobility;

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

cleaving the cleavable linkages of each electrophoretic probe forming such complex so that eTag reporters are released; and

separating and identifying the released eTag reporters based on electrophoretic mobility to determine the presence or absence of the one or more target compounds.

2. The method of claim 1 further including a step prior to said step of cleaving, the step comprising separating said complexes from unbound said electrophoretic probes.

3. The method of claim 2 wherein said cleavable linkages are each an olefin, a thioether, a sulfoxide, or a selenium analog of the thioether or sulfoxide.

4. The method according to claim 1, 2, 3 wherein each of said electrophoretic probes is selected from a group defined by the formula:

5. The method of claim 4 wherein said mass/charge ratio is in the range of −

0.001 and 0.5, and wherein said step of providing includes providing a plurality of from 5 to 100 said electrophoretic probes.

6. The method of claim 5 wherein k is in the range of from 1 to 3, and wherein M is a mobility modifier consisting of from 1 to 300 atoms selected from the group consisting of carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus, and boron.

7. The method of claim 6 wherein said plurality of said electrophoretic probes is in the range of from 5 to 50.

8. The method of claim 1 wherein said step of cleaving includes providing a second reagent specific for each of said one or more target compounds, each second reagent being capable of generating an active species for oxidizing said cleavable linkage.

9. The method of claim 8 wherein said active species is singlet oxygen and said cleavable linkage is an olefin, a thioether, a sulfoxide, or a selenium analog of the thioether or sulfoxide.

10. The method according to claim 8 or 9 wherein said step of providing includes providing a plurality of from 5 to 100 said electrophoretic probes.

11. The method of claim 10 wherein said mobility modifier consisting of from 1 to 300 atoms selected from the group consisting of carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus, and boron.

12. The method of claim 11 wherein said detection group comprises a fluorescent label or an electrochemical label.

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

providing one or more electrophoretic probes specific for each of the one or more target compounds, each electrophoretic probe having one or more eTag reporters attached thereto by a cleavable linkage, the one or more eTag reporters of each electrophoretic probe being distinguished from those of other binding compounds by electrophoretic mobility;

providing a second reagent specific for each of the one or more target compounds, each second reagent being capable of generating an active species;

combining with the sample one or more electrophoretic probes and a second reagent for each of the one or more target compounds such that in the presence of a target compounds a complex is formed between the target compound, the one or more electrophoretic probes specific therefor, and the second reagent specific therefor, and such that the second regent causes the generation of an active species and the cleavage of one or more cleavable linkages to release one or more eTag reporters, and

electrophoretically separating and identifying the one or more released eTag reporters to determine the presence or absence of the one or more target compounds.

14. The method of claim 13 wherein said cleavable linkage is cleaved by oxidation.

15. The method of claim 14 wherein said active species is singlet oxygen and said cleavable linkage is an olefin, a thioether, a sulfoxide, or a selenium analog of the thioether or sulfoxide.

16. The method of claim 15 wherein each of said electrophoretic probes comprises a target-binding moiety and wherein the target-binding moiety and said second reagent are each antibodies or fragments thereof.

17. The method according to claim 13, 14, 15 or 16 wherein said eTag reporter are identified by fluorescence or by an electrochemical label, and wherein said step of providing one or more electrophoretic probes includes providing a plurality of from 5 to 100 said electrophoretic probes.

18. The method according to 13, 14, 15 or 16 further including, prior to said step of electrophoretically separating, a step of separating said released eTag reporters from any components that interfere with electrophoretic analysis.