Multiplexed Analyses of Test Samples

• US 20170176422A1
• Filed: 03/09/2017
• Published: 06/22/2017
• Est. Priority Date: 06/07/2012
• Status: Abandoned Application

• Current Assignee: Somalogic Incorporated
• Original Assignee: Somalogic Incorporated
• Inventors: Sanders, Glenn, Katilius, Evaldas, Kraemer, Stephan
• Application Number:
  US15/454,080
• Publication Number:
  US 20170176422A1
• Time in Patent Office: Days
• 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 1/6804 Nucleic acid analysis using immunogens immunoassay G01N33/53
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/113 incorporating modified backbone
• CPC Class Codes: C12Q 2525/205 Aptamer
• CPC Class Codes: C12Q 2561/101 Taqman
• CPC Class Codes: G01N 2570/00 Omics, e.g. proteomics, glycomics or lipidomics; Methods of analysis focusing on the entire complement of classes of biological molecules or subsets thereof, i.e. focusing on proteomes, glycomes or lipidomes
• CPC Class Codes: G01N 33/5308 for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
• CPC Class Codes: G01N 33/543 with an insoluble carrier for immobilising immunochemicals
• CPC Class Codes: G01N 33/54306 Solid-phase reaction mechanisms
• CPC Class Codes: G01N 33/54393 Improving reaction conditions or stability, e.g. by coating or irradiation of surface, by reduction of non-specific binding, by promotion of specific binding
• CPC Class Codes: G01N 33/68 involving proteins, peptides or amino acids involving lipoproteins G01N33/92
• CPC Class Codes: G01N 33/6803 General methods of protein analysis not limited to specific proteins or families of proteins

Abstract

The present disclosure describes methods, devices, reagents, and kits for the detection of one or more target molecules that may be present in a test sample. The described methods, devices, kits, and reagents facilitate the detection and quantification of a non-nucleic acid target (e.g., a protein target) in a test sample by detecting and quantifying a nucleic acid (i.e., an aptamer) where the aptamer-aptamer interactions are significantly reduced or eliminated while maintaining the aptamer-target interaction.

Claims

1. A method comprising:

providing an aptamer that is immobilized on a first solid support, the aptamer having a specific binding affinity for the target molecule and bearing a first tag having an affinity to a first capture element, the first solid support comprising a first capture element, and the first tag being associated with the first capture element to immobilize the aptamer on the first solid support,

said first solid support having been washed with one or more solutions that dissociate aggregated aptamers;

contacting said immobilized aptamer with the test sample, wherein an aptamer-target affinity complex is formed if said target molecule is present in said test sample;

removing one or more components of the mixture not associated with said first solid support;

attaching a second tag with an affinity to a second capture element to said target molecule in the aptamer-target affinity complex;

releasing the aptamer-target affinity complex from said first solid support;

exposing the released aptamer-target affinity complex to a second solid support comprising a second capture element and allowing the second tag to associate with said second capture element;

removing any components of the mixture not associated with said second solid support; and

eluting aptamers from said second solid support with one or more solutions comprising a chaotropic salt that disrupts aptamer/analyte interactions.

2. The method of claim 1, wherein said aptamer comprises at least one C-5 modified nucleotide.

3. The method of claim 1, wherein said aptamer comprises at least one chemical modification comprising a chemical substitution at one or more positions independently selected from a ribose position, a deoxyribose position, a phosphate position, and a base position, wherein optionally said chemical modification is independently selected from the group consisting of a 2′

-position sugar modification, a 2′

-amino (2′

-NH2), a 2′

-fluoro (2′

-F), a 2′

-O-methyl (2′

-OMe), a 5-position pyrimidine modification, an 8-position purine modification, a modification at a cytosine exocyclic amine, a substitution of 5-bromouracil, a substitution of 5-bromodeoxyuridine, a substitution of 5-bromodeoxycytidine, a backbone modification, methylation, a 3′

cap, and a 5′

cap.

4. The method of claim 1, further comprising a kinetic challenge.

5. The method of claim 1, wherein the rate of dissociation of said aptamer-target affinity complex (t1/2) is:

(a) greater than or equal to 30 minutes;

(b) between about 30 minutes and about 240 minutes;

or

(c) selected from the group consisting of ≧

30 minutes, ≧

60 minutes, ≧

90 minutes, ≧

120 minutes, ≧

150 minutes, ≧

180 minutes, ≧

210 minutes, and ≧

240 minutes.

6. The method of claim 1, wherein one or more of said buffered solutions comprises an organic solvent, optionally glycerol

7. The method of claim 1, wherein said chaotropic salt is selected from the group consisting of sodium perchlorate, lithium chloride, magnesium chloride and sodium chloride.

8. The method of claim 1, wherein said aptamer is detected and optionally quantified using a method selected from the group consisting of Q-PCR, MS, nextgeneration sequencing and hybridization, wherein said Q-PCR is optionally performed using TaqMan®

PCR, an intercalating fluorescent dye during the PCR process, or a molecular beacon during the PCR process.

9. The method of claim 1, wherein the aptamer comprises a detectable moiety, wherein said detectable moiety is optionally selected from the group consisting of a dye, a quantum dot, a radiolabel, a electrochemical functional group, and an enzyme plus a detectable enzyme substrate, wherein said dye is preferably a fluorescent dye.

10. The method of claim 1, wherein said aptamer comprises DNA, RNA or both DNA and RNA.

11. The method of claim 1, wherein said target molecule is selected from the group consisting of a protein, a peptide, a carbohydrate, a polysaccharide, a glycoprotein, a hormone, a receptor, an antigen, an antibody, a virus, a substrate, a metabolite, a transition state analog, a cofactor, an inhibitor, a drug, a dye, a nutrient, a growth factor, a tissue, and a controlled substance, preferably wherein said target molecule is a protein or a peptide.

12. The method of claim 1, wherein said test sample is selected from the group consisting of a biological sample, an environmental sample, a chemical sample, a pharmaceutical sample, a food sample, an agricultural sample, and a veterinary sample, wherein optionally the biological sample selected from the group consisting of blood, whole blood, leukocytes, peripheral blood mononuclear cells, plasma, serum, sputum, breath, urine, semen, saliva, meningeal fluid, amniotic fluid, glandular fluid, lymph fluid, nipple aspirate, bronchial aspirate, synovial fluid, joint aspirate, cells, a cellular extract, stool, tissue, a tissue extract, a tissue biopsy, and cerebrospinal fluid, preferably plasma or serum.

13. The method of claim 1, wherein said first tag and said second tag, said first capture element and said second capture element each comprises at least one component independently selected from the group consisting of a polynucleotide, a polypeptide, a peptide nucleic acid, a locked nucleic acid, an oligosaccharide, a polysaccharide, an antibody, an affibody, an antibody mimic, a cell receptor, a ligand, a lipid, biotin, avidin, streptavidin, Extravidin, neutravidin, Traptavidin, a metal, histidine, and any portion of any of these structures.

14. The method of claim 1, wherein the first tag comprises a releasable moiety, preferably wherein the releasable moiety comprises a photocleavable moiety.

15. The method of claim 1, wherein said first solid support and second solid support each is independently selected from the group consisting of a polymer bead, an agarose bead, a polystyrene bead, an acrylamide bead, a solid core bead, a porous bead, a paramagnetic bead, glass bead, controlled pore bead, a microtitre well, a cyclo-olefin copolymer substrate, a membrane, a plastic substrate, nylon, a Langmuir-Blodgett film, glass, a germanium substrate, a silicon substrate, a silicon wafer chip, a flow through chip, a microbead, a nanoparticle, a polytetrafluoroethylene substrate, a polystyrene substrate, a gallium arsenide substrate, a gold substrate, and a silver substrate.

16. The method of claim 1, further comprising quantifying said target by quantifying said aptamer.

17. The method of claim 1, wherein detection of the aptamer comprises hybridizing the aptamer to a third solid support wherein the third solid support comprises a plurality of addressable features and wherein at least one of said features comprises at least capture element disposed thereon that is complementary to any sequence contained within the aptamer and/or further comprising the step of detecting said target molecule by detecting the aptamer portion of said aptamer-target affinity complex.

18. A method of detecting the presence of, or determining the amount of, a target molecule in a sample, the method comprising:

providing a plurality of immobilized aptamers, wherein each of said aptamers is specific to a target molecule, and wherein each of said plurality of aptamers comprises a first cleavable capture tag, said aptamers being immobilized on a solid support having probes adhered to the surface thereof, the probes binding to the first tag, such that the aptamers are immobilized onto the solid support through binding of the first tag and the probe;

contacting the immobilized aptamers with a sample containing target molecules to form a mixture containing aptamer-target molecule complexes bound to the solid support;

partitioning aptamer-target molecule complexes bound to the solid support from the remainder of the mixture;

introducing a second capture tag to the target molecule component of the aptamer-target molecule complexes;

dissociating the aptamer-target molecule complexes from the surface of the solid support by

cleaving the first cleavable capture tag;

providing a second solid support having probes adhered to the surface of the support, wherein the probes are capable of binding to the second capture tag on target molecules;

contacting the dissociated aptamer-target molecule complexes with the second solid support such that the aptamer-target molecule complexes become bound to the second support through binding of the second capture tag and probe;

eluting aptamers from said second solid support with one or more buffered solutions comprising a chaotropic salt that disrupts aptamer/analyte interactions but supports aptamer/aptamer interactions and DNA hybridization;

dissociating the aptamer-target molecule; and

detecting the free aptamers.

19. The method of claim 18, wherein said aptamers comprise at least one C-5 modified nucleotide.

20. The method of claim 18, wherein said aptamer comprises at least one chemical modification comprising a chemical substitution at one or more positions independently selected from a ribose position, a deoxyribose position, a phosphate position, and a base position, wherein optionally said chemical modification is independently selected from the group consisting of a 2′

-position sugar modification, a 2′

-amino (2′

-NH2), a 2′

-fluoro (2′

-F), a 2′

-O-methyl (2′

-OMe), a 5-position pyrimidine modification, an 8-position purine modification, a modification at a cytosine exocyclic amine, a substitution of 5-bromouracil, a substitution of 5-bromodeoxyuridine, a substitution of 5-bromodeoxycytidine, a backbone modification, methylation, a 3′

cap, and a 5′

cap.

21. The method of claim 18, further comprising a kinetic challenge.

22. The method of claim 18, wherein the rate of dissociation of said aptamer-target affinity complex (t1/2) is:

(a) greater than or equal to 30 minutes;

(b) between about 30 minutes and about 240 minutes;

or

(c) selected from the group consisting of ≧

30 minutes, ≧

60 minutes, ≧

90 minutes, ≧

120 minutes, ≧

150 minutes, ≧

180 minutes, ≧

210 minutes, and ≧

240 minutes.

23. The method of claim 18, wherein said aptamer is detected and optionally quantified using a method selected from the group consisting of Q-PCR, MS, nextgeneration sequencing and hybridization, wherein said Q-PCR is optionally performed using TaqMan®

PCR, an intercalating fluorescent dye during the PCR process, or a molecular beacon during the PCR process.

24. The method of claim 18, wherein the aptamer comprises a detectable moiety, wherein said detectable moiety is optionally selected from the group consisting of a dye, a quantum dot, a radiolabel, a electrochemical functional group, and an enzyme plus a detectable enzyme substrate, wherein said dye is preferably a fluorescent dye.

25. The method of claim 18, wherein said aptamer comprises DNA, RNA or both DNA and RNA.

26. The method of claim 18, wherein said target molecule is selected from the group consisting of a protein, a peptide, a carbohydrate, a polysaccharide, a glycoprotein, a hormone, a receptor, an antigen, an antibody, a virus, a substrate, a metabolite, a transition state analog, a cofactor, an inhibitor, a drug, a dye, a nutrient, a growth factor, a tissue, and a controlled substance, preferably wherein said target molecule is a protein or a peptide.

27. The method of claim 18, wherein said test sample is selected from the group consisting of a biological sample, an environmental sample, a chemical sample, a pharmaceutical sample, a food sample, an agricultural sample, and a veterinary sample, wherein optionally the biological sample selected from the group consisting of blood, whole blood, leukocytes, peripheral blood mononuclear cells, plasma, serum, sputum, breath, urine, semen, saliva, meningeal fluid, amniotic fluid, glandular fluid, lymph fluid, nipple aspirate, bronchial aspirate, synovial fluid, joint aspirate, cells, a cellular extract, stool, tissue, a tissue extract, a tissue biopsy, and cerebrospinal fluid, preferably plasma or serum.

28. The method of claim 18, wherein said first tag and said second tag, said first capture element and said second capture element each comprises at least one component independently selected from the group consisting of a polynucleotide, a polypeptide, a peptide nucleic acid, a locked nucleic acid, an oligosaccharide, a polysaccharide, an antibody, an affibody, an antibody mimic, a cell receptor, a ligand, a lipid, biotin, avidin, streptavidin, Extravidin, neutravidin, Traptavidin, a metal, histidine, and any portion of any of these structures.

29. The method of claim 18, wherein the first tag comprises a releasable moiety, preferably wherein the releasable moiety comprises a photocleavable moiety.

30. The method of claim 18, wherein said first solid support and second solid support each is independently selected from the group consisting of a polymer bead, an agarose bead, a polystyrene bead, an acrylamide bead, a solid core bead, a porous bead, a paramagnetic bead, glass bead, controlled pore bead, a microtitre well, a cyclo-olefin copolymer substrate, a membrane, a plastic substrate, nylon, a Langmuir-Blodgett film, glass, a germanium substrate, a silicon substrate, a silicon wafer chip, a flow through chip, a microbead, a nanoparticle, a polytetrafluoroethylene substrate, a polystyrene substrate, a gallium arsenide substrate, a gold substrate, and a silver substrate.

31. The method of claim 18, further comprising quantifying said target by quantifying said aptamer.

32. The method of claim 18, wherein detection of the aptamer comprises hybridizing the aptamer to a third solid support wherein the third solid support comprises a plurality of addressable features and wherein at least one of said features comprises at least capture element disposed thereon that is complementary to any sequence contained within the aptamer and/or further comprising the step of detecting said target molecule by detecting the aptamer portion of said aptamer-target affinity complex.