Method for tagging and screening molecules

• US 6,319,668 B1
• Filed: 06/24/1996
• Issued: 11/20/2001
• Est. Priority Date: 04/25/1995
• Status: Expired due to Fees

• Current Assignee: Irori Technologies Incorporated
• Original Assignee: Discovery Partners International, Inc. (Infinity Pharmaceuticals, Inc.)
• Inventors: David, Gary S., Parandoosh, Zahra, Nova, Michael P., Xiao, Xiao-Yi, Potash, Hanan
• Primary Examiner(s): Zitomer, Stephanie W.
• Application Number:
  US08/669,252
• Time in Patent Office: 1,975 Days
• Field of Search: 435/6, 435/5, 435/7--, 435/282.1, 435/287.2, 435/288.1, 435/288.3, 435/288.4, 435/288.7, 530/333, 530/211, 530/334, 536/24.37, 536/24.33, 536/25.3, 585/502, 365/183, 365/94, 395/401
• US Class Current: 506/28
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00295 the reactor vessels having pervious side walls
• CPC Class Codes: B01J 2219/00299 Generally cylindrical reactor vessels
• CPC Class Codes: B01J 2219/00308 interchangeably mounted in racks or blocks
• CPC Class Codes: B01J 2219/00333 Closures attached to the reactor vessels
• CPC Class Codes: B01J 2219/00344 Caps
• CPC Class Codes: B01J 2219/00461 Beads and reaction vessel together
• CPC Class Codes: B01J 2219/00463 Directed sorting
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00502 Particles of irregular geometry
• CPC Class Codes: B01J 2219/0054 Means for coding or tagging the apparatus or the reagents
• CPC Class Codes: B01J 2219/00542 Alphanumeric characters
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00549 2-dimensional
• CPC Class Codes: B01J 2219/00551 3-dimensional
• CPC Class Codes: B01J 2219/0056 Raised or sunken areas
• CPC Class Codes: B01J 2219/00563 Magnetic means
• CPC Class Codes: B01J 2219/00567 Transponder chips
• CPC Class Codes: B01J 2219/00569 EEPROM memory devices
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 : Sequential processes
• CPC Class Codes: B01J 2219/00596 : Solid-phase processes
• CPC Class Codes: B01J 2219/00689 : using computers
• CPC Class Codes: B01J 2219/00695 : Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/0072 : Organic compounds
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01L 2300/022 : Transponder chips
• CPC Class Codes: B01L 2300/024 : Storing results with means integrated into the container
• CPC Class Codes: B01L 2300/0609 : Holders integrated in container to position an object
• CPC Class Codes: B01L 3/50825 : Closing or opening means, corks, bungs closures for containers B65D; means for removing stoppers B67B7/02
• CPC Class Codes: B01L 3/5453 : for test tubes
• CPC Class Codes: B82Y 10/00 : Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• CPC Class Codes: C07K 1/00 : General methods for the preparation of peptides , i.e. processes for the organic chemical preparation of peptides or proteins of any length
• CPC Class Codes: C07K 1/04 : on carriers C07K1/003, C07K1/006 take precedence
• CPC Class Codes: C07K 1/047 : Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• 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 15/149 : specially adapted for sorting particles, e.g. by their size or optical properties
• CPC Class Codes: G01N 2035/00782 : reprogrammmable code
• CPC Class Codes: G01N 35/00732 : Identification of carriers, materials or components in automatic analysers
• CPC Class Codes: G01N 35/00871 : Communications between instruments or with remote terminals
• CPC Class Codes: G11C 13/0014 : comprising cells based on organic memory material
• CPC Class Codes: G11C 13/0019 : comprising bio-molecules
• CPC Class Codes: G11C 13/025 : using fullerenes, e.g. C60, or nanotubes, e.g. carbon or silicon nanotubes

Abstract

Combinations, called matrices with memories, of matrix materials that are encoded with an optically readable code are provided. The matrix materials are those that are used in as supports in solid phase chemical and biochemical syntheses, immunoassays and hybridization reactions. The matrix materials may additionally include fluophors or other luminescent moieties to produce luminescing matrices with memories. The memories include electronic and optical storage media and also include optical memories, such as bar codes and other machine-readable codes. By virtue of this combination, molecules and biological particles, such as phage and viral particles and cells, that are in proximity or in physical contact with the matrix combination can be labeled by programming the memory with identifying information and can be identified by retrieving the stored information. Combinations of matrix materials, memories, and linked molecules and biological materials are also provided. The combinations have a multiplicity of applications, including combinatorial chemistry, isolation and purification of target macromolecules, capture and detection of macromolecules for analytical purposes, selective removal of contaminants, enzymatic catalysis, cell sorting, drug delivery, chemical modification and other uses. Methods for tagging molecules, biological particles and matrix support materials, immunoassays, receptor binding assays, scintillation proximity assays, non-radioactive proximity assays, and other methods are also provided.

Claims

1. A method for tagging molecules comprising a target product produced in a synthesis comprising at least one synthesis step, the method comprising:

(a) first linking a first molecule to a matrix material;

(b) either prior to, during or after first linking, imprinting an optically-readable symbol on a surface of the matrix material or on a microvessel containing the matrix material, wherein the optically-readable symbol provides a unique identifier corresponding to each first molecule;

(c) first programming a remote memory with a first data point that creates a first record correlating the optically-readable symbol to the first molecule;

(d) second linking at least one second molecule to the first linked molecule in a first synthesis step;

(e) second programming the memory with a second data point that creates a second record correlating the optically-readable symbol and the at least one second linked molecule; and

(f) if the synthesis comprises a plurality of synthesis steps, repeating steps (d) and (e) until the synthesis is complete.

2. The method of claim 1, wherein the matrix material is continuous and is in the form of a container, microvessel or laboratory glassware or chromatography column.

3. The method of claim 1, wherein the matrix material is continuous and is in the form of a container or microplate or test tube, culture dish, vial or beaker.

4. The method of claim 1, wherein:

the container is a plate with a plurality of wells; and

one or more of the wells is (are) imprinted with the optically-readable symbol.

5. The method of claim 1, wherein the matrix material is in the form of a cube or other parallelepiped having at least one outer surface adapted for linkage of biological particles or molecules.

6. The method of claim 1, wherein the matrix material is selected from the group consisting of a polystyrene, a cellulose, a glass, a polyacrylamide, a polysaccharide, a rubber, silicon, a plastic, sand, pumice, agarose, halogenated hydrocarbon polymers, polyvinyltoluene, and any polymer used as a matrix in solid phase syntheses, wherein at least a portion of the surface of the matrix material has been activated or derivatized for linkage of biological particles or molecules.

7. The method of claim 1, wherein the matrix material contains a scintillating material suitable for use in a scintillation proximity assay (SPA).

8. The method of claim 7, wherein the scintillating material is selected from the group consisting of doped glass and calcium fluoride.

9. The method of claim 8, wherein the scintillating material is a doped glass and a dopant within the doped glass is selected from the group consisting of Mn, Cu, Pb, Sn, Au, Ag, Sm and Ce.

10. The method of claim 7, wherein the scintillating material is yttrium silicate.

11. The method of claim 1, further comprising directing the sequence of steps (a) and (c) through (f) using a computer program.

12. The method of claim 1, wherein the matrix material comprises a luminescent moiety.

13. The method of claim 12, wherein the luminescent moiety is selected from among fluorophores.

14. The method of claim 12, wherein the luminescent moiety is selected from the group consisting of 2,5-diphenyloxazole (PPO), anthracene, 2-(4′

-tert-butylphenyl)-5-(4″

-biphenyl)-1,3,4-oxadiazole (butyl-PBD);

1-phenyl-3-mesityl-2-pyrazoline (PMP).

15. The method of claim 12, wherein the luminescent moiety is selected from the group consisting of rare earth metal cryptate allopycocyanin (APC), allophycocyanin B, phycocyanin C or phycocyanin R, a rhodamine, thiomine, phycocyanin R, phycoerythrocyanin, phycoerythrin C, phycoerythrin B, phycoerythrin R.

16. The method of claim 12, wherein the luminescent moiety is selected from the group consisting of Eu trisbipyridine diamine (EuTBP) and Tb tribipyridine diamine (TbTBP).

17. The method of claim 1, wherein a target product is an organic molecule.

18. The method of claim 1, wherein the synthesis is repeated using a plurality of matrices to produce a library of target products linked to matrices, wherein each matrix of the plurality of matrices is tagged with a unique optically-readable symbol.

19. The method of claim 18, wherein the memory is in a computer.

20. The method of claim 1, wherein the target product is an oligonucleotide.

21. The method of claim 20, wherein the oligonucleotide contains 6, 7 or 8 nucleotide base pairs.

22. The method of claim 1, further comprising screening the target product for activity or analyzing a structure of the target product or assessing an activity of the target product.

23. The method of claim 1, wherein the target product is a peptide and each added molecule is an amino acid.

24. The method of claim 1, wherein the target product is an oligonucleotide and each added molecule is an nucleotide.

25. The method of claim 1, wherein the target product is an oligomer and each added molecule is a monomer.

26. The method of claim 1, the target product is an organic molecule and each added molecule is a substituent on the organic molecule.

41. The method of claim 1 wherein the matrix material comprises a plurality of matrix particles contained within a microvessel and the microvessel comprises a substantially rigid structure which is partially porous.

42. The method of claim 41, wherein the optically-readable symbol is imprinted on the microvessel.

43. The method of claim 42, wherein the optically-readable symbol is a two-dimensional bar code.

44. The method of claim 1, wherein the optically-readable symbol is a two-dimensional bar code.

27. A multiplexed method for high throughput screening of synthesized compounds, comprising:

preparing a library of synthesized compounds comprising molecules or biological particles linked to a solid support matrix in combination with an optically-readable symbol, wherein the optically-readable symbol uniquely identifies each linked synthesized compound; and

screening test compounds by contacting samples of test compounds with the library.

28. The method of claim 27, wherein the library is synthesized on the solid support matrix and during synthesis the identity of the synthesized compounds, or a component of the synthesized compound is written to memory.

29. The method of claim 27 wherein the library is a combinatorial library.

30. The method of claim 27, wherein the components of the library are molecules that are peptides, peptoids or organic molecules.

31. The method of claim 27, wherein the library is a phage display library.

32. In a non-radioactive energy transfer proximity assay, the improvement comprising adding a combination to the assay, the combination comprising:

a) an optically-readable symbol comprising a unique identifier;

b) a matrix comprising a matrix material selected from the group consisting of a solid continuous surface, wherein a first portion of the surface is for linking biological particles or molecules and a second portion of the surface is imprinted with the optically-readable symbol, and a plurality of particles for linking biological particles or molecules contained inside a microvessel, wherein an outer surface of the microvessel is imprinted with the optically-readable symbol;

c) at least one moiety linked to the first portion of the surface of the solid continuous surface or to the plurality of particles, the at least one moiety selected from a molecule, a biological particle, a mixture of molecules, a mixture of biological particles, or a mixture of molecules and biological particles,

wherein the at least one moiety comprises at least one fluorescent moiety.

33. In a non-radioactive energy transfer proximity assay, the improvement comprising adding a combination to the assay, wherein the combination comprises:

a) a matrix material that forms a continuous surface, a first portion of the continuous surface adapted for use as a support matrix to which biological particles or molecules can be linked; and

b) an optically-readable symbol imprinted on a second portion of the continuous surface, wherein the optically-readable comprises a unique identifier;

wherein at least one fluorescent moiety is linked to the first portion of the continuous surface.

34. In a scintillation proximity assay, the improvement comprising, including an optical memory as part of the matrix material, wherein the matrix material contains a scintillant.

35. In a scintillation proximity assay, the improvement comprising:

(a) adding a radiolabel to the matrix material in a combination comprising;

(i) an optically-readable symbol that comprises a unique identifier;

(ii) a matrix comprising a matrix material selected from the group consisting of a solid continuous surface, wherein a first portion of the surface is for linking biological particles or molecules and a second portion of the surface is imprinted with the optically-readable symbol, and a plurality of particles for linking biological particles or molecules contained inside a microvessel, wherein an outer surface of the microvessel is imprinted with the optically-readable symbol;

(iii) at least one moiety linked to the first portion of the surface of the solid continuous surface or to the plurality of particles, the at least one moiety selected from a molecule, a biological particle, a mixture of molecules, a mixture of biological particles, or a mixture of molecules and biological particles;

(b) coating the matrix with a ligand and recording an association between an identity of the ligand and the optically-readable symbol imprinted on the matrix;

(c) linking a receptor to a second matrix particle that contains a scintillant; and

(d) reacting the receptor with the radio-labeled matrix, whereby light is produced.

36. In the scintillation proximity assay of claim 35, further comprising using a computer program to direct a sequence of steps (b) through (d).

37. In a scintillation proximity assay, the improvement comprising:

(a) adding a radiolabel to a matrix material in a combination comprising;

(i) a matrix material that forms a continuous surface, a first portion of the continuous surface adapted for use as a support matrix to which biological particles or molecules can be linked; and

(ii) an optically-readable memory comprising a optically-readable symbol imprinted on a second portion of the continuous surface;

wherein the optically-readable memory is readable by an optical detector;

(b) coating the matrix material with a receptor and recording an association between an identity of the receptor with data contained within the optically-readable memory imprinted on the matrix material;

(c) linking a ligand to a second matrix that contains a scintillant; and

(d) reacting the ligand with the radio-labeled matrix, whereby light is produced.

38. In the scintillation proximity assay of claim 37, further comprising using a computer program to direct a sequence of steps (b) through (d).

39. In a scintillation proximity assay, the improvement comprising:

(a) adding a radiolabel to the matrix material in a combination comprising;

(i) a matrix material that forms a continuous surface, a first portion of the continuous surface adapted for use as a support matrix to which biological particles or molecules can be linked; and

(ii) an optically-readable memory comprising a optically-readable symbol imprinted on a second portion of the continuous surface;

wherein the optically-readable memory is readable by an optical detector;

(b) coating the matrix material with a ligand and recording an association between an identity of the ligand with data contained within the optically-readable memory imprinted on the matrix material;

(c) linking a receptor to a second matrix that contains a scintillant; and

(d) reacting the receptor with the radio-labeled matrix, whereby light is produced.

40. In the scintillation proximity assay of claim 39, further comprising using a computer program to direct a sequence of steps (b) through (d).