Matrices with memories and uses thereof

• US 5,961,923 A
• Filed: 09/30/1996
• Issued: 10/05/1999
• Est. Priority Date: 04/25/1995
• Status: Expired due to Term

• Current Assignee: Irori Technologies Incorporated
• Original Assignee: Irori
• Inventors: Zhao, Chanfeng, David, Gary S., Parandoosh, Zahra, Nova, Michael P., Senyei, Andrew E., Xiao, Xiao-Yi, Potash, Hanan, Satoda, Yozo
• Primary Examiner(s): Zitomer, Stephanie W.
• Application Number:
  US08/723,423
• Time in Patent Office: 1,100 Days
• Field of Search: 435/91.2, 435/6, 435/91.1, 435/5.4, 435/7.1-7.9, 422/68.1, 340/572, 340/825.54, 424/85.17, 424/85.2, 530/399, 530/333, 530/335, 530/350, 530/306, 364/496-499
• US Class Current: 506/4
• 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 2219/00283 Reactor vessels with top opening
• 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 2219/00554 Physical means
• 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 2219/00592 : Split-and-pool, mix-and-divide 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 2300/0609 : 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: 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: 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 1/047 : 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 2333/9121 : with an alcohol group as acceptor (2.7.1), e.g. general tyrosine, serine or threonine kinases
• CPC Class Codes: G01N 2500/00 : Screening for compounds of potential therapeutic value
• 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 13/02 : using elements whose operation depends upon chemical change G11C13/0009 takes precedence
• 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 system for writing and reading data from an optical memory device, comprising:

(a) a decoder/encoder instrument having a memory for storing data;

(i) relating to one or a plurality of process steps, to the identity of a molecule or biological particle, or information categorizing or tracking the molecule or biological particle;

(ii) identifying one or a plurality of unique indicators representative of each of the process steps or the identity or category of a molecule or biological particle; and

(iii) for generating a data signal representative of each unique indicator;

(b) optical writing means for receiving a data signal and writing an optically-encoded symbol on a surface, the optically-encoded symbol comprising a plurality of optically-contrasting symbols in a write sequence and having a decode orientation for decoding the optically-encoded symbol according to the write sequence;

(c) a matrix material in contact with a solution containing a molecule or a biological particle or in contact with a molecule or biological particle, the matrix material comprising;

a write surface formed from a material on which a contrast can be created by the optical writing means so that the optically-encoded symbol can be written thereupon;

a binding surface for retaining molecules or biological particles;

(d) an optical detector for detecting the optically-encoded symbol, generating an electrical signal representative of the detected optically-encoded symbol, and providing the electrical signal to the decoder/encoder.

2. The system of claim 1, further comprising:

(e) orientation means for determining an orientation of the optically-encoded symbol and for rotating the optically-encoded symbol into a machine-readable decode orientation, wherein the matrix further includes an orientation indicator for indicating the orientation of the optically-encoded symbol.

3. The system of claim 1, wherein the optically-encoded symbol indicates exposure of the device to one of a combination of process steps or the identity or category of the molecule or biological particle.

4. The system of claim 2, wherein:

the orientation indicator of the optically-encoded symbol comprises a mechanically-detectable feature disposed on the matrix; and

the orientation means comprises a feeder means for physically rotating the recording device to position the optically-encoded symbol to the machine-readable decode orientation.

5. The system of claim 2, wherein the orientation indicator of the optically-encoded symbol comprises optically-detectable orientation indicia and the orientation means comprises software within the encoder/decoder instrument for rotating an image of the optically-encoded symbol into the machine-readable decode orientation.

6. The system of claim 5, wherein the optically-readable symbol comprises a bar code symbol comprising at least one row having a plurality of optically-contrasting lines and spaces.

7. The system of claim 6, wherein the bar code symbol is a two-dimensional bar code having a plurality of rows of optically-contrasting lines and spaces.

8. The system of claim 1, wherein the matrix material or portion thereof on which the optically-readable symbol is imprinted comprises a material selected from the group consisting of polypropylene, glass, polytetrafluoroethylene, polyethylene, high density polyethylene, polystyrene, polyester, ceramic, and composites thereof.

9. The system of claim 1, wherein the matrix material or portion on which the optically-readable symbol is imprinted comprises a ceramic.

10. The system of claim 1, wherein the one binding surface is recessed to form at least one cavity.

11. The system of claim 10, wherein the surface of the cavity is derivatized or activated to render it suitable for use a support for molecules or biological particles.

12. The system of claim 10, wherein the cavity further comprises a biological particle or molecule linked to the surface of the cavity.

13. The system of claim 10, wherein the cavity contains a plurality of matrix particles.

14. The system of claim 10, wherein the cavity is covered with a porous material that contains pores of a size that retain the matrix particles but are permeable to molecules and biological particles.

15. The system of claim 1, wherein the matrix comprises an assembly of a binding unit having the first surface and an information unit having the second surface, the information unit and the binding unit being adapted to interfit with each other.

16. The system of claim 1, wherein the encoder/decoder includes compensation software for compensating for a degraded contrast of the optically-encoded symbol.

17. The system of claim 1, wherein the optical writing means comprises a laser and the plurality of optically-contrasting symbols are formed by selectively carbonizing the write surface with a beam from the laser.

18. The system of claim 17, wherein the laser is a CO₂ laser.

19. The system of claim 1, wherein the optical detector comprises a CCD array.