Remotely programmable matrices with memories

• US 6,416,714 B1
• Filed: 06/07/1995
• Issued: 07/09/2002
• Est. Priority Date: 04/25/1995
• Status: Expired due to Term

• Current Assignee: Irori Technologies Incorporated
• Original Assignee: Discovery Partners International, Inc. (Infinity Pharmaceuticals, Inc.)
• Inventors: Nova, Michael P., Senyei, Andrew E.
• Primary Examiner(s): ZITOMER, STEPHANIE W
• Application Number:
  US08/484,486
• Time in Patent Office: 2,589 Days
• Field of Search: 435/6, 435/5, 435/7--, 436/501, 436/182, 436/183, 436/518, 436/578, 436/523, 436/524, 436/525, 436/526, 436/527, 436/528, 340/572, 336/24-- 2, 422/68.1, 422/50, 422/57, 422/58, 422/82.05, 422/99, 422/102, 422/104, 530/334, 530/333, 530/335, 530/388.1, 364/496, 364/497, 364/498, 364/499, 257/225, 257/390, 395/430, 438/131
• US Class Current: 506/39
• 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 2219/00344 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 2219/00549 2-dimensional
• CPC Class Codes: B01J 2219/00551 3-dimensional
• CPC Class Codes: B01J 2219/0056 Raised or sunken areas
• CPC Class Codes: B01J 2219/00567 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: 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 with remotely addressable or remotely programmable recording devices that contain at least one data storage unit 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 data storage units are preferably non-volatile antifuse memories. 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, chemical modification and other uses.

Claims

1. A method for electromagnetically tagging molecules or biological particles, comprising:

(a) contacting the molecules or biological particles with a combination, wherein;

the combination comprises;

(A) a recording device, comprising a data storage unit; and

(B) a matrix

the biological particles comprise a virus, viral vector, viral capsid with or without packaged nucleic acid, phage, phage vector or phage casid with or without encapsulated nucleic acid, a eukaryotic or prokaryotic cell or fragments of the virus, viral capsid, phage, phage capsid or cell;

the molecules comprise macromolecules or monomeric constituents of macromolecules or organic compounds;

the matrix is either comprised of particles of a size such that at least one dimension is no more than 100 mm or the matrix material is in the form of a container selected from the group consisting of vials, test tubes, culture dishes, vessels of a volume of about 100 ml or less, and microtiter plates;

the recording device is in contact with the matrix or is in a solution that is in contact with the matrix; and

the contacting is effected by placing the molecules in proximity to the combination or by placing the combination in physical contact with the molecules or biological particles;

(b) storing identifying information in the data storage unit of the recording device or reading identifying information in the data storage unit, wherein the information identifies the molecules or biological particles;

(c) repeating steps (a) and (b) once or a plurality of times;

, and then;

(d) separating the combinations from each other, individually exposing the combinations to electromagnetic signals, reading stored information.

11. The method of claim 1, wherein the signals are radiofrequency signals.

2. A method for electromagnetically tagging a support matrix, comprising:

contacting the support matrix with a recording device, wherein;

the contact may be direct or may be effected indirectly, and the matrix is in the form of a substantially continuous sheet or in the form of a container selected from the group consisting of vials, test tubes, culture dishes, vessels of a volume of about 100 ml or less, and microtiter plates; and

entering information or reading information that identifies molecules or biological particles that are linked to or proximate to the support matrix into the the recording device;

the biological particles comprise a virus, viral vector, viral capsid with or without packaged nucleic acid, phage, phage vector or phage capsid with or without encapsulated nucleic acid, a eukaryotic or prokaryotic cell or fragments of the virus, viral capsid, phage, phage capsid or cell; and

the molecules comprise macromolecules or monomeric constituents of macromolecules or organic compounds.

3. The method of claim 2, wherein:

the recording device comprises a data storage unit comprising a non-volatile memory means for storing a plurality of data points and means for receiving a transmitted electromagnetic signal so that a write signal causes a stored data point corresponding to the data signal to be stored within the non-volatile memory means.

4. A method for electromagnetically tagging a support matrix, comprising:

(a) contacting the support matrix with a memory device, wherein;

the contact may be direct or may be effected indirectly;

(b) storing information that identifies molecules or biological particles that are linked to or proximate to the support matrix in the memory, wherein;

the biological particles comprise a virus, viral vector, viral capsid, with or without packaged nucleic acid, phage, phage vector or phage capsid with or without encapsulated nucleic acid, a eukaryotic or prokaryotic cell or fragments or the virus, viral capsid, phage, phage capsid or cell;

the molecules comprise macromolecules or monomeric constituents of macromolecules or organic compounds; and

the memory device includes an optical recording medium.

5. The method of claim 4, wherein the optical recording medium is for storing a plurality of data points and comprises means for receiving a projected optical signal comprising a first intensity for forming a plurality of spectral holes in the optical recording medium, wherein each spectral hole of the plurality of spectral holes corresponds to a stored data point.

12. The method of claim 5, wherein the projected optical signal has a second intensity for reading the stored data point by detecting the presence of each spectral hole in the optical recording medium.

13. The method of claim 4, wherein:

steps (a) and (b) are repeated once or a plurality of times; and

the combinations are separated from each other, and stored information is read.

6. A method for identifying and tracking molecules and biological particles, comprising:

(a) providing at least one recording device that is linked to, in contact with, or in proximity to, a molecule or biological particle;

(b) programming the recording device with;

(i) one or more indicators representative of the identity of the molecule or biological particle;

(ii) one or more indicators representative of physical or chemical properties of the molecule or biological particle

(c) retrieving the at least one recording device and linked, contacted or proximate molecule or biological particle, individually exposing the at least one recording device to an electromagnetic signal, and reading stored information, thereby determining the identity of and tracking the molecule or biological particle linked, contacted or proximate to the recording device, wherein;

the biological particles comprise a virus, viral vector, viral capsid, with or without packaged nnucleic acid, phage, phage vector or phage capsid with or without encapsulated nucleic acid, a eukaryotic or prokaryotic cell or fragments or the virus, viral capsid, phage, phage capsid or cell; and

the molecules comprise macromolecules or monomeric constituents of macromolecules or organic compounds.

7. The method of claim 6, wherein programming is effected by:

exposing the recording device to electromagnetic radiation; and

transmitting to a host computer or decoder/encoder instrument the indicator(s) representative of the identity of the molecule or biological particle, or physical or chemical properties of the molecule or biological particle, or other identifying information for tracking and identifying the molecule or biological particle.

8. The method of claim 6, further comprising reading the information in each memory and separating the devices and linked or proximate molecules and biological particles.

14. The method of claim 6, wherein a plurality of recording devices are provided;

and the method further comprises, after the retrieving in step (c);

separating the devices and linked, contacted or proximate molecules or biological particles from each other, and individually exposing each recording device to an electromagnetic signal, and reading the stored information, thereby determining the identity of and tracking the molecules or biological particles.

9. A method for tracking molecules or biological particles, comprising:

(a) labeling the molecules or biological particles with electromagnetic tags comprising recording devices, wherein each tag comprises data identifying said molecules or biological particles, and each tag is proximate to or linked directly or indirectly to the molecules or biological particles;

(b) separating the tags and linked or proximate molecules or biological particles;

(c) individually exposing each tag to an electromagnetic signal, and reading data stored in memory thereby tracking said molecules or biological particles;

wherein the biological particles comprise a virus, viral vector, viral capsid, with or without packaged nucleic acid, phage, phage vector or phage capsid with or without encapsulated nucleic acid, a eukaryotic or prokaryotic cell or fragments or the virus, viral capsid, phage, phage capsid cell; and

the molecules comprise macromolecules or monomeric constituents of macromolecules or organic compounds.

10. The method of claim 9, wherein labeling of the molecules is effected during synthesis of the molecules.