Method for marking samples

• US 6,544,739 B1
• Filed: 06/02/2000
• Issued: 04/08/2003
• Est. Priority Date: 12/06/1990
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Solas, Dennis W., Dower, William J., Fodor, Stephen P. A.
• Primary Examiner(s): ZITOMER, STEPHANIE W
• Application Number:
  US09/585,556
• Time in Patent Office: 1,040 Days
• Field of Search: 435/6, 435/91.2, 435/287.2, 435/288.3, 435/288.7, 435/287.9, 435/252.3, 435/325, 435/419, 530/300, 530/350, 530/387.1, 536/23.1, 536/24.3
• 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 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00434 Liquid crystal masks
• CPC Class Codes: B01J 2219/00436 Maskless processes
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/00475 Sheets
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00531 essentially square
• 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 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 : Covalent
• CPC Class Codes: B01J 2219/0063 : Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 : by coating it with another layer
• CPC Class Codes: B01J 2219/00641 : the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00648 : by the use of solid beads
• CPC Class Codes: B01J 2219/00659 : Two-dimensional arrays
• 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 2219/00711 : Light-directed synthesis
• 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: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• 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: C07K 1/042 : characterised by the nature of the carrier
• CPC Class Codes: C07K 1/045 : using devices to improve synthesis, e.g. reactors, special vessels
• CPC Class Codes: C07K 17/06 : attached to the carrier via a bridging agent
• CPC Class Codes: C07K 17/14 : Peptides being immobilised on, or in, an inorganic carrier
• CPC Class Codes: C12Q 1/6804 : Nucleic acid analysis using immunogens immunoassay G01N33/53
• CPC Class Codes: C12Q 1/6809 : Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6816 : characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6827 : for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6834 : Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6874 : involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/151 : repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2525/179 : incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2525/185 : incorporating bases where the precise position of the bases in the nucleic acid string is important
• CPC Class Codes: C12Q 2525/204 : specific length of the oligonucleotides
• CPC Class Codes: C12Q 2545/101 : with an internal standard/control
• CPC Class Codes: C12Q 2563/119 : the label being proteinic
• CPC Class Codes: C12Q 2563/149 : Particles, e.g. beads
• CPC Class Codes: C12Q 2563/173 : staining/intercalating agent, e.g. ethidium bromide
• CPC Class Codes: C12Q 2565/507 : characterised by the density of the capture oligonucleotide
• CPC Class Codes: C12Q 2565/513 : characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C12Q 2565/514 : characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• 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: G01N 15/1433 : using image recognition
• CPC Class Codes: G03F 7/00 : Photomechanical, e.g. photolithographic, production of textured or patterned surfaces, e.g. printing surfaces; Materials therefor, e.g. comprising photoresists; Apparatus specially adapted therefor using photoresist structures for special production processes, see the relevant places, e.g. B44C, H01L, e.g. H01L21/00, H05K
• CPC Class Codes: G03F 7/265 : Selective reaction with inorganic or organometallic reagents after image-wise exposure, e.g. silylation
• CPC Class Codes: G03F 7/38 : Treatment before imagewise removal, e.g. prebaking G03F7/265 takes precedence
• CPC Class Codes: G11C 13/0014 : comprising cells based on organic memory material
• CPC Class Codes: G11C 13/0019 : comprising bio-molecules

Abstract

The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.

Claims

1. A method of identifying or distinguishing between different biological materials comprising:

(a) providing a plurality of marker polymers, each of which comprises a different and unique determinable polymer sequence;

(b) combining a different marker polymer with a unique determinable polymer sequence with each different biological material; and

(c) identifying a biological material by determining the polymer sequence of the marker for said material.

2. The method of claim 1, wherein each marker polymer consists essentially of between 10 and 1000 molecules of polymer.

3. The method of claim 1, wherein the marker polymers are nucleic acids and the polymer sequences are nucleotide sequences.

4. The method of claim 3 wherein the nucleic acids are amplified prior to sequence determination.

5. The method of claim 1, wherein the marker polymer does not have biological activity.

6. The method of claim 1, wherein each marker polymer consists essentially of between 10 and 100 molecules of polymer.

7. The method of claim 1, wherein each marker polymer consists essentially of between 100 and 1000 molecules of polymer.

8. The method of claim 1, wherein the marker polymer comprises nucleic acid and the unique determinable sequence is a nucleotide sequence which further identifies the manufacturer of the biological material.

9. The method of claim 1, wherein the marker polymer comprises nucleic acid and the unique determinable sequence is a nucleotide sequence which futher identifies the date of manufacture of the biological material.

10. The method of claim 1, wherein the marker polymer comprises nucleic acid and the unique determinable sequence is a nucleotide sequence which further identifies the location of manufacture of the biological material.

11. The method of claim 1 wherein the marker polymer comprises a polypeptide, carbohydrate or nucleic acid.

12. A method of identifying a biological material by determining complementarity of a nucleic acid marker combined with said biological material comprising:

(a) providing a substrate having attached thereto a plurality of different nucleic acid probes in positionally determinable locations wherein at least some of the probes are complementary to the nucleic acid marker;

(b) applying said material with its nucleic acid marker to the probes under hybridization conditions; and

(c) determining complementarity of the nucleic acid marker to at least some of the plurality of different probes in the positionally determinable locations and thereby identifying said biological material.

13. The method of claim 12, wherein the substrate is glass.

14. The method of claim 12, wherein the substrate comprises beads.

15. The method of claim 12, wherein the substrate comprises fibers.

16. The method of claim 12, wherein the substrate comprises glass surfaces and the probes are attached to the glass surfaces by amine groups on said surfaces.

17. The method of claim 12, wherein the probes are attached to the substrate through hydroxyl groups on the substrate.

18. The method of claim 12, wherein the substrate comprises beads, each of which has a surface with an organic hydrophilic layer thereon terminating in hydroxyl groups, the probes are linked to said hydroxyl groups through nucleic acid phosphates, and each nucleic acid probe comprises a different and unique determinable nucleotide sequence.

19. A method of identifying different biological entities comprising:

(a) providing a plurality of markers, each of which comprises a different and unique nucleic acid sequence;

(b) combining each biological entity with a different marker having a unique and determinable nucleic acid sequence; and

(c) identifying a biological entity by determining the identity of the unique nucleic acid sequence of the marker for said entity.

20. The method of claim 19 wherein combining comprises attaching each marker to a different biological entity.

21. The method of claim 19 wherein the biological entity is a bacterium, a plant or an animal.

22. The method of claim 19, wherein the identifying step comprises providing a glass substrate having a plurality of nucleic acid probes attached thereto and contacting said biological entity with said probes under hybridization conditions.

23. The method of claim 19, wherein the identifying step comprises providing beads having a plurality of nucleic acid probes attached thereto, and contacting said biological entity with said probes under hybridization conditions.

24. The method of claim 19, wherein the identifying step comprises providing fibers having a plurality of nucleic acid probes attached thereto, and contacting said biological entity with said probes under hybridization conditions.

25. The method of claim 19 wherein combining the biological entity with said marker comprises transforming the biological entity with the marker.