Products for detecting nucleic acids

• US 6,355,432 B1
• Filed: 06/02/2000
• Issued: 03/12/2002
• Est. Priority Date: 06/07/1989
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix Lnc.
• Inventors: Solas, Dennis W., Dower, William J., Fodor, Stephen P. A.
• Primary Examiner(s): Zitomer, Stephanie W.
• Application Number:
  US09/585,659
• Time in Patent Office: 648 Days
• Field of Search: 536/23.1, 536/24.3, 435/6, 435/287.2, 435/288.3, 435/7.1, 530/300, 530/350, 530/387.1
• US Class Current: 506/9
• 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 2219/00621 : by physical means, e.g. trenches, raised areas
• 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 2219/00644 : the porous medium being present in discrete locations, e.g. gel pads
• 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: C07C 229/14 : to carbon atoms of carbon skeletons containing rings
• CPC Class Codes: C07C 229/16 : to carbon atoms of hydrocarbon radicals substituted by amino or carboxyl groups, e.g. ethylenediamine-tetra-acetic acid, iminodiacetic acids
• CPC Class Codes: C07D 263/44 : Two oxygen atoms
• CPC Class Codes: C07D 317/62 : with hetero atoms or with carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals, directly attached to atoms of the carbocyclic ring
• CPC Class Codes: C07H 19/04 : Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
• 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 1/047 : Simultaneous synthesis of different peptide species; Peptide libraries
• 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: C07K 7/06 : having 5 to 11 amino acids
• 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 2535/131 : Allele specific probes
• CPC Class Codes: C12Q 2563/149 : Particles, e.g. beads
• CPC Class Codes: C12Q 2565/626 : being a flow cytometer
• 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: G01N 21/6428 : Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/6452 : Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 21/6458 : Fluorescence microscopy fluorescence microscopes per se G02B21/0076 and G02B21/16
• 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 collection of beads comprising a plurality of beads which have binding polymers of different target specific sequence attached thereto;

said beads being coded with an encoding system whereby the target specific sequence of the polymer attached to the beads can be identified.

2. The collection of claim 1, wherein the binding polymer is an oligonucleotide having a given length and is selected from the group consisting of all possible oligonucletide sequences having t he same number of nucleotides.

3. The collection of claim 2, wherein at least about 20% of all possible oligonucleotide sequences having the same number of nucleotides are each attached to a different single bead.

4. The collection of claim 2, wherein at least about 70% of all possible oligonucleotide sequences having the same number of nucleotides are each attached to a different single bead.

5. The collection of claim 2, wherein the oligonucleotide sequences having the same number of nucleotides are at least 5 nucleotides long.

6. The collection of claim 2, wherein the oligonucleotide sequences having the same number of nucleotides are 8 nucleotides long.

7. The collection of claim 2, wherein the oligonucleotide sequences having the same number of nucleotides are 9 nucleotides long.

8. The collection of claim 2, wherein the oligonucleotide sequences having the same number of nucleotides are at least 10 nucleotides long.

9. The collection of claim 2, wherein at least 10,000 of all the possible oligonucleotide sequences having the same number of nucleotides are each attached to a different single bead.

10. The collection of claim 2, wherein at least 100,000 of all the possible oligonucleotide sequences having the same number of nucleotides are each attached to a different single bead.

11. The collection of claim 2, wherein at least 1,000,000 of all the possible oligonucleotide sequences having the same number of nucleotides are each attached to a different single bead.

12. The collection of claim 1, wherein the polymer is selected from the group consisting of polynucleotides and polypeptides.

13. The collection of claim 1, wherein the binding polymer is a protein selected from the group consisting of proteins having enzyme binding sites and proteins having antibody binding sites.

14. The collection of claim 1, wherein the beads are comprised of a glass surface and the binding polymers are attached through amines on the glass surface.

15. The collection of claim 1, wherein the beads are comprised of a surface and the binding polymers are attached th rough hydroxyl groups on the surface.

16. The collection of claim 1, wherein the binding polymers are oligodeoxyribonucleotides, a plurality of the beads are comprised of a surface and a coating of an organic hydrophilic layer terminating in hydroxl groups, and phosphates of the oligodeoxyribonucleotides are immediately linked to the hydroxyl groups.

17. The collection of claim 1, wherein the encoding system is selected from the group consisting of a magnetic system, a shape encoding system, a color encoding system, and combinations thereof.

18. The collection of claim 1, wherein the polymer attached to a single bead is an oligonucleotide probe having a given length.

19. The collection of claim 1, wherein a plurality of beads are comprised of a TEFLON copolymer graft surface and a coating of a hydrophilic organic layer terminating in hydroxyl sites.

20. The collection of claim 2, wherein a plurality of the attached oligonucleotides are comprised of at least one nucleotide analogue.

21. The collection of claim 2, wherein the plurality of different beads is reusable.

22. The collection of claim 2, wherein the given length of the oligonucleotide attached to a plurality of beads is selected from the group consisting of oligonucleotide sequences having a variable number of nucleotides.