Multiplex decoding of array sensors with microspheres

• US 8,460,865 B2
• Filed: 04/24/2007
• Issued: 06/11/2013
• Est. Priority Date: 06/24/1998
• Status: Expired due to Fees

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Chee, Mark S., Stuelpnagel, John R., Czarnik, Anthony W.
• Primary Examiner(s): Strzelecka, Teresa E
• Application Number:
  US11/739,668
• Publication Number:
  US 20070231824A1
• Time in Patent Office: 2,240 Days
• Field of Search: None
• US Class Current: 435/6.1
• 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 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00466 in a slurry
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00572 Chemical means
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00585 Parallel 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 2219/0061 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 2219/00619 using hydrophilic or hydrophobic regions
• 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 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• 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 2219/00677 : Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00702 : Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01L 3/5085 : for multiple samples, e.g. microtitration plates
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6816 : characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6825 : Nucleic acid detection involving sensors
• 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 2521/313 : Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2527/137 : Concentration of a component of medium
• CPC Class Codes: C12Q 2537/143 : Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2563/107 : fluorescence
• CPC Class Codes: C12Q 2563/155 : Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2563/179 : the label being a nucleic acid
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, 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 33/54313 : the carrier being characterised by its particulate form
• CPC Class Codes: Y10S 977/924 : using nanostructure as support of dna analysis

Abstract

The invention relates to compositions and methods for multiplex decoding of microsphere array sensors.

Claims

1. A method of decoding an array, said method comprising:

a) providing an array comprising a plurality of bioactive agents randomly distributed at sites of said array, wherein each of a plurality of said sites further comprises at least a first and a second identifier binding ligand (IBL);

b) detecting binding of a first decoder binding ligand (DBL) to the first IBL;

c) detecting binding of a second DBL to the second IBL; and

d) determining the location of the first and second IBLs, thereby decoding the position of one or more bioactive agents on said array; and

wherein said first IBL and said second IBL each comprise different nucleic acid sequences.

2. The method of claim 1, wherein said array comprises glass or plastic.

3. The method of claim 1, wherein said array comprises a fiber optic bundle.

4. The method of claim 1, wherein said array comprises a flat planar surface.

5. The method of claim 4, wherein said flat planar surface comprises one or more depressions.

6. The method of claim 1, wherein said plurality of bioactive agents and said first and second IBLs each comprise a nucleic acid.

7. The method of claim 6, wherein said nucleic acid is selected from the group consisting of DNA and RNA.

8. The method of claim 6, wherein said nucleic acid is single-stranded.

9. The method of claim 6, wherein said one of said first and second IBLs comprises substantially the same nucleic acid sequence as one or more bioactive agents.

10. The method of claim 1, wherein said sites of are divided into a first and a second subpopulation of sites, and wherein said first and second IBLs are attached to said first subpopulation of sites at a first ratio and are attached to said second subpopulation of sites at a second ratio.

11. The method of claim 6, wherein said nucleic acid is an oligonucleotide of about 8 to about 40 nucleotides in length.

12. The method of claim 1, wherein said DBL comprises a fluorophore.

13. The method of claim 1, wherein said sites are regularly arrayed on said array.

14. The method of claim 13, wherein said regularly arrayed sites are addressable in an X-Y format.

15. The method of claim 1, wherein said sites are depressions.

16. The method of claim 15, wherein said depressions are wells.

17. The method of claim 1, wherein step a) comprises randomly distributing said bioactive agents to an array substrate comprising an etched surface having sites.

18. The method of claim 17, wherein said sites are wells.

19. The method of claim 6, wherein said first and second IBLs each comprise a different nucleic acid sequence from said bioactive agents.

20. A method of decoding an array comprising:

a) providing an array comprising a population of microspheres randomly distributed at sites of said array, wherein each microsphere is associated with a bioactive agent, a first identifier binding ligand (IBL), and a second IBL, and wherein said first IBL and said second IBL each comprise a different nucleic acid sequence;

b) detecting binding of a first decoder binding ligand (DBL) to the first IBL;

c) detecting binding of a second DBL to the second IBL; and

d) determining the site having the microsphere comprising the first and second IBLs, thereby decoding the position of one or more bioactive agents on said array.

21. The method of claim 20, wherein said bioactive agent comprises a nucleic acid that is substantially the same as the first IBL.

22. The method of claim 20, wherein the bioactive agent comprises a nucleic acid that is different from the first IBL and the second IBL.

23. The method of claim 20, wherein the array comprises an etched surface.