Multiplex decoding of array sensors with microspheres

• US 8,795,967 B2
• Filed: 05/13/2013
• Issued: 08/05/2014
• Est. Priority Date: 06/24/1998
• Status: Expired due to Term

• 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:
  US13/893,273
• Publication Number:
  US 20130310280A1
• Time in Patent Office: 449 Days
• Field of Search: None
• US Class Current: 435/6.11
• 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 system for decoding the position of one or more bioactive agents on an array, comprising:

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), wherein said first IBL and said second IBL each comprise different nucleic acid sequences;

a first decoder binding ligand (DBL) adapted to bind to the first IBL, wherein binding of the first DBL with the first IBL comprises a detectable signal indicative of the location of the first IBL;

a second DBL adapted to bind to the second IBL, wherein binding of the second DBL with the second IBL comprises a detectable signal indicative of the location of the second IBL; and

wherein the location of the first and second IBLs is indicative of the position of one or more bioactive agents on said array.

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

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

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

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

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

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

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

9. The system of claim 1, wherein one of said first and second IBLs comprises substantially the same nucleic acid sequence as one or more bioactive agents.

10. The system of claim 1, wherein the first IBL and the second IBL each comprise different nucleic acid sequences.

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

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

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

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

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

16. The system of claim 1, wherein said sites are wells.

17. The system of claim 1, wherein said first and second IBLs each comprise a different nucleic acid sequence from said bioactive agents.

18. The system of claim 1, wherein the first DBL is bound to the first IBL.

19. The system of claim 1, wherein a plurality of particles are randomly distributed at sites of said array, wherein each particle is associated with a bioactive agent, a first IBL and a second IBL.

20. The system of claim 19, wherein the particle is a microsphere.

22. The system of claim 20, wherein a plurality of particles are randomly distributed at sites of said array, wherein each particle is associated with a bioactive agent, a first IBL and a second IBL.

21. A system for determining the presence of a target analyte in a sample, comprising:

an array comprising a plurality of bioactive agents randomly distributed at sites of said array, wherein binding of a target analyte to said bioactive agent comprises a detectable signal;

at least a first and a second identifier binding ligand (IBL) at each of a plurality of said sites, wherein said first IBL and said second IBL each comprise different nucleic acid sequences;

a first decoder binding ligand (DBL) adapted to bind to the first IBL, wherein binding of the first DBL with the first IBL comprises a detectable signal indicative of the location of the first IBL;

a second DBL adapted to bind to the second IBL, wherein binding of the second DBL with the second IBL comprises a detectable signal indicative of the location of the second IBL; and

wherein the location of the first and second IBLs is indicative of the position of one or more bioactive agents on said array, wherein said first and second IBLs identify the one or more bioactive agents on said array such that the presence of an analyte can be determined.