Decoding of array sensors with microspheres

• US 7,033,754 B2
• Filed: 12/22/2000
• Issued: 04/25/2006
• Est. Priority Date: 06/24/1998
• Status: Expired due to Term

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Czarnik, Anthony W., Chee, Mark S., Stuelpnagel, John R.
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US09/748,706
• Publication Number:
  US 20050233318A1
• Time in Patent Office: 1,950 Days
• Field of Search: 435/6, 435/7, 435/174, 435/283.1, 435/287.2, 435/288.4, 435/288.7, 422/68.1, 536/24.3, 530/350
• US Class Current: 506/17
• 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 decoding microsphere array sensors.

Claims

1. A method of decoding the position of bioactive agents attached to microspheres on an array substrate comprising:

a) providing an array substrate comprising a population of microspheres comprising at least a first and a second subpopulation, wherein the microspheres of each subpopulation comprise;

i) a bioactive agent;

ii) at least a first and a second identifier binding ligand (IBL), wherein said first and second IBLs are different from said bioactive agent and wherein said IBLs are attached to each microsphere; and

b) detecting both the first and second IBLs to decode the position of each of said bioactive agents on said substrate.

2. The method according to claim 1, wherein said detecting comprises detecting binding of a first decoder binding ligand (DBL) to said first IBL and a second decoder binding ligand to said second IBL.

3. The method according to claim 1, wherein said first and second IBLs comprise a nucleic acid.

4. The method according to claim 1, wherein said first and second IBLs are attached to said first subpopulation of microspheres at a first ratio and are attached to said second population of microspheres at a second ratio.

5. A method of decoding the position of a bioactive agent on an array substrate comprising:

a) providing an array substrate comprising randomly distributed microspheres, wherein each microsphere comprises;

i) a bioactive agent; and

ii) a combination of different identifier binding ligands (IBLs),

wherein said combination uniquely identifies said bioactive agent;

b) adding a first decoder binding ligand (DBL) to the array substrate, wherein the first DBL binds to an IBL in said combination;

c) identifying the position of the IBL that binds to the first DBL;

d) adding a second DBL to the array, wherein the second DBL binds to another IBL in said combination;

e) identifying the position of the IBL that binds to the second DBL; and

f) decoding the position of said bioactive agent on said array substrate based on the position on the array substrate of the IBLs that bind the first and the second DBLs.

6. The method of claim 5, wherein said combination of IBLs and said first and second DBLs each comprise single strand nucleic acid.

7. The method of claim 6, wherein said nucleic acid is DNA.

8. The method of claim 6, wherein said nucleic acid is RNA.

9. The method of claim 6, wherein said combination of IBLs and said first and second DBLs are oligonucleotides of about 8 to about 40 basepairs in length.

10. The method of claim 5, wherein said microspheres comprise 10 IBLs.

11. The method of claim 5, wherein said first DBL binds to said IBL with a dissociation constant of less than about 10⁻

5–

10<sup>−

9</sup> M<sup>−

1</sup>.

12. The method of claim 5, wherein said second DBL binds to said IBL with a dissociation constant of less than about 10⁻

510<sup>−

9</sup> M<sup>−

1</sup>.

13. The method of claim 5, wherein said first and second DBLs comprise a fluorophore.