DECODING OF ARRAY SENSORS WITH MICROSPHERES

• US 20020132221A1
• Filed: 06/24/1999
• Published: 09/19/2002
• Est. Priority Date: 06/24/1998
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: CZARNIK, ANTHONY W., CHEE, MARK S., STUELPNAGEL, JOHN R.
• Granted Patent: US 7,060,431 B2
• Time in Patent Office: Days
• US Class Current: 435/4
• 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 2219/00317 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. An array composition comprising:

a) a substrate with a surface comprising discrete sites; and

b) a population of microspheres comprising at least a first and a second subpopulation, wherein each subpopulation comprises;

i) a bioactive agent; and

ii) an identifier binding ligand that will bind a decoder binding ligand such that the identification of the bioactive agent can be elucidated;

wherein said microspheres are distributed on said surface.

3. A composition according to claim 1 or 2 further comprising at least one decoder binding ligand.

4. A composition according to claim 1 or 2 wherein said bioactive agents are nucleic acids.

5. A composition according to claim 1 or 2 wherein said bioactive agents are proteins.

2. An array composition comprising:

a) a substrate with a surface comprising discrete sites; and

b) a population of microspheres comprising at least a first and a second subpopulation, wherein each subpopulation comprises a bioactive agent and does not comprise an optical signature, wherein said microspheres are distributed on said surface.

6. A method of making a composition comprising:

a) forming a surface comprising individual sites on a substrate;

b) distributing microspheres on said surface such that said individual sites contain microspheres, wherein said microspheres comprise at least a first and a second subpopulation each comprising a bioactive agent and do not comprise an optical signature.

7. A method of making a composition comprising:

a) forming a surface comprising individual sites on a substrate;

b) distributing microspheres on said surface such that said individual sites contain microspheres, wherein said microspheres comprise at least a first and a second subpopulations each comprising;

i) a bioactive agent; and

ii) an identifier binding ligand that will bind at least one decoder binding ligand such that the identification of the bioactive agent can be elucidated.

8. A method of decoding an array composition comprising

a) providing an array composition comprising:

i) a substrate with a surface comprising discrete sites; and

ii) a population of microspheres comprising at least a first and a second subpopulation, wherein each subpopulation comprises a bioactive agent;

wherein said microspheres are distributed on said surface;

b) adding a plurality of decoding binding ligands to said array composition to identify the location of at least a plurality of the bioactive agents.

9. A method according to claim 8 wherein at least one subpopulation of microspheres comprises an identifier binding ligand to which a decoding binding ligand can bind.

10. A method according to claim 8 wherein said decoding binding ligands bind to said bioactive agents.

11. A method according to claim 8 wherein said decoding binding ligands are labeled.

12. A method according to claim 8 wherein the location of each subpopulation is determined.

17. A method according to claim 16 wherein said discrete sites comprise wells.

18. A method according to claim 16 wherein said energy is in the form of agitation.

13. A method of determining the presence of a target analyte in a sample comprising:

a) contacting said sample with a composition comprising;

i) a substrate with a surface comprising discrete sites; and

ii) a population of microspheres comprising at least a first and a second subpopulation each comprising a bioactive agent and do not comprise an optical signature;

wherein said microspheres are distributed on said surface such that said discrete sites contain microspheres; and

b) determining the presence or absence of said target analyte.

14. A method of determining the presence of a target analyte in a sample comprising:

a) contacting said sample with a composition comprising;

i) a substrate with a surface comprising discrete sites; and

ii) a population of microspheres comprising at least a first and a second subpopulation each comprising;

1) a bioactive agent; and

2) an identifier binding ligand that will bind a decoder binding ligand such that the identification of the bioactive agent can be elucidated;

wherein said microspheres are distributed on said surface such that said discrete sites contain microspheres; and

b) determining the presence or absence of said target analyte.

15. An array composition comprising:

a) a substrate with a surface comprising discrete sites;

b) a population of microspheres distributed on said sites and comprising at least a first and a second subpopulation, each subpopulation comprising a bioactive agent, wherein said first subpopulation comprises at least a first optical dye with a first pKa and said second subpopulation comprises at least a second optical dye with a second pKa, wherein said first and second pKas are different.

16. A method of making a microsphere array comprising:

a) contacting a substrate with a surface comprising discrete sites with a solution comprising a population of particles; and

b) applying energy to said substrate or said solution, or both, such that at least a subpopulation of said particles associate onto sites.