Nanoarrays and methods of use thereof

1. A solid support comprising two or more wells, wherein each well is separated by about 0.2 μm to about 2.0 μm from any adjacent well and each well comprises at least one particle, said particle comprising a plurality of oligonucleotide moieties covalently attached to said particle via a bioconjugate linker, wherein the bioconjugate linker is formed via a reaction between a particle polymer comprising a first bioconjugate reactive moiety and an oligonucleotide comprising a second bioconjugate reactive moiety, and wherein the average longest dimension of the particle is from about 100 nm to about 1000 nm, wherein

said solid support comprises a polymer layer comprising polymerized units of alkoxysilyl methacrylate, alkoxysilyl acrylate, alkoxysilyl methylacrylamide, alkoxysilyl acrylamide, or a copolymer thereof.

2. The solid support of claim 1 , wherein the solid support comprises a photoresist, wherein the photoresist is a silsesquioxane resist, an epoxy-based polymer resist, poly(vinylpyrrolidone-vinyl acrylic acid) copolymer resist, an Off-stoichiometry thiol-enes (OSTE) resist, amorphous fluoropolymer resist, a crystalline fluoropolymer resist, polysiloxane resist, or a organically modified ceramic polymer resist.

3. The solid support of claim 1 , wherein the particle comprises silica, glass, ceramic, metal, magnetic material, or a paramagnetic material.

4. The solid support of claim 1 , wherein the particle polymer comprises polymerized units of polyacrylamide (AAm), poly-N-isopropylacrylamide, poly N-isopropylpolyacrylamide, sulfobetaine acrylate (SBA), carboxybetaine acrylate (CBA), phosphorylcholine acrylate (PCA), sulfobetaine methacrylate (SBMA), carboxybetaine methacrylate (CBMA), phosphorylcholine methacrylate (PCMA), polyethylene glycol acrylate, methacrylate, polyethylene glycol (PEG)-thiol/PEG-acrylate, acrylamide/N,N′-bis(acryloyl)cystamine (BACy), PEG/polypropylene oxide (PPO), polyacrylic acid, poly(hydroxyethyl methacrylate) (PHEMA), poly(methyl methacrylate) (PMMA), poly(N-isopropylacrylamide) (PNIPAAm), poly(lactic acid) (PLA), poly(lactic-co-glycolic acid) (PLGA), polycaprolactone (PCL), poly(vinylsulfonic acid) (PVSA), poly(L-aspartic acid), poly(L-glutamic acid), polylysine, agar, agarose, alginate, heparin, alginate sulfate, dextran sulfate, hyaluronan, pectin, carrageenan, gelatin, chitosan, cellulose, collagen, glicydyl methacrylate (GMA), glicydyl methacrylate (GMA) azide, hydroxyethylmethacrylate (HEMA), hydroxyethylacrylate (HEA), hydroxypropylmethacrylate (HPMA), polyethylene glycol methacrylate (PEGMA), polyethylene glycol acrylate (PEGA), isocyanatoethyl methacrylate (IEM), or a copolymer thereof.

5. The solid support of claim 1 , wherein the particle polymer comprises polymerized units of polyacrylamide (AAm), glicydyl methacrylate (GMA), glicydyl methacrylate (GMA) azide, polyethylene glycol methacrylate (PEGMA), polyethylene glycol acrylate (PEGA), isocyanatoethyl methacrylate (IEM), or a copolymer thereof.

6. The solid support of claim 1 , wherein the particle polymer comprises polymerized units of a) polyethylene glycol methacrylate (PEGMA) and glicydyl methacrylate (GMA), b) polyethylene glycol methacrylate (PEGMA) and isocyanatoethyl methacrylate (IEM), or c) polyethylene glycol methacrylate (PEGMA) and glicydyl methacrylate (GMA) azide.

7. The solid support of claim 1 , wherein the particle is a polymeric particle comprising polymerized units of polyacrylamide (AAm), poly-N-isopropylacrylamide, poly N-isopropylpolyacrylamide, sulfobetaine acrylate (SBA), carboxybetaine acrylate (CBA), phosphorylcholine acrylate (PCA), sulfobetaine methacrylate (SBMA), carboxybetaine methacrylate (CBMA), phosphorylcholine methacrylate (PCMA), polyethylene glycol acrylate, methacrylate, polyethylene glycol (PEG)-thiol/PEG-acrylate, acrylamide/N,N′-bis(acryloyl)cystamine (BACy), PEG/polypropylene oxide (PPO), polyacrylic acid, poly(hydroxyethyl methacrylate) (PHEMA), poly(methyl methacrylate) (PMMA), poly(N-isopropylacrylamide) (PNIPAAm), poly(lactic acid) (PLA), poly(lactic-co-glycolic acid) (PLGA), polycaprolactone (PCL), poly(vinylsulfonic acid) (PVSA), poly(L-aspartic acid), poly(L-glutamic acid), polylysine, agar, agarose, alginate, heparin, alginate sulfate, dextran sulfate, hyaluronan, pectin, carrageenan, gelatin, chitosan, cellulose, collagen, glicydyl methacrylate (GMA), hydroxyethylmethacrylate (HEMA), hydroxyethylacrylate (HEA), hydroxypropylmethacrylate (HPMA), polyethylene glycol methacrylate (PEGMA), polyethylene glycol acrylate (PEGA), isocyanatoethyl methacrylate (IEM), or a copolymer thereof.

8. The solid support of claim 1 , wherein the solid support further comprises an amphiphilic copolymer layer.

9. The solid support of claim 8 , wherein the amphiphilic copolymer comprises a poloxamer.

10. The solid support of claim 8 , wherein the amphiphilic copolymer comprises a brush copolymer or a comb polymer.

11. The solid support of claim 1 , wherein the average longest dimension of the particle is from about 150 nm to about 600 nm.

12. The solid support of claim 1 , wherein the average longest dimension of the particle is from about 350 nm to about 600 nm.

13. The solid support of claim 1 , wherein the average longest dimension of the particle is from about 400 nm to about 500 nm.

14. The solid support of claim 1 , wherein the solid support comprises about 1×10 5 to about 5×10 10 wells.

15. The solid support of claim 1 , wherein the wells are separated from each other by about 0.5 μm to about 2.0 μm.

16. The solid support of claim 1 , wherein the wells are from about 0.2 μm to about 2 μm in diameter, and wherein the wells are about 0.5 μm to about 2 μm in depth.

17. The solid support of claim 14 , wherein greater than 50%, 60%, 70%, 80%, 90% or 95% of the wells comprise a particle.

18. The solid support of claim 1 , wherein each of the particles comprise at least two populations of substantially the same oligonucleotide moieties.

19. The solid support of claim 1 , wherein each of the oligonucleotide moieties is capable of hybridizing to a complementary sequence of a template nucleic acid.

20. A method of amplifying a target polynucleotide, the method comprising: contacting the solid support of claim 1 with a sample comprising a target polynucleotide; and amplifying the target polynucleotide to produce an amplification product, wherein amplifying comprises hybridizing an oligonucleotide moiety of said plurality of oligonucleotide moieties and extending the oligonucleotide moiety hybridized to the target polynucleotide.