OLIGONUCLEOTIDE ENCODED CHEMICAL LIBRARIES

1 . A system for screening chemical compounds, comprising:

(a) A picowell array plate comprising a plurality of picowells, wherein each picowell has a top aperture that defines an opening at the top of the picowell, a bottom that is defined by a floor, wherein the top aperture is separated by a wall from the floor, and wherein the wall resides in between the top aperture and the floor,

(b) A bead disposed in a picowell, wherein the bead comprises a plurality of substantially identical bead-bound DNA barcodes, and a plurality of substantially identical bead-bound compounds,

(c) Wherein the bead comprises a bead-bound DNA barcode that takes the form of either a concatenated DNA barcode or an orthogonal DNA barcode, and wherein if the DNA barcode takes the form of a concatenated DNA barcode the concatenated DNA barcode is made by a method that uses one or both of:

(i) Uses click chemistry, or

(ii) Uses a repeating cycle of steps, wherein the repeating cycle of steps comprises using a splint oligonucleotide (splint oligo) that is capable of hybridizing to a partially made bead-bound DNA barcode, and wherein the hybridizing is mediated by an annealing site on the splint oligo and a corresponding, complementary annealing site in the partially made bead-bound DNA barcode,

wherein the annealed splint oligo is used as a template for extending the partially made DNA barcode using DNA polymerase, and wherein the splint oligo contains bases that are complementary to a DNA barcode module that is to be polymerized to the partially made bead-bound DNA barcode, and wherein the splint oligo also contains bases that are complementary to an annealing site that is to be polymerized to the partially made bead-bound DNA barcode, and

(d) Wherein each one of the plurality of substantially identical bead-bound compounds comprises one or more chemical library monomers, and wherein each bead-bound DNA barcode module identifies a corresponding chemical library monomer, wherein the term “compound” is used to refer to a completed product that comprises one or more chemical library members, and wherein the completed DNA barcode identifies the compound.

2 . The system of claim 1 , further comprising an oligonucleotide sequencing primer that is capable of guiding the sequencing of one or more DNA barcode modules that is comprised by a bead-bound DNA barcode, where optionally the system comprises a DNA sequencing machine, and where the DNA sequencing machine is not a luminescence-based sequencer and not a pH-based DNA sequencing machine.

3 . The system of claim 1 , further comprising a plurality of spherical caps, wherein each cap is capable of fitting into the aperture of a picowell wherein the aperture is circular, and each cap is capable of minimizing or preventing evaporation of fluid that is inside of the picowell, and each cap is capable of minimizing or preventing leakage of fluid that is inside of the picowell.

4 . The system of claim 1 , wherein the at least one bead disposed in the at least one picowell comprises at least one response capture element that is coupled to said at least one bead.

5 . The system of claim 1 , wherein the at least one of the a bead disposed in a picowell comprises at least one response capture element that is coupled to said at least one bead, wherein the at least one response capture element comprises:

(a) Poly(dT);

(b) An exon-targeting RNA probe;

(c) An antibody; or

(d) An aptamer.

6 . The system of claim 1 , wherein the DNA barcode is either a concatenated DNA barcode or an orthogonal DNA barcode, and wherein the DNA barcode comprises one or more DNA barcode modules, wherein each of the one or more DNA barcode modules encodes information that identifies a chemical library monomer, and wherein the concatenated DNA barcode or the orthogonal DNA barcode further includes one or both of:

(a) One or more functional nucleic acids; and

(b) One or more nucleic acids that encode information of a type other than the identity of a chemical library monomer.

7 . The system of claim 1 , wherein the bead-bound concatenated DNA barcode comprises:

(i) a 1 st DNA barcode module; or

(i) a 1 st DNA barcode module, a 1 st annealing site, and a 2 nd DNA barcode module; or

(ii) a 1 st DNA barcode module, a 1 st annealing site, a 2 nd DNA barcode module, a 2 nd annealing site, and a 3 rd DNA barcode module; or

(iii) a 1 st DNA barcode module, a 1 st annealing site, a 2 nd DNA barcode module, a 2 nd annealing site, a 3 rd DNA barcode module, a 3 rd annealing site, and a 4 th DNA barcode module; or

(iv) a 1 st DNA barcode module, a 1 st annealing site, a 2 nd DNA barcode module, a 2 nd annealing site, a 3 rd DNA barcode module, a 3 rd annealing site, a 4 th DNA barcode module, a 4 th annealing site, and a 5 th DNA barcode module; or

(v) a 1 st DNA barcode module, a 1 st annealing site, a 2 nd DNA barcode module, a 2 nd annealing site, a 3 rd DNA barcode module, a 3 rd annealing site, a 4 th DNA barcode module, a 4 th annealing site, a 5 th DNA barcode module, a 5 th annealing site, and a 6 th DNA barcode module.

8 . The system of claim 1 , wherein the bead comprises a DNA barcode that is an orthogonal DNA barcode, wherein the bead comprises an external surface, and wherein the orthogonal DNA barcode comprises:

(a) A first nucleic acid that comprises a first DNA barcode module and an annealing site for a sequencing primer, wherein the first nucleic acid is coupled to the bead at a first position,

(b) A second nucleic acid that comprises a second DNA barcode module and an annealing site for a sequencing primer, wherein the second nucleic acid is coupled to the bead at a second position, and

(c) A third nucleic acid that comprises a third DNA barcode module and an annealing site for a sequencing primer, wherein the second nucleic acid is coupled to the bead at a third position, and

wherein the first, second, and third position on the bead are each located at different location on the bead's external surface.

9 . The system of claim 1 , wherein the concatenated DNA barcode is made by a method that uses:

(i) Both click chemistry and the repeating cycle of steps that uses the splint oligo;

(ii) Both click chemistry and chemical methods that are not click chemistry methods;

(iii) Only click chemistry; or

(iv) Only the repeating cycle of steps that uses the splint oligo.

10 . The system of claim 1 , wherein each of the plurality of substantially identical bead-bound compounds is coupled to the bead by way of a cleavable linker, or by way of a cleavable linker that is a light-cleavable linker, or by way of a non-cleavable linker.

11 . The system of claim 1 , wherein the at least one bead comprises grafted copolymers consisting of a low crosslinked polystyrene matrix on which polyethylene glycol (PEG) is grafted.

12 . The system of claim 1 , wherein at least one picowell comprises at least one cell,

wherein the plurality of substantially identical bead-bound compounds are bound to the at least one bead by way of a cleavable linker, and wherein cleaving the cleavable linker releases the bead-bound compound from the bead to produce a released compound, and

wherein the released compound is capable of contacting the at least one cell, and wherein the at least one cell is:

(i) a mammalian cell that is not a cancer cell,

(ii) a mammalian cancer cell,

(iii) a dead mammalian cell,

(iv) an apoptotic mammalian cell,

(v) a necrotic mammalian cell,

(vi) a bacterial cell,

(vii) a plasmodium cell,

(vii) a cell that is metabolically active but has a cross-linked genome and is unable to undergo cell division, or

(ix) a mammalian cell that is infected with a virus.

13 . The system of claim 1 , wherein each picowell has a top aperture that defines an opening at the top of the picowell, a bottom that is defined by a floor, wherein the top aperture is separated from the floor, and wherein a wall resides in between the top aperture and the floor, and

wherein the aperture is round, wherein the floor is round, and wherein the wall takes the form of a truncated cone, and wherein the aperture has a first diameter, the floor has a second diameter, and wherein the first diameter is greater than the second diameter.

14 . The system of claim 1 , wherein each picowell has a top aperture that defines an opening at the top of the picowell, a bottom that is defined by a floor, wherein the top aperture is separated from the floor, and wherein a wall resides in between the top aperture and the floor, and

wherein the aperture is round, wherein the floor is round, and wherein the wall takes the form of a truncated cone, and wherein the aperture has a first diameter, the floor has a second diameter, and wherein the first diameter is greater than the second diameter,

further comprising a cap that snuggly fits into the aperture, wherein the aperture is comprised by a polymer having a greater durometer (harder) and wherein the cap is made of a polymer having a lesser durometer (softer), and wherein the relative durometers of the cap and aperture allow the cap to be reversibly and snuggly fit into the aperture, and

wherein the cap is:

(i) a cap intended only to plug the picowell and prevent leakage,

(ii) a cap that is a passive cap and that is capable of absorbing metabolites that are released by a cell, in the situation where a cell in a cell medium is cultured in the picowell,

(iii) a cap that is an active cap, and that takes the form of a bead that comprises a plurality of essentially identical compounds, and

wherein each of the plurality of essentially identical compounds is coupled to the bead with a cleavable linker;

(iv) a cap that is an active cap, and that takes the form of a bead that comprises a plurality of identical reagents, and wherein each of the plurality of essentially identical reagents is coupled to the bead with a cleavable linker.

15 . The system of claim 14 , further comprising at least one spherical cap.

16 . The system of claim 14 , further comprising at least one non-spherical cap.

17 . The system of claim 1 , wherein the DNA barcode comprises one or more nucleic acids that do not encode any chemical monomer but instead identify one or more of:

(a) The class of chemical compounds that is cleavably attached to the bead;

(b) The step in a multi-step pathway of organic synthesis, wherein a bead-bound nucleic acid corresponds to a given chemical monomer that is used to make a bead-bound compound, and wherein the bead-bound nucleic acid that corresponds to a given chemical monomer identifies that chemical monomer;

(c) The date that the bead-bound compound was synthesized;

(d) The disease that the bead-bound compound is intended to treat;

(e) The cellular event that the bead-bound compound is intended to stimulate or inhibit; or

(f) The reaction conditions that were used to couple a given chemical library monomer to the bead.

18 . The system of claim 1 , wherein there does not exist any headpiece that links any of the bead-bound compounds to any of the bead-bound DNA barcodes.

19 . The system of claim 1 , wherein the concatenated DNA barcode comprises at least one nucleic acid that is a DNA barcode module, and at least one functional nucleic acid that:

(a) Is capable of being used as an annealing site for a sequencing primer,

(b) Is capable of forming a hairpin structure, and wherein the hairpin structure comprises a sequencing primer, an annealing site for the sequencing primer, and a bend in the hairpin structure wherein the bend is 5-prime to the sequencing primer and is 3-prime to the annealing site for the sequencing primer, or

(c) Is a spacer nucleic acid.

20 . The system of claim 1 , wherein the orthogonal DNA barcode contains a plurality of DNA barcode modules, wherein each of the DNA barcode modules is coupled to a different site on the bead either directly or via a linker, and wherein each of the plurality of DNA barcode modules contains at least one functional nucleic acid that is:

(a) Capable of being used as an annealing site for a sequencing primer,

(b) Capable of forming a hairpin structure, and wherein the hairpin structure comprises a sequencing primer, an annealing site for the sequencing primer, and a bend in the hairpin structure wherein the bend is 5-prime to the sequencing primer and is 3-prime to the annealing site for the sequencing primer, or

(c) A spacer nucleic acid.

21 . A method for controlling the concentration of a compound in a solution that resides in a picowell, wherein the method is applied to a bead-bound compound in a picowell, wherein the picowell contains a solution, and wherein the bead-bound compound is coupled to the bead by way of a cleavable linker, the method comprising:

(a) The step of exposing the bead-bound compound to a condition that effects cleavage of the cleavable linker, wherein the condition comprises light that is capable of cleaving the cleavable linker,

(b) The step of allowing release of the bead-bound compound from the bead to generate a released compound, wherein release is followed by diffusion or dispersion of the released compound in the solution to result in a substantially uniform concentration of the compound in the solution,

(c) The step of adjusting the condition to produce a determined concentration of the substantially uniform concentration, wherein the determined concentration is made with regard to the concentration of a released fluorophore that is released by from a bead-bound release-monitor.

22 . The method of claim 21 , wherein the condition is adjusted by adjusting one or more of the wavelength of the light, the intensity of the light, and by the duration of light exposure and wherein, optionally:

(i) The concentration of a released fluorophore that is released from a bead-bound release-monitor is determined at the same time as effecting release of the bead-bound compound from the bead to generate a released compound, or

(ii) The concentration of a released fluorophore that is released from a bead-bound release-monitor is determined at a time substantially before effecting release of the bead-bound compound from the bead to generate a released compound.

23 . A cap in combination with a picowell plate that comprises a plurality of picowells,

wherein the cap is capable of use with said picowell plate,

wherein each of the plurality of picowells is definable by an aperture, a floor, and a wall, wherein the wall is defined by the aperture on top and the floor on the bottom, and wherein the aperture is round, wherein the floor is round, and wherein the wall takes the form of a surface of a truncated cone, and

wherein the aperture has a first diameter, the floor has a second diameter, and wherein the first diameter is greater than the second diameter,

wherein the cap is a spherical cap that is capable of snuggly fitting into the aperture, wherein the aperture is comprised by a polymer having a greater durometer (harder) and wherein the cap is made of a polymer having a lesser durometer (softer),

and wherein the relative durometers of the cap and aperture allow the spherical cap to be reversibly and snuggly fit into the aperture, and wherein the cap is:

(i) capable of plugging the picowell and preventing leakage,

(ii) a passive cap and that is capable of absorbing metabolites that are released by a cell, in the situation where a cell in a cell medium is cultured in the picowell,

(iii) an active cap that takes the form of a bead that comprises a plurality of essentially identical compounds, and

wherein each of the plurality of essentially identical compounds is coupled to the bead with a cleavable linker, wherein at least one of the plurality of picowells contains an aqueous medium, and wherein cleavage of the cleavable linker releases at least some of the plurality of essentially identical compounds from the bead into the aqueous medium.

24 . A system comprising a picowell array plate comprising an upper generally planar surface, a plurality of picowells, wherein each picowell has a top aperture that defines an opening at the top of the picowell, a bottom that is defined by a floor, wherein the top aperture is separated by a wall from the floor, and wherein the wall resides in between the top aperture and the floor,

and optionally, a bead disposed in at least one of said plurality of picowells, wherein the bead comprises a plurality of substantially identical bead-bound DNA barcodes, and a plurality of substantially identical bead-bound compounds,

wherein the picowell array plate further comprises a mat that is capable of securely covering the opening at the top of at least one or all of the plurality of picowells, or that is actually securely covering the opening at the top of at least one or all of the plurality of picowells, wherein the securely covering is reversible, wherein the mat optionally comprises one or all of:

(a) An absorbant surface that, when positioned in contact with the upper generally planar surface of the picowell array plate, is capable of absorbing any metabolites, biochemicals, or proteins that may be comprised by one or more of the plurality of picowells,

(b) An adhesive surface that is capable of maintaining reversible adhesion to the top generally planar surface of the picowell array plate.

25 . A method for determining a signal from an assay and a sequencing readout on a bead, thereby identifying one or more compounds of interest from the assay, comprising the steps:

(a) providing a plurality of beads, wherein each bead comprises a plurality of compounds attached to the bead that are related substantially to each other, and a plurality of oligonucleotides, wherein the plurality of oligonucleotides attached to each bead identify the plurality of compounds attached to the same bead;

(b) performing the assay involving the plurality of compounds attached to the beads;

(c) determining at least one signal that reflects the performance of the compounds in the assay of step b;

(d) sequencing the plurality of oligonucleotides attached to the beads, without removing the oligonucleotides from the bead, thereby determining a sequencing readout for each bead; and

(e) identifying the compounds attached to the bead by the sequencing readout of step d and relating it to the assay performance contained in the determined signal of step c, wherein beads having a signal from the assay and the sequencing readout identify the compound of interest.

26 . A method for screening a compound library for compounds having desired properties, comprising:

(a) providing a plurality of beads, wherein each bead comprises a plurality of oligonucleotides attached to the bead surface and a plurality of substantially related compounds attached to the bead surface, and wherein the sequence of the oligonucleotides attached to the beads encodes the identity of the plurality of substantially related compounds attached to the bead surface;

(b) incorporating the plurality of beads in an assay for desired properties of compounds in the compound library;

(c) capturing a signal from at least one bead, wherein the signal reflects the performance of the compounds on the bead in the assay;

(d) sequencing the plurality of oligonucleotides attached to the at least one bead for which assay signal was also captured, without removing the oligonucleotides from the bead; and

(e) identifying at least one compound from the sequencing readout of step (d) and relating it to its corresponding assay performance captured in the signal of step (c).

27 . The method of claim 26 , wherein each bead comprises a different plurality of oligonucleotides and a different plurality of substantially related compounds.

28 . The method of claim 25 , wherein the plurality of oligonucleotides is a plurality of DNA oligonucleotides.

29 . The method of claim 25 , wherein the plurality of compounds is attached to the bead surface by joining multiple compound building blocks in tandem, wherein all the compound building blocks together make up the compound.

30 . The method of claim 29 , wherein each DNA module and each compound building block are assembled sequentially and alternatively.

31 . The method of claim 25 , wherein each compound in the plurality of identical compounds is attached to the bead surface by way of a cleavable linker.

32 . The method of claim 31 , wherein the cleavable linker is a photocleavable linker, a protease cleavable linker, or an acid cleavable linker.

33 . The method of claim 25 , wherein the compounds are cleaved from the bead surface after step (a) and prior to step (d).

34 . The method of claim 25 , wherein the signal that reflects the desired property of the compound is a fluorescent signal.

35 . The method of claim 25 , wherein the size of each bead is between 1 μm and 100 μm.

36 . The method of 35, wherein the size of each bead is between 1 μm and 10 μm.

37 . The method of 36, wherein the size of each bead is about 3 μm.

38 . The method of claim 25 , wherein the method further comprises identifying a target candidate in a plurality of potential targets, and wherein the compound having the desired property binds to the target candidate.

39 . The method of claim 38 , wherein step (b) comprises incubating the plurality of beads in the plurality of potential targets.

40 . The method of claim 38 , wherein the potential targets are proteins or nucleic acids.

41 . The method of claim 25 , wherein the sequencing is performed by single-molecule real-time sequencing, ion semiconductor sequencing, pyrosequencing, sequencing by synthesis, sequencing by bridge amplification, sequencing by ligation, nanopore sequencing, chain termination sequencing, massively parallel signature sequencing, polony sequencing, heliscope single molecule sequencing, shotgun sequencing, SOLiD sequencing, Illumina sequencing, tunneling currents DNA sequencing, sequencing by hybridization, sequencing with mass spectrometry, microfluidic Sanger sequencing, and oligonucleotide extension sequencing.

42 . A method for screening a compound library for compounds having desired properties, comprising:

(a) providing a plurality of beads, wherein each bead comprises a plurality of oligonucleotides attached to the bead surface and a plurality of substantially related compounds attached to the bead surface, and wherein the sequence of the oligonucleotides attached to the beads encodes the synthesis history of the plurality of substantially related compounds attached to the bead surface;

(b) incorporating the plurality of beads in an assay for desired properties of compounds in the compound library;

(c) capturing a signal from at least one bead, wherein the signal reflects the performance of the compounds on the bead in the assay;

(d) sequencing the plurality of oligonucleotides attached to the at least one bead for which assay signal was also captured, without removing the oligonucleotides from the bead; and

(e) identifying at least one compound from the sequencing readout of step (d) and relating it to its corresponding assay performance captured in the signal of step (c).

43 . The method of claim 42 , wherein the assay comprises a binding assay.

44 . The method of claim 42 , wherein the assay comprises an activity assay.

45 . The method of claim 42 , wherein the assay comprises a competitive binding assay or a competitive inhibition assay.

46 . The method of claim 42 , wherein the assay comprises interaction of untethered compounds with other assay reagents, wherein the untethered compounds are compounds released from the bead surface.

47 . The method of claim 45 , wherein the compounds are released by cleaving a cleavable linker that connects the compounds to the beads.

48 . The method of claim 42 , wherein the assay occurs in a plurality of confined volumes, wherein nominally one bead is dispersed per confined volume.

49 . The method of claim 48 , wherein the confined volume comprises an aqueous droplet.

50 . The method of claim 49 , wherein the aqueous droplet is suspended in an oil medium or a hydrophobic liquid medium.

51 . The method of claim 48 , wherein the confined volume comprises a picowell.

52 . The method of claim 50 , wherein the picowells are organized in a regular array.

53 . The method of claim 51 , wherein the plurality of confined volumes are organized in a regular array.

54 . The method of claim 48 , wherein the confined volume comprises a layer of adherent aqueous medium around the bead, wherein the bead is suspended in a hydrophobic medium.

55 . The method of claim 42 , wherein the assay reagents are washed away before sequencing the oligonucleotides.

56 . The method of claim 42 , wherein the sequencing step (d) is performed before the assay step (b).

57 . The method of claim 56 , wherein the oligonucleotides on the beads are removed after the sequencing step, but before the assay step.

58 . The method of claim 57 , wherein the removing of the oligonucleotide comprises an enzymatic digestion, a chemical cleavage, a thermal degradation or a physical shearing.

59 . The method of claim 43 , wherein the binding assay comprises binding of RNA molecules to the beads.

60 . The method of claim 43 , wherein the signal from the bead comprises sequencing of the bound RNA molecules.

61 . The method of claim 42 , wherein the binding assay comprises a fluorescently labeled binding assay, wherein the molecules binding to the compounds on the beads comprise fluorophores.

62 . The method of claim 42 , wherein the binding assay comprises nucleic-acid labeled binding assay, wherein the molecules binding to the compounds on the beads comprise nucleic-acid tags, wherein further the signal from the assay comprises sequencing of the nucleic acid tags attached to the molecules binding to the compounds on the beads.

63 . The method of claim 42 , wherein the desired properties include one or more of:

(i) Inhibiting or stimulating the catalytic activity of an enzyme,

(ii) Stimulating Th1-type immune response, as measurable by cell-based assays or by in vivo assays,

(iii) Stimulating Th2-type immune response, as measurable by cell-based assays or by in vivo assays,

(iv) Inhibiting Th1-type immune response, as measurable by cell-based assays or by in vivo assays,

(v) Inhibiting Th2-type immune response, as measurable by cell-based assays or by in vivo assays,

(vi) Stimulating or inhibiting ubiquitin-mediated degradation of a protein, as measurable by purified proteins, by cell-based assays, or by in vivo assays.

64 . A system for screening a compound library for a compound having a desired activity, comprising:

(a) a sample compartment for receiving a plurality of compound-attached, oligonucleotide-encoded beads;

(b) a plurality of encapsulation compartments within the sample compartment, each encapsulation compartment nominally comprising a single bead dispersed in an assay medium, wherein further the assay medium comprises reagents whose interaction with the compounds on the beads is being assayed resulting in a measurable signal;

(c) a detector for measuring signals;

(d) a sequencing platform; and

(e) a user interface for receiving one or more commands from a user.

65 . The system of claim 64 , wherein the encapsulation compartment comprises a liquid droplet.

66 . The system of claim 64 , wherein the encapsulation compartment comprises a picowell.

67 . The system of claim 64 , wherein further the encapsulation compartment comprises assay reagents.

68 . The system of claim 64 , wherein the detector comprises an optical detector.

69 . The system of claim 64 , wherein the sequencer comprises the optical detector.

70 . The system of claim 1 , further comprising a plurality of caps, each cap capable of fitting into the opening of a different picowell, and each cap capable of minimizing or preventing evaporation of fluid that is inside of the picowell, and each cap is capable of minimizing or preventing leakage of fluid that is inside of the picowell.