Spatially encoded polymer matrix

• US 8,791,053 B2
• Filed: 09/26/2003
• Issued: 07/29/2014
• Est. Priority Date: 09/27/2002
• Status: Active Grant

• Current Assignee: MPM-Holding ApS
• Original Assignee: MPM-Holding ApS
• Inventors: Christensen, Soren Flygenring, Truelsen, Jens Hog, Meldal, Morten, Michael, Roice, Johannsen, Ib
• Primary Examiner(s): Steele, Amber D
• Application Number:
  US10/529,397
• Publication Number:
  US 20060127369A1
• Time in Patent Office: 3,959 Days
• Field of Search: 506/4, 506/6, 506/12, 506/13, 506/15, 506/22
• US Class Current: 506/13
• 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 2219/005 Beads
• CPC Class Codes: B01J 2219/0054 Means for coding or tagging the apparatus or the reagents
• CPC Class Codes: B01J 2219/00551 3-dimensional
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00698 Measurement and control of process parameters
• 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: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 2219/00731 Saccharides
• CPC Class Codes: B01J 2219/0074 Biological products

Abstract

The invention relates to a spatially encoded polymer matrix in the form of a bead or a granule for combinatorial solid phase synthesis, assaying, functional proteomics and diagnostic use. Compositions of such beads or granules are also provided. Each beaded polymer matrix of the composition comprises a plurality of spatially immobilized particles. The spatial immobilization of the particles confers on each beaded polymer matrix a “fingerprint” which enables identification of unique beads in a population of beads. The unique identification of individual beads makes it possible to perform combinatorial chemistry strategies while logging individual chemical transformation. Also provided are methods for detection of relative positions in space of particles, methods for generating matrices, methods for distance matrix determination, methods for identifying individual matrices and devices for recording and storing images of matrices.

Claims

1. A composition comprising a plurality of different, spatially encoded beads, comprising

a polymer matrix and from 3 to not more than 10 spatially immobilized, individually detectable particles held in the polymer matrix,

wherein each bead has a diameter of from 0.5 millimeter to less than 2.0 millimeter,

wherein the diameter of the particles is less than 30 micrometer, the particles being disposed in a spatial configuration relative to one another that constitutes the code serving to identify each bead.

2. The composition according to claim 1 in which the polymer matrix has different optical or spectroscopic properties from those of the particles.

3. The composition according to claim 1 in which the particles are monodisperse.

4. The composition according to claim 1 in which the particles are heterodisperse.

5. The composition according to claim 1 in which the particles are spherical.

6. The composition according to claim 1, wherein the polymer matrix is selected from the group consisting of polyethers, polyvinyls, polyacrylates, polyacylamides, polyacrylamides, polystyrenes, polycarbonates, polyesters, polyamides, and combinations thereof.

7. The composition according to claim 1, wherein the polymer matrix is selected from the group consisting of SPOCC, PEGA, HYDRA, POEPOP, PEG polyacrylate copolymers/polyether-polyamine copolymers, crosslinked polyethylene diamines, and combinations thereof.

8. The composition according to claim 1, wherein the composition comprises at least 10² individually identifiable beads.

9. The composition according to claim 1, wherein the composition comprises at least 10⁹ individually identifiable beads.

10. The composition according to claim 1, wherein the spatial positions of particles in each bead are defined by sets of coordinates (x,y,z) of particle centers of said particles, relative to a reference point of detection.

11. The composition of claim 1, wherein said beads are prepared by a process, which comprises:

suspending the particles in a polymerizable liquid,

polymerizing the liquid to obtain the polymer matrix, and

forming beads with embedded particles from said matrix.

12. The composition according to claim 1 comprising 3 to 4 particles.

13. The composition according to claim 1 comprising from 4 to 8 particles.

14. The composition according to claim 1 comprising from 4 to 10 particles.

15. The composition according to claim 14, said bead being essentially spherical.

16. The composition according to claim 15, wherein all of said particles are essentially monodisperse.

17. The composition according to claim 14 wherein said particles are less than 10 micrometer in diameter.

18. The composition according to claim 17, wherein said particles are less than 5 micrometer in diameter.

19. The composition according to claim 17, wherein said particles are less than 1 micrometer in diameter.

20. The composition according to claim 17, wherein said particles are less than 0.1 micrometer in diameter.

21. The composition according to claim 14, wherein said particles comprise a spectroscopically detectable marker.

22. The composition according to claim 14, wherein said particles comprise a fluorescently detectable marker.

23. The composition according to claim 22, wherein the fluorescently detectable marker is selected from the group consisting of fluorescein, oregon green, rhodamine, aminobenzoic acid, a sulfonated aminocoumarin probe, a sulfonated rhodamine probe, BODIPY dyes, cascade blue dye, coumarine, naphthalenes, dansyl, indoles, pyrenes, pyridyloxazole, cascade yellow dye, fluorescamine, aromatic ortho dialdehydes, OPA, NDA, ATTO-Tag, 7-nitrobenz-2-oxa-1,3-diazole, and derivatives thereof.

24. The composition according to claim 22, wherein said fluorescently detectable marker is selected from the group consisting of fluorescent organic polycyclic compounds, conjugated vinylic compounds, heterocyclic transition metal complexes, rare earth metal compounds, inorganic oxides and glasses.

25. The composition according to claim 22, wherein the polymer matrix is optically transparent in the optical excitation of said fluorescent marker and/or the emission wavelength ranges of said fluorescent marker.

26. The composition according to claim 1, wherein each bead comprises at least one site for functionalisation to which a ligand or a bioactive species can be attached.

27. The composition according to claim 26, wherein the site for functionalisation comprises a reactive group or a scaffold comprising two or more of such reactive groups.

28. The composition according to claim 26 further comprising a plurality of ligands or bioactive species attached to the polymer matrix, wherein different ligands or different bioactive species are attached to different beads, wherein more than about 95% of all of said different beads are individually identifiable.

29. A method for the detection of relative positions in space of centers (x,y,z) of immobilized particles of the composition according to claim 1, said method comprising the step of recording of at least two 2D-projections of the particles, said method optionally comprising the further step of determining, on the basis of the relative positions in space of centers (x,y,z) of immobilized particles, the distance matrix for individual beads, or a set of geometrical figures derivable from the relative positions in space of centers (x,y,z) of the immobilized particles.

30. The method according to claim 29, wherein a fluorescently detectable marker is attached to the particles of the composition and is detectable by a fluorescent spectroscopic method.

31. The method according to claim 29, wherein a marker is attached to the particles of the composition and said marker is detected by fast spectroscopic techniques other than fluorescence spectroscopy.

32. The method according to claim 31, wherein said fast spectroscopic technique is selected from the group consisting of Infrared spectroscopy, raman spectroscopy, visible light spectroscopy, UV spectroscopy, electron spin resonance, and nuclear magnetic resonance.

33. The method according to claim 29, wherein a marker is attached to the particles of the composition and said marker is detected by fast detection techniques, other than spectroscopy, selected from the group consisting of light scattering, reflection, diffraction and light rotation.

34. The method according to claim 29, wherein a marker is attached to the particles of the composition and the marker is detected by probing the marker with a range of frequencies differing by less than 10% based on the numerical highest frequency value.

35. The method according to claim 29, wherein a marker is attached to the particles of the composition and the marker is detected by probing the marker with one or more predetermined frequencies.

36. The method according to claim 29 wherein 3 2D-projections are recorded along 3 orthogonal axes x, y and z to generate 3 sets of 2D-coordinates (y,z), (x,z) and (x,y), respectively, from which the 3D-coordinates (x,y,z) of particle centers can be derived.

37. The method according to claim 29, wherein a plurality or stack of 2D projections are generated by confocal or focal microscopy to recreate the 3D image matrix of the bead from which the relative particle position (x,y,z) in space can be determined.

38. The method of claim 29 employing at least one focused scanning laser for detection of relative positions in space of centers (x,y,z) of immobilized particles and laminar fluidics for bead manipulation.

39. The method of claim 38 in which the coordinates x and y of a particle position are determined by fast scanning two orthogonally aligned lasers over two cross sections of the moving bead while the z coordinate is determined by the time of flight of the bead at known flow rates.

40. The method of claim 29 in which the coordinates x and y of a particle position are determined by using a single laser and particle position a rotating mirror are determined by using a single laser and a rotating mirror that via 2 or 3 geometrically arranged static mirrors reflects the laser beam along 2 or 3 orthogonal axes.

41. A method for distance matrix determination of at least one bead in the composition of claim 1, each bead comprising a plurality of spatially immobilised particles comprising an optically detectable label, said method comprising the steps of

i) providing at least one composition according to claim 1,

ii) providing at least one device for recording and storing at least one image of the at least one bead, said device comprising

a) at least one source of illumination,

b) at least one flow system comprising a flow cell comprising an imaging section,

c) at least one pulse generator,

d) at least one image intensifier,

e) at least one CCD camera,

iii) activating at least one source of illumination,

iv) introducing the at least one encoded bead comprising a plurality of particles into the flow cell comprising an imaging section,

v) recording at least one image of the at least one bead by sending substantially simultaneously a pulse generated by a pulse generator to both a) the at least one image intensifier, and b) the at least one CCD camera capable of recording said at least one image, and

vi) determining for individual beads a distance matrix based on the at least one image obtained for each bead in step v),

wherein the distance matrix for an individual bead is determined by a method comprising the steps of

determining for each particle of the encoded bead the 2D coordinates in the XZ-plane and in the YZ-plane, thereby generating a first set of data and a second set of data,

combining the first set of data and the second set of data and thereby obtaining 3D coordinates for each particle, and

calculating the distance matrix as the full set of distances between particles for which preferably only one set of 3D coordinates is obtained.

42. The method of claim 41, wherein steps iv), v), and vi) are repeated for individual steps entering the flow cell.

43. The method of claim 41 comprising the further step of detecting a bead entering the flow cell by using a photo-sensor.

44. The method of claim 41, wherein the pulse generator is activated by the activation of the photo-sensor, and wherein the photo sensor is activated by an encoded bead entering the flow cell.

45. The method of claim 41 comprising the further step of storing the at least one image on a data storage medium.

46. The method of claim 41, wherein two CCD cameras and two image intensifiers are employed for recording the at least one image of the at least one bead.

47. The method of claim 41, wherein the source of illumination comprises a continuous wave laser capable of illuminating the imaging section of the flow cell.

48. The method of claim 41, wherein the photo-sensor for detecting the entry of an encoded bead into the imaging section of the flow cell comprises an optical objective for focusing said imaging section of said flow cell onto the photo-sensitive area of said photo-sensor, wherein said optical objective of said photo-sensor comprises a fluorescence filter capable of blocking the light of said laser, and wherein said fluorescence filter transmits the fluorescence emission from the particles.

49. The method of claim 41, wherein the at least one CCD camera for recording the at least one image of the at least one encoded bead comprises at least one gated image intensifier for amplifying the fluorescence emission from the encoded bead, and wherein each of said image intensifiers comprises at least one optical objective for focussing said imaging section of said flow cell onto the photo-sensitive area of each image intensifier, and wherein each optical objective comprises a fluorescence filter for blocking the light of said laser, and wherein the fluorescence filter transmits the fluorescence emission from the particles.

50. The method of claim 49, wherein the size distribution of the beads is in the range of from 0.1 millimeter to less than 2 millimeter.

51. The method of claim 50, wherein the majority of the beads are in the range of from 0.5 millimeter to 1 millimeter, and independently thereof, wherein the diameter of the particles is in the range of from 5 to 15 micrometer.

52. The method of claim 41, wherein a plurality of encoded beads are provided and wherein multiple distance matrices are determined based on individual distances recorded for individual beads.

53. The method of claim 52, wherein a set of multiple distance matrices is determined for a subpopulation of the beads based on more than one set of individual distances recorded for the subpopulation of beads.

54. The method of claim 52, wherein each distance matrix is recorded individually.

55. The method of claim 41, wherein at least one image of each bead is recorded per second.

56. The method of claim 41, wherein a total of more than 4000 beads are recorded per hour.

57. The method of claim 41, wherein the optical power of the laser is in the range of from 1 mWatt to less than about 200 mWatt.

58. The method of claim 41, wherein the wave length of the laser is in the range of from about 450 nm to less than 700 nm.

59. The method of claim 41, wherein the exposure time of the image intensifiers is less than about 1 millisecond.

60. The method of claim 41, wherein the exposure time of the CCD cameras is less than about 1 millisecond.

61. The method of claim 41, wherein the response time of the photo-sensor is less than about 1 millisecond.

62. The method of claim 41, wherein the flow rate of the beads through the flow cell of the flow system is more than 0.01 meter per second.

63. The method of claim 41, wherein the dimensions of the imaging section is preferably less than 1 milliliter.

64. The method of claim 41, wherein the flow cell comprises a material which does not absorb the illumination light from the source of illumination and/or the emission light emitted from the particles.

65. The method of claim 41, wherein the optically detectable label is selected from the group consisting of light reflecting particles, light absorbing particles, dyes, fluorescent particles, and autofluorescent particles.

66. The method of claim 41 comprising the further steps of

i) comparing the Z-coordinates of different particles within each bead, and

ii) selecting particles wherein the difference between Z-coordinates is less than a predetermined threshold value, delta-Z,

iii) pairwise grouping the selected particles according to delta-Z values,

iv) maintaining the X-coordinate and the Z-coordinate for each of the pairwise grouped particles, and

v) switching the Y-coordinate between pairwise grouped particles, thereby obtaining an alternative set of 3D coordinates from which an alternative distance matrix can be calculated.

67. A method for identifying individual beaded polymer matrices in the composition, said method comprising the steps of

i) determining the distance matrix for individual beads according to the method of claim 41,

ii) deriving from each of the distance matrices generated in step i) all of the possible geometrical figures selected from triangles and quadrangles, which can be generated by connecting particle coordinates with straight lines, and

iii) recording and storing the set of geometrical figures obtained in step ii) for each bead of the composition to be identified,

iv) selecting a subset of beads,

v) identifying one or more of the selected beads on the basis of a comparison of the set of possible geometrical figures selected from triangles and quadrangles of said bead(s) with all sets of possible geometrical figures selected from triangles and quadrangles recorded for the composition in step iii).

68. The method of claim 67, wherein the geometrical figures are triangles.

69. The method of claim 67, wherein each bead comprises 3 or 4 spatially immobilised particles.

70. The method of claim 67, wherein the geometrical figures are quadrangles.

71. The method of claim 67 comprising the further step of performing a digital 3D registration of at least some of the identified beads, said 3D registration comprising generating a digital 3D reconstruction of the at least some identified beads based on the orthogonal pairs of images, and wherein the identification of individual beads is aided by an analysis of which of the generated 3D reconstructions represents the best fit to the original 3D registration.

72. A method for identifying an individually identifiable, spatially encoded, bead in the composition according to claim 1, comprising the steps of

i) determining the unique, spatial position of the particles in the bead to be identified,

ii) deriving from the positions, a matrix of the distances between the particles,

iii) deriving from the matrix, a set of all possible triangles defined by the particles,

iv) identifying said bead based on comparison of the set of possible triangles with all sets of possible triangles capable of being stored for the composition.

73. A method for recording individual reaction steps involved in a step-wise synthesis of a chemical compound in a library comprising the composition according to claim 1, said method comprising the steps of

a) spatially immobilizing a plurality of particles in polymer beads,

b) isolating at least a subset of the spatially encoded beads provided in step a) and

c) recording and storing a distance matrix or a geometrical figure derivable from the distance matrix for each bead or granule,

d) stepwise synthesising chemical compounds on functional groups of the encoded beads, wherein the identity of each bead is recorded and stored for each reaction step,

e) obtaining for each bead a record of individual reaction steps.

74. A method for identifying a chemical compound being synthesised on the polymer matrix said method comprising the steps of

a) performing the recording method of claim 73,

b) selecting beaded polymer matrices or granules of interest by using an assay or a diagnostic screen selective for the chemical compound having been synthesised on the beaded polymer matrix,

c) recording the distance matrix for each of the beaded polymer matrices selected in step b),

d) comparing the distance matrix recorded in step c) with all of the distance matrices recorded and stored in step c) of claim 73, thereby obtaining information about the identity of the selected bead,

e) identifying for each selected bead the sequence of individual steps having lead to the synthesis of the chemical compound, and

f) identifying, based the sequence of individual steps, the chemical structure of the compound.

75. The method of claim 74, wherein the assay is a binding assay performed by measuring the binding of a protein to a ligand bound to the polymer matrix.

76. The method of claim 74, wherein the assay is performed by measuring an enzyme activity on a substrate bound to the polymer matrix.

77. The method of claim 74, wherein the assay is performed by measuring enzyme inhibition of a molecule bound to the polymer matrix.

78. The method of claim 74, wherein the assay is performed by measuring receptor interaction with a compound bound to the polymer matrix.

79. The method of claim 74, wherein said plurality of particles comprise a fluorescently detectable marker.

80. The method of claim 79, wherein said fluorescently detectable marker is a uv or visible light-excitable microspheres.