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The invention includes devices and methods for forming random arrays of magnetic particles, arrays formed using these devices and methods, and to methods of using the arrays. The invention provides an assembly (chip) with magnetic domains that produce localized magnetic fields capable of immobilizin

The invention includes devices and methods for forming random arrays of magnetic particles, arrays formed using these devices and methods, and to methods of using the arrays. The invention provides an assembly (chip) with magnetic domains that produce localized magnetic fields capable of immobilizing magnetic particles such as commercially available magnetic beads. Probe or sensor molecules can be coupled to the beads, which are then dispersed on the assembly, forming a random order array. The arrays can be used for analyzing samples, targets, and/or the interaction between samples and targets. The invention finds particular use in processes such as high-throughput genotyping and other nucleic acid hybridization-based assays.

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We claim: 1. A device for forming an array of magnetic particles, the device comprising: a substrate comprising a plurality of magnetic regions having gaps between them, wherein the substrate comprises a surface, wherein the magnetic regions have a maximum length parallel to the surface of the subs

We claim: 1. A device for forming an array of magnetic particles, the device comprising: a substrate comprising a plurality of magnetic regions having gaps between them, wherein the substrate comprises a surface, wherein the magnetic regions have a maximum length parallel to the surface of the substrate and a maximum width parallel to the surface of the substrate with the maximum length being greater than the maximum width, and wherein the magnetic regions produce a plurality of localized magnetic fields when magnetized, and wherein adjacent magnetic regions are so aligned with one another in the directions of their maximum length that the localized magnetic fields are sufficient to trap a magnetic particle between adjacent magnetic regions with a trapping energy at least three times greater than the thermal energy of the particle at room temperature and the gaps are available for fluid flow among them and are also available for occupancy by magnetic particles prior to introduction of magnetic particles to the device so that forces generated by the localized magnetic fields between adjacent regions can trap magnetic particles in the gaps between them, wherein the magnetic regions project above the surface of the substrate, and wherein the magnetic regions comprise a layer of magnetic material and a layer of nonmagnetic material, wherein the layer of nonmagnetic material is located between the substrate and the layer of magnetic material. 2. The device of claim 1, wherein the localized magnetic fields are sufficient to trap a magnetic particle with a trapping energy at least an order of magnitude greater than the thermal energy of the particle at room temperature. 3. The device of claim 1, wherein the magnetic material regions are arranged in a pattern of mutually perpendicular rows and columns. 4. The device of claim 1, wherein the magnetic regions are arranged in an array of subarrays configuration. 5. The device of claim 1, wherein the magnetic regions are substantially uniform in shape. 6. The device of claim 1, wherein the magnetic regions are substantially rectangular in shape. 7. The device of claim 1, wherein the magnetic regions are substantially uniform in size. 8. The device of claim 1, wherein the number of magnetic regions is at least 1000 per centimeter squared. 9. The device of claim 1, wherein the number of magnetic regions is at least 10,000 per centimeter squared. 10. The device of claim 1, wherein the number of magnetic regions is at least 100,000 per centimeter squared. 11. The device of claim 1, wherein the number of magnetic regions is at least 250,000 per centimeter squared. 12. The device of claim 1, wherein the number of magnetic regions is at least 1,000,000 per centimeter squared. 13. The device of claim 1, wherein adjacent magnetic regions are separated by a gap approximately equal in size to the size of a magnetic particle having a largest dimension of less than approximately 200 μm. 14. The device of claim 13, wherein the magnetic particle has a greatest dimension selected from the group consisting of: 30 nm, 100 nm, 300 nm, 500 nm, 1 μm, 3 μm, 5 μm, and 10 μm. 15. The device of claim 14 wherein the magnetic particle is substantially spherical, and the greatest dimension of the particle is the diameter of the particle. 16. The device of claim 13, wherein the gap has a minimum length of approximately 1 micron. 17. The device of claim 13, wherein the gap has a minimum length of approximately 3 microns. 18. The device of claim 13, wherein the gap has a minimum length of approximately 5 microns. 19. The device of claim 1, wherein adjacent magnetic regions are separated by a gap having a greatest dimension approximately equal in size to the greatest dimension of a magnetic particle. 20. The device of claim 19, wherein the gap has a greatest dimension approximately equal in size to the greatest dimension of a magnetic particle having a greatest dimension selected from the group consisting of: 30 nm, 100 nm, 300 nm, 500 nm, 1 μm, 3 μm, 5 μm, and 10 μm. 21. The device of claim 20, wherein the magnetic particle is substantially spherical, and the greatest dimension of the particle is the diameter of the particle. 22. The device of claim 1, wherein the magnetic regions comprise a magnetic material. 23. The device of claim 22, wherein the magnetic material is a ferromagnetic material. 24. The device of claim 1, wherein the substrate comprises a nonmagnetic material. 25. The device of claim 24, wherein the magnetic regions are surrounded by nonmagnetic material. 26. The device of claim 1, wherein the magnetic regions comprise cobalt. 27. The device of claim 1, wherein the magnetic regions are formed using photolithography. 28. The device of claim 1, wherein the magnetic particles are magnetic beads. 29. The device of claim 1, wherein the magnetic particles are paramagnetic particles. 30. The device of claim 1, wherein the magnetic particles are superparamagnetic particles. 31. The device of claim 1, further comprising a magnet for magnetizing and demagnetizing the magnetic regions. 32. The device of claim 1, wherein the size, shape, and spacing of the regions are selected to increase the likelihood of trapping only a single magnetic particle within the gaps. 33. The device of claim 1, wherein the distance between the ends of adjacent magnetic regions in the dimension of the maximum length is 200 microns or less. 34. A device for forming an array of magnetic particles, the device comprising: a substrate comprising a plurality of magnetic regions having gaps between them, wherein the substrate comprises a surface, and wherein the magnetic regions produce a plurality of localized magnetic fields when magnetized, wherein the magnetic regions have a maximum length parallel to the surface of the substrate and a maximum width parallel to the surface of the substrate, and wherein a plurality of regions are spaced apart along the dimension of the maximum length and a plurality of regions are spaced apart along the dimension of the maximum width, so that the distance separating adjacent regions in the dimension of the maximum length is less than the distance separating adjacent regions in the dimension of the maximum width, and, wherein the localized magnetic fields are sufficient to trap a magnetic particle with a trapping energy at least three times greater than the thermal energy of the particle at room temperature, wherein the magnetic regions project above the surface of the substrate, and wherein the magnetic regions comprise a layer of magnetic material and a layer of nonmagnetic material, wherein the layer of nonmagnetic material is located between the substrate and the layer of magnetic material. 35. A device for forming an array of magnetic particles, the device having an upper surface and comprising: a substrate comprising a plurality of magnetic regions having gaps between them, wherein the magnetic regions have north and south poles that produce a plurality of localized magnetic fields when magnetized, wherein adjacent magnetic regions have ends with opposite magnetic polarities facing each other across a gap between them, wherein the magnetic regions are appropriately shaped and have an appropriate size so as to generate localized magnetic fields that exist substantially in a volume between adjacent north and south poles of adjacent magnetic regions above and parallel to the upper surface of the device and wherein the magnetic fields are sufficient to trap a magnetic particle with a trapping energy at least three times greater than the thermal energy of the particle at room temperature and the gaps are available for fluid flow among them and are also available for occupancy by magnetic particles prior to introduction of magnetic particles to the device so that forces generated by the localized magnetic fields between adjacent regions can trap magnetic particles in the gaps between them, wherein the magnetic regions project above the surface of the substrate, and wherein the magnetic regions comprise a layer of magnetic material and a layer of nonmagnetic material, wherein the layer of nonmagnetic material is located between the substrate and the layer of magnetic material. 36. The device of any of claims 1, 2, 34, or 35, wherein the thermal energy of the particle is approximately 0.025 eV. 37. The device of any of claims 1, 2, 34, or 35, wherein the magnetic regions have walls that are substantially perpendicular to the substrate. 38. A device for forming an array of magnetic particles, the device comprising: a substrate comprising a plurality of magnetic regions having gaps between them, wherein the substrate comprises a surface, wherein the magnetic regions have a maximum length parallel to the surface of the substrate and a maximum width parallel to the surface of the substrate with the maximum length being greater than the maximum width, and wherein the magnetic regions produce a plurality of localized magnetic fields when magnetized, and wherein adjacent magnetic regions are so aligned with one another in the directions of their maximum length that the localized magnetic fields are sufficient to trap a magnetic particle between adjacent magnetic regions with a trapping energy at least three times greater than the thermal energy of the particle at room temperature and the gaps are available for fluid flow among them and are also available for occupancy by magnetic particles prior to introduction of magnetic particles to the device so that forces generated by the localized magnetic fields between adjacent regions can trap magnetic particles in the gaps between them, wherein at least a portion of the device comprises a biocompatible material. 39. The device of claim 38, wherein at least the surface of the substrate and the magnetic regions comprises a biocompatible material. 40. A device for forming an array of magnetic particles, the device comprising: a substrate comprising a plurality of magnetic regions having gaps between them, wherein the substrate comprises a surface, wherein the magnetic regions have a maximum length parallel to the surface of the substrate and a maximum width parallel to the surface of the substrate with the maximum length being greater than the maximum width, and wherein the magnetic regions produce a plurality of localized magnetic fields when magnetized, and wherein adjacent magnetic regions are so aligned with one another in the directions of their maximum length that the localized magnetic fields are sufficient to trap a magnetic particle between adjacent magnetic regions with a trapping energy at least three times greater than the thermal energy of the particle at room temperature and the gaps are available for fluid flow among them and are also available for occupancy by magnetic particles prior to introduction of magnetic particles to the device so that forces generated by the localized magnetic fields between adjacent regions can trap magnetic particles in the gaps between them, wherein the magnetic regions project above the surface of the substrate, and wherein the magnetic regions comprise a layer of magnetic material and a layer of nonmagnetic material, wherein the layer of nonmagnetic material is located between the substrate and the layer of magnetic material, wherein the substrate comprises silicon. 41. A device for forming an array of magnetic particles, the device comprising: a substrate comprising a plurality of magnetic regions having gaps between them, wherein the substrate comprises a surface, wherein the magnetic regions have a maximum length parallel to the surface of the substrate and a maximum width parallel to the surface of the substrate with the maximum length being greater than the maximum width, and wherein the magnetic regions produce a plurality of localized magnetic fields when magnetized, and wherein adjacent magnetic regions are so aligned with one another in the directions of their maximum length that the localized magnetic fields are sufficient to trap a magnetic particle between adjacent magnetic regions with a trapping energy at least three times greater than the thermal energy of the particle at room temperature and the gaps are available for fluid flow among them and are also available for occupancy by magnetic particles prior to introduction of magnetic particles to the device so that forces generated by the localized magnetic fields between adjacent regions can trap magnetic particles in the gaps between them, further comprising a flux circulator disposed around the magnetic regions. 42. A device for forming an array of magnetic particles, the device comprising: a substrate comprising a plurality of magnetic regions having gaps between them, wherein the substrate comprises a surface, wherein the magnetic regions have a maximum length parallel to the surface of the substrate and a maximum width parallel to the surface of the substrate with the maximum length being greater than the maximum width, and wherein the magnetic regions produce a plurality of localized magnetic fields when magnetized, and wherein adjacent magnetic regions are so aligned with one another in the directions of their maximum length that the localized magnetic fields are sufficient to trap a magnetic particle between adjacent magnetic regions with a trapping energy at least three times greater than the thermal energy of the particle at room temperature and the gaps are available for fluid flow among them and are also available for occupancy by magnetic particles prior to introduction of magnetic particles to the device so that forces generated by the localized magnetic fields between adjacent regions can trap magnetic particles in the gaps between them, farther comprising a plurality of photodetectors located in proximity to locations for trapping the magnetic particles so as to detect an optical signal from trapped particles. 43. A device for forming an array of magnetic particles, the device comprising: a substrate comprising a plurality of magnetic regions having gaps between them, wherein the substrate comprises a surface, wherein the magnetic regions have a maximum length parallel to the surface of the substrate and a maximum width parallel to the surface of the substrate with the maximum length being greater than the maximum width, and wherein the magnetic regions produce a plurality of localized magnetic fields when magnetized, and wherein adjacent magnetic regions are so aligned with one another in the directions of their maximum length that the localized magnetic fields are sufficient to trap a magnetic particle between adjacent magnetic regions with a trapping energy at least three times greater than the thermal energy of the particle at room temperature and the gaps are available for fluid flow among them and are also available for occupancy by magnetic particles prior to introduction of magnetic particles to the device so that forces generated by the localized magnetic fields between adjacent regions can trap magnetic particles in the gaps between them, farther comprising a microfluidic assembly, wherein the microfluidic assembly comprises channels positioned in communication with the magnetic regions so as to allow introduction of fluids to the magnetic regions via the channels so that the fluids contact the magnetic regions following introduction of the fluids via the channels. 44. A device for forming an array of magnetic particles, the device comprising: a substrate comprising a plurality of magnetic regions having gaps between them, wherein the substrate comprises a surface, wherein the magnetic regions have a maximum length parallel to the surface of the substrate and a maximum width parallel to the surface of the substrate with the maximum length being greater than the maximum width, and wherein the magnetic regions produce a plurality of localized magnetic fields when magnetized, and wherein adjacent magnetic regions are so aligned with one another in the directions of their maximum length that the localized magnetic fields are sufficient to trap a magnetic particle between adjacent magnetic regions with a trapping energy at least three times greater than the thermal energy of the particle at room temperature and the gaps are available for fluid flow among them and are also available for occupancy by magnetic particles prior to introduction of magnetic particles to the device so that forces generated by the localized magnetic fields between adjacent regions can trap magnetic particles in the gaps between them, wherein the magnetic regions project above the surface of the substrate, and wherein the magnetic regions comprise a layer of magnetic material and a layer of nonmagnetic material, wherein the layer of nonmagnetic material is located between the substrate and the layer of magnetic material, further comprising a plurality of magnetic particles. 45. The device of claim 44, wherein the magnetic particles are substantially uniform in size and shape and are magnetic beads. 46. The device of claim 44, wherein the magnetic particles are substantially uniform in size and shape and are paramagnetic beads. 47. The device of claim 44, wherein the magnetic particles are substantially uniform in size and shape and are superparamagnetic beads. 48. The device of claim 44, wherein the magnetic particles are trapped by the localized magnetic fields. 49. The device of claim 44, wherein each of a plurality of the magnetic particles comprises a detectable moiety. 50. The device of claim 49, wherein the detectable moiety comprises a fluorescent or luminescent molecule. 51. The device of claim 49, wherein the detectable moiety comprises a nucleic acid. 52. The device of claim 51, wherein the nucleic acid comprises a hybridization tag. 53. The device of claim 44, wherein each of a plurality of the magnetic particles has a probe attached thereto. 54. The device of claim 53, wherein the probe comprises a binding ligand. 55. The device of claim 53, wherein the probe comprises a nucleic acid molecule. 56. The device of claim 53, wherein the probe comprises a protein. 57. A device for forming an array of magnetic particles, the device comprising: a substrate comprising a plurality of magnetic regions, wherein the substrate comprises a surface, and wherein the localized magnetic regions produce a plurality of localized magnetic fields concentrated in gaps between the regions, and wherein the magnetic regions project above the surface of the substrate and have a maximum length parallel to the surface of the substrate and a maximum width parallel to the surface of the substrate, with the maximum length being greater than the maximum width, wherein a plurality of regions are spaced apart along the dimension of the maximum length and a plurality of regions are spaced apart along the dimension of the maximum width, and wherein the distance separating adjacent regions in the dimension of the length is less than the distance separating adjacent regions in the dimension of the width, further comprising a plurality of magnetic particles wherein the magnetic regions project above the surface of the substrate, and wherein the magnetic regions comprise a layer of magnetic material and a layer of nonmagnetic material, wherein the layer of nonmagnetic material is located between the substrate and the layer of magnetic material. 58. The device of claim 57, wherein the magnetic regions are substantially uniform in size and shape. 59. The device of claim 57, wherein the magnetic regions are arranged in a pattern of mutually perpendicular rows and columns. 60. The device of claim 57, comprising: a nonmagnetic substrate; and a plurality of magnetic regions located on the substrate, wherein a localized magnetic field exists between adjacent magnetic material regions when magnetized. 61. The device of claim 60, further comprising a plurality of magnetic particles. 62. The device of claim 60, wherein the magnetic regions are substantially uniform in size and shape. 63. The device of claim 60, wherein the magnetic regions are arranged in a pattern of mutually perpendicular rows and columns. 64. The device of claim 60, wherein the magnetic regions project above the surface of the substrate. 65. The device of claim 1, 34, or 57, wherein the magnetic regions have a maximum length that is between 3 and 5 times as great as the maximum width or between 5 and 10 times as great as the maximum width. 66. The device of claim 1, 34, or 57, wherein adjacent magnetic regions are separated by a gap of between 1 and 5 microns or between 5 and 15 microns. 67. The device of claim 1, 34, or 57, wherein the magnetic regions are not rectangular.