Encoded beads having oligonucleotides attached in arrays on a patterned surface

• US 8,124,402 B2
• Filed: 05/17/2006
• Issued: 02/28/2012
• Est. Priority Date: 04/25/1996
• Status: Expired due to Fees

• Current Assignee: BioArray Solutions Limited (Werfen SA)
• Original Assignee: BioArray Solutions Limited (Werfen SA)
• Inventors: Seul, Michael
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US11/436,717
• Publication Number:
  US 20060228740A1
• Time in Patent Office: 2,113 Days
• Field of Search: None
• US Class Current: 435/283.1
• 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 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00448 using microlens arrays
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00653 the compounds being bound to electrodes embedded in or on the solid supports
• 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 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 2219/00743 Cells
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2563/155 Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: C40B 50/18 : using a particular method of attachment to the solid support
• CPC Class Codes: C40B 60/14 : for creating libraries

Abstract

A method and apparatus for the manipulation of colloidal particles and biomolecules at the interface between an insulating electrode such as silicon oxide and an electrolyte solution. Light-controlled electrokinetic assembly of particles near surfaces relies on the combination of three functional elements: the AC electric field-induced assembly of planar aggregates; the patterning of the electrolyte/silicon oxide/silicon interface to exert spatial control over the assembly process; and the real-time control of the assembly process via external illumination. The present invention provides a set of fundamental operations enabling interactive control over the creation and placement of planar arrays of several types of particles and biomolecules and the manipulation of array shape and size. The present invention enables sample preparation and handling for diagnostic assays and biochemical analysis in an array format, and the functional integration of these operations. In addition, the present invention provides a procedure for the creation of material surfaces with desired properties and for the fabrication of surface-mounted optical components.

Claims

1. An ordered planar array comprising several different particle types with different oligonucleotides attached to different particle types, said particles up to 10 microns in diameter, wherein the relative positions of particular particle types with respect to other particular particle types in the array are random and are not determined before the planar array is formed, and said particles are encoded with a characteristic that permits identification of the oligonucleotides attached thereto and permits distinguishing and identifying the different particle types without removing the particles from the array, and wherein said particles are immobilized on a substrate in a spatially non-random, crystalline configuration such that the particles have portions of their surfaces facing corresponding portions of surfaces of other particles without physical barriers between said corresponding portions of surfaces.

2. The ordered planar array according to claim 1, wherein the oligonucleotides hybridize with target complementary oligonucleotides under appropriate conditions.

3. The ordered planar array according to claim 1, wherein the target oligonucleotides are single nucleic acid strands.

4. The ordered planar array according to claim 3, wherein the nucleic acid strands comprise DNA derived from a human being or complementary or homologous to DNA derived from a human being.

5. The ordered planar array according to claim 3, wherein the nucleic acid strands include fragments of DNA or RNA.

6. The ordered planar array according to claim 1, wherein the substrate comprises a semiconductor.

7. The ordered planar array of claim 6 wherein the semiconductor is silicon.

8. The ordered planar array according to claim 1, wherein the substrate comprises an electrode.

9. The ordered planar array according to claim 1, wherein the characteristic is chemical tags associated with individual particles.

10. The ordered planar array according to claim 9, wherein the chemical tags are capable of being interrogated optically.

11. The ordered planar array of claim 9 wherein the chemical tags are oligonucleotides.

12. The ordered planar array of claim 11 wherein the oligonucleotides encode the particles with a binary code.

13. The ordered planar array of claim 10 wherein the chemical tags are oligonucleotides.

14. The ordered planar array of claim 11 or 13 wherein the chemical tags are fluorescent oligonucleotides.

15. The ordered planar array of claim 14 wherein the oligonucleotides encode the particles with a binary code.

16. The ordered planar array of claim 9 wherein the chemical tags are fluorescent.

17. The ordered planar array according to claim 1, wherein the particles are affixed to the substrate.

18. The ordered planar array according to claim 17, wherein the affixing is by chemical bonding.

19. The ordered planar array of claim 17 wherein the affixing is permanent.

20. The ordered planar array according to claim 1, wherein the oligonucleotides are exposed to a contiguous liquid phase containing nucleic acid strands complementary to the oligonucleotides.

21. The ordered planar array according to claim 1, further comprising a multiplicity of subarrays of ordered planar arrays, wherein the location of a particular subarray on said substrate in combination with the encoding uniquely identifies the types of particles located therein.

22. The ordered planar array of claim 1 wherein the particles range in diameter from 1 to 10 microns.

23. Several ordered planar arrays of claim 1 each in a different area of the substrate.