Methods for transport in molecular biological analysis and diagnostics

• US 6,238,624 B1
• Filed: 10/04/1996
• Issued: 05/29/2001
• Est. Priority Date: 11/01/1993
• Status: Expired due to Term

• Current Assignee: Gamida for Life B.V.
• Original Assignee: Nanogen, Inc.
• Inventors: Evans, Glen A., Tu, Eugene, Heller, Michael J., Sosnowski, Ronald G.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US08/726,278
• Time in Patent Office: 1,698 Days
• Field of Search: 422/50, 422/68.1, 435/6, 435/7.1, 435/7.2, 530/333, 530/334, 436/501, 935/77.78, 536/25.3
• US Class Current: 422/68.1
• 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 19/0093 Microreactors, e.g. miniaturised or microfabricated reactors laboratory containers with capillary fluid transport in microfabricated channels or chambers B01L3/5027
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• 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 2219/00686 Automatic
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00713 : Electrochemical synthesis
• CPC Class Codes: B01J 2219/0072 : Organic compounds
• 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 2219/00822 : Metal
• CPC Class Codes: B01J 2219/00828 : Silicon wafers or plates
• CPC Class Codes: B01J 2219/00844 : Comprising porous material
• CPC Class Codes: B01J 2219/00853 : Employing electrode arrangements
• CPC Class Codes: B01L 2300/0636 : Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0645 : Electrodes
• CPC Class Codes: B01L 2300/0816 : Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0819 : Microarrays; Biochips
• CPC Class Codes: B01L 2300/0829 : Multi-well plates; Microtitration plates
• CPC Class Codes: B01L 2300/0877 : Flow chambers
• CPC Class Codes: B01L 2400/0421 : electrophoretic flow
• CPC Class Codes: B01L 3/502707 : characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B01L 3/502715 : characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/502761 : specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: B01L 3/5085 : for multiple samples, e.g. microtitration plates
• CPC Class Codes: B82Y 10/00 : Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• CPC Class Codes: B82Y 5/00 : Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 : Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07K 1/04 : on carriers C07K1/003, C07K1/006 take precedence
• CPC Class Codes: C07K 1/045 : using devices to improve synthesis, e.g. reactors, special vessels
• CPC Class Codes: C07K 1/047 : Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C12Q 1/6813 : Hybridisation assays
• CPC Class Codes: C12Q 1/6816 : characterised by the detection means C12Q1/6804 takes precedence
• 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 2565/515 : characterised by the interaction between or sequential use of two or more arrays
• CPC Class Codes: C12Q 2565/607 : being a sensor, e.g. electrode
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 40/12 : Libraries containing saccharides or polysaccharides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G11C 13/0014 : comprising cells based on organic memory material
• CPC Class Codes: G11C 13/0019 : comprising bio-molecules
• CPC Class Codes: G11C 19/00 : Digital stores in which the information is moved stepwise, e.g. shift registers
• CPC Class Codes: H01L 2224/45144 : Gold (Au) as principal constituent
• CPC Class Codes: H01L 2224/95144 : Magnetic alignment, i.e. using permanent magnetic parts in the semiconductor or solid-state body
• CPC Class Codes: H01L 2224/95145 : Electrostatic alignment, i.e. polarity alignment with Coulomb charges
• CPC Class Codes: H01L 2224/95147 : by molecular lock-key, e.g. by DNA
• CPC Class Codes: H01L 25/50 : Multistep manufacturing processes of assemblies consisting of devices, each device being of a type provided for in group H01L27/00 or H01L29/00 H01L21/50 takes precedence
• CPC Class Codes: H01L 29/6656 : using multiple spacer layers, e.g. multiple sidewall spacers
• CPC Class Codes: H01L 29/6659 : with both lightly doped source and drain extensions and source and drain self-aligned to the sides of the gate, e.g. lightly doped drain [LDD] MOSFET, double diffused drain [DDD] MOSFET
• CPC Class Codes: H01L 29/66628 : recessing the gate by forming single crystalline semiconductor material at the source or drain location
• CPC Class Codes: H01L 29/7834 : with a non-planar structure, e.g. the gate or the source or the drain being non-planar
• CPC Class Codes: H01L 2924/00 : Indexing scheme for arrangements or methods for connecting or disconnecting semiconductor or solid-state bodies as covered by H01L24/00
• CPC Class Codes: H01L 2924/01019 : Potassium [K]
• CPC Class Codes: H01L 2924/0102 : Calcium [Ca]
• CPC Class Codes: H01L 2924/01046 : Palladium [Pd]
• CPC Class Codes: H01L 2924/01078 : Platinum [Pt]
• CPC Class Codes: H01L 2924/01079 : Gold [Au]
• CPC Class Codes: H01L 2924/10253 : Silicon [Si]
• CPC Class Codes: Y10S 435/808 : Optical sensing apparatus
• CPC Class Codes: Y10S 435/814 : Enzyme separation or purification
• CPC Class Codes: Y10S 436/805 : Optical property
• CPC Class Codes: Y10T 436/25125 : Digestion or removing interfering materials

Abstract

A self-addressable, self-assembling microelectronic device is designed and fabricated to actively carry out and control multi-step and multiplex molecular biological reactions in microscopic formats. These reactions include nucleic acid hybridizations, antibody/antigen reactions, diagnostics, and biopolymer synthesis. The device can be fabricated using both microlithographic and micro-machining techniques. The device can electronically control the transport and attachment of specific binding entities to specific micro-locations. The specific binding entities include molecular biological molecules such as nucleic acids and polypeptides. The device can subsequently control the transport and reaction of analytes or reactants at the addressed specific micro-locations. The device is able to concentrate analytes and reactants, remove non-specifically bound molecules, provide stringency control for DNA hybridization reactions, and improve the detection of analytes. The device can be electronically replicated.

Claims

1. A method for electronically transporting a charged entity in a solution from a first microlocation to a second microlocation, each individual microlocation serving to electronically control transport of said charged entity to a microlocation, comprising the steps of:

contacting said first and second microlocations with said solution;

placing said first microlocation at an opposite charge to said charged entity relative to said second microlocation, thereby transporting said charged entity to said first microlocation;

thereafter, placing said second microlocation at an opposite charge to said charged entity, relative to said first microlocation, thereby transporting said charged entity from said first microlocation to said second microlocation; and

attaching said charged entity to one or more of said microlocations.

2. The method of claim 1, wherein said charged entity is a nucleic acid.

3. The method of claim 1 further including the step of placing the second microlocation at a like charge to said charged entity when the first microlocation is at an opposite charge to said charged entity.

4. The method of claim 3 further including the step of placing the first microlocation at a like charge to said charged entity when the second microlocation is at an opposite charge to said charged entity.

5. The method of claim 1 wherein the charged entity is a charged functionalized specific binding entity.

6. The method of claim 3 or 5 wherein the charged functionalized specific binding entity is transported to the first microlocation and coupled to the first microlocation.

7. The method of claim 6 wherein the coupling is non-covalent coupling.

8. The method of claim 6 further including the step of transporting and coupling a second, different charged functionalized specific binding entity to said second microlocation.

9. The method of claim 1 wherein the first microlocation includes a coupled binding entity and electronically enhanced hybridization is effected between said coupled binding entity and said charged entity.

10. The method of claim 9 wherein the first microlocation is placed at a like charge to said charged entity.

11. The method of claim 10 wherein electronic stringency control is effected.

12. The method of claim 1 wherein the first microlocation has first binding entities bound thereto and the second microlocation has second binding entities bound thereto, where the first binding entities and second binding entities differ, whereby at least some of said charged entities are sequentially reacted at the first microlocation and then the second microlocation.

13. The method of claim 6 wherein the coupling between the charged functionalized specific binding entity and the first microlocation is covalent coupling.

14. A method for producing a complement of a master electronic device containing multiple microlocations having specific nucleic acid sequences, comprising the steps of:

providing complementary sequences to said specific nucleic acid sequences and hybridizing said complementary sequences to said specific nucleic acid sequences on said master device;

aligning microlocations on a recipient device containing multiple microlocations with the microlocations on said master device; and

placing the microlocations on said master device repulsive to said complementary sequences and the microlocations on said recipient device attractive to said complementary sequences, thereby transporting said complementary sequences to said microlocations on said recipient device.

15. The method for producing a complement of a master electronic device of claim 14, further comprising the step of providing a positively charged chaotropic agent or denaturant to denature the complementary sequences from the master template.

16. The method for producing a complement of a master electronic device of claim 14 wherein the transporting of said complementary sequences to said microlocations on said recipient device is performed in series.

17. The method for producing a complement of a master electronic device of claim 14 wherein the microlocations on said master device are placed sufficiently negative to denature the said complementary sequences from said specific nucleic acid sequences.

18. A method for producing a complement of an electronic device having specific DNA sequences, comprising the steps of:

hybridizing the complementary sequences to the specific DNA sequences on a master electronic device;

aligning locations at a recipient electronic device with the locations on a said master device; and

placing the locations on said master device negative and the locations on said recipient device positive, transporting the complementary sequences to said recipient device.

19. The method for producing a complement of patterned sequences of claim 18, further comprising denaturing the complementary sequences from the master electronic device in parallel.

53. The method for producing a complement of a master electronic device of claim 18 wherein the transporting of said complementary sequences to said microlocations on said recipient device is performed in parallel.

20. A method for electronically transporting charged entities in a solution from a first microlocation having first binding entities bound thereto to a second microlocation, having second binding entities bound thereto, where the first binding entities and second binding entities differ, each individual microlocation serving to electronically control transport of said charged entities to a microlocation, comprising the steps of:

contacting said first and second microlocations with said solution;

placing said first microlocation at an opposite charge to said charged entities, relative to said second microlocation, thereby transporting said charged entities to said first microlocation and reacting the charged entities with said first binding entities;

thereafter, placing said second microlocation at an opposite charge to said charged entities, relative to said first microlocation, thereby transporting said charged entities from said first microlocation to said second microlocation and reacting the charged entities with said second binding entities.

21. A method for operating an active biological device having an array of microlocations, including at least a first microlocation having a first probe and a second microlocation having a second probe, the first probe and the second probe not being equal, the device adapted to receive a solution including one or more charged entities, the method comprising the steps of:

placing the first microlocation attractive to affect the free field electrophoretic transport certain of said charged entities to the first microlocation and simultaneously

placing the second microlocation repulsive to cause the repulsion of said certain of said charged entities from the second microlocation.

22. The method of claim 21 wherein the solution includes charged functionalized specific binding entities.

23. The method of claim 22 wherein the charged functionalized binding entity is attracted to the first microlocation and coupled to the first microlocation.

24. The method of claim 23 wherein the coupling is covalent coupling.

25. The method of claim 23 wherein the coupling is non-covalent coupling.

26. The method of claim 23 further including the step of providing second charged functionalized specific binding entity to the second microlocation.

27. The method of claim 21 wherein the charged entities are concentrated at the first microlocation relative to the second microlocation.

28. The method of claim 21 wherein the first microlocation includes a bound specific binding entity and the placing of the first microlocation effects electronically enhanced hybridization between said specific binding entity and said charged entities.

29. The method of claim 21 wherein the microlocation continues to affect free field electrophoretic transport of charged binding entities after charged binding entity has been transported to the microlocation.

30. The method of claim 21 further including the step of placing the first microlocation at a like charge to said charged entity when the second microlocation is at an opposite charge to said charged entity.

31. The method of claim 21 wherein the placing of the first microlocation is equal to and opposite that of the second microlocation.

32. The method of claim 21 wherein all of the microlocations are at said opposite potential except the first microlocation.

33. The method of claim 21 wherein the microlocations are arranged in an array of rows and columns.

34. The method of claim 33 wherein all of the microlocations are at said opposite potential except for selected rows of microlocations, which are placed to affect the free field electrophoretic transport of the charged specific binding entity to that row.

35. The method of claim 33 wherein all of the microlocations are at said opposite potential except for selected columns of microlocations, which are placed to affect the free field electrophoretic transport of the charged specific binding entity to that column.

36. The method of claim 33 wherein the microlocations are arranged in an array of M rows and N columns.

37. The method of claim 36 wherein M=N.

38. The method of claim 36 wherein the array is at least an eight by eight array of microlocations.

39. The method of claim 33 wherein the microlocations are at said opposite potential except for a selected set of microlocations, which are placed in a condition to affect the free field electrophoretic transport of the charged specific binding entity to that set.

40. The method of claim 21 further comprising the step of, after the charged specific binding entity has been transported to the first microlocation, reversing the state of the first microlocation.

41. The method of claim 40 wherein reversing the state of the first microlocation effects electronic stringency control.

42. The method of claim 40 further comprising the step of reversing the state at the second microlocation.

43. The method of claim 21 wherein charged specific binding entities are transported from the first microlocation to the second microlocation.

44. A method for serial hybridization with a charged entity on an active programmable matrix device having at least a first location including a first specific binding entity and a second location including a second binding entity, the first binding entity being different from the second binding entity, comprising the steps of:

placing a solution containing the charged entity in contact with the device, including the said first location and the second location,

providing an attractive potential on said first location relative to other locations, transporting the charged entity to said first location, and thereafter,

providing an attractive potential on said second location relative to said first location, transporting at least a portion of said charged entity to said second location.

45. The method for serial hybridization of claim 44 further including the step of providing a repulsive potential on the said first location when said attractive potential is applied to said second location.

46. The method of claim 44 wherein placing of the microlocations attractive relative to the charged entity effects electronically enhanced hybridization between said specific binding entities and said charged entities.

47. The method of claim 44 further including the step of placing the first microlocation at a like charge to said charged entity when the second microlocation is at an opposite charge to said charged entity.

48. The method of claim 47 wherein the placing of the first microlocation is equal to and opposite that of the second microlocation.

49. The method of claim 44 further comprising the step of, after the charged specific binding entity has been transported to the first microlocation, changing to a repulsive potential on the first microlocation.

50. The method of claim 49 wherein reversing the state of the first microlocation effects electronic stringency control.

51. The method of claim 44 further comprising the step of reversing the potential at the second microlocation.

52. The method of claim 49 wherein charged specific binding entities are transported from the first microlocation to the second microlocation.

54. A method for producing a complement of a master electronic device having multiple microlocations, the microlocations including specific binding sequences, comprising the steps of:

hybridizing complementary sequences to said binding sequences on said master device;

aligning microlocations on a recipient electronic device having multiple microlocations with the microlocations on said master device; and

placing the microlocations on said master device to be repulsive to said complementary sequences, thereby transporting the complementary sequences to said microlocations on said recipient device.

55. The method for producing a complement of a master electronic device of claim 54, further comprising the step of providing a positively charged chaotropic agent or denaturant to denature the complementary sequences from the master template.

56. The method for producing a complement of a master electronic device of claim 54 where in the transporting of said complementary sequences to said microlocations on said recipient device is performed in parallel.

57. The method for producing a complement of a master electronic device of claim 54 wherein the transporting of said complementary sequences to said microlocations on said recipient device is performed in series.

58. The method for producing a complement of a master electronic device of claim 54 wherein the microlocations on said master device are placed sufficiently negative to denature the said complementary sequences from said specific nucleic acid sequences.

59. A method for producing a complement of an electronic device addressed with DNA sequences, comprising the steps of:

addressing specific DNA sequences to a master electronic device;

aligning locations at a recipient electronic device with the locations on a said master device; and

placing the locations on said master device negative and the locations on said recipient device positive, transporting the complementary sequences to said recipient device.

60. The method for producing a complement of patterned sequences of claim 59, further comprising denaturing the complementary sequences from the master template in parallel.