Droplet-based microfluidic oligonucleotide synthesis engine

• US 20030170698A1
• Filed: 01/03/2003
• Published: 09/11/2003
• Est. Priority Date: 01/04/2002
• Status: Abandoned Application

• Current Assignee: Board of Regents of the University of Texas System (University of Texas System)
• Original Assignee: Board of Regents of the University of Texas System (University of Texas System)
• Inventors: Vykoukal, Jody V., Becker, Frederick F., Gascoyne, Peter, Schwartz, Jon
• Application Number:
  US10/336,609
• Publication Number:
  US 20030170698A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 2219/00358 electrode driven
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00704 integrated with the reactor apparatus
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 2200/10 Integrating sample preparation and analysis in single entity, e.g. lab-on-a-chip concept
• CPC Class Codes: B01L 2300/0819 Microarrays; Biochips
• CPC Class Codes: B01L 2400/0424 Dielectrophoretic forces
• CPC Class Codes: B01L 2400/0427 Electrowetting
• CPC Class Codes: B01L 2400/043 magnetic forces
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 3/502792 for moving individual droplets on a plate, e.g. by locally altering surface tension
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites

Abstract

Devices, systems, and methods for an oligonucleotide synthesis engine. In on embodiment, the invention involves a microfluidic device including: an oligonucleotide synthesis subunit including a reaction surface and means for generating a manipulation force and routing for packet delivery; an analysis or diagnostic subunit; and a control subunit including a program to direct oligonucleotide synthesis. In another embodiment, the invention involves a method for analyzing a sample. An oligonucleotide is synthesized in a solid-phase oligonucleotide synthesis subunit, wherein the subunit includes a reaction surface and means for generating a manipulation force and routing for packet delivery. The synthesis is controlled with a control subunit, wherein the control subunit is programmed for the automatic synthesis of oligonucleotides. The sample is analyzed in an analysis or diagnostic subunit.

Claims

1. A microfluidic device comprising:

an oligonucleotide synthesis subunit comprising a reaction surface and means for generating a manipulation force and routing for packet delivery;

an analysis or diagnostic subunit; and

a control subunit comprising a program to direct oligonucleotide synthesis.

2. The device of claim 1, comprising a programmable fluidic processor (PFP).

3. The device of claim 2, wherein a sequence to be synthesized is downloaded to the control electronics of said PFP.

4. The device of claim 3, wherein sequences are downloaded to the control electronics of said PFP.

5. The device of claim 2, wherein said PFP is configured to act as a program manifold.

6. The device of claim 5, wherein said program manifold routes and delivers one or more reagents.

7. The device of claim 1, wherein said synthesis subunit comprises wall-less channels.

8. The device of claim 1, wherein said synthesis subunit is adapted for use with phosphoramidite chemistry.

9. The device of claim 8, wherein said phosphoramidite chemistry is modified phosphoramidite chemistry.

10. The device of claim 1, wherein said synthesis subunit comprises a bead or reagent reservoir.

11. The device of claim 1, wherein said routing for packet delivery comprises using dielectrophoresis.

12. The device of claim 1,wherein said analysis or diagnostic subunit comprises wall-less channels.

13. The device of claim 1, wherein said analysis or diagnostic subunit is adapted for measuring impedance, conductance, electrophoretic movements, fluorescence, mass ion peaks, hybridization, ligase, base addition, and/or fluocytometry.

14. A method of using the device of claim 1.

15. A method for analyzing a sample comprising:

synthesizing an oligonucleotide in a solid-phase oligonucleotide synthesis subunit, wherein said subunit comprises a reaction surface and means for generating a manipulation force and routing for packet delivery;

controlling said synthesis with a control subunit wherein said control subunit is programmed for the automatic synthesis of oligonucleotides; and

analyzing said sample in an analysis or diagnostic subunit.

16. The method of claim 15, wherein said synthesis subunit or said analysis or diagnostic subunit comprises a programmable fluidic processor (PFP).

17. The method of claim 16, further comprising downloading the sequence of said oligonucleotide to the control electronics of the PFP.

18. The method of claim 17, further comprising downloading 2-1000 oligonucleotide sequences to the control electronics of said PFP.

19. The method of claim 16, wherein said PFP is configured to act as a program manifold.

20. The method of claim 19, wherein said program manifold is used for reagent routing and delivery.

21. The method of claim 15, wherein said analysis is controlled by said control subunit.

22. The method of claim 15, wherein said oligonucleotide is 10-20 base pairs in length.

23. The method of claim 15, wherein synthesizing comprises using phosphoramidite chemistry.

24. The device of claim 23, wherein said phosphoramidite chemistry is modified phosphoramidite chemistry.

25. The method of claim 15, further comprising using a protecting group during oligonucleotide synthesis.

26. The method of claim 25, wherein said protecting group comprises a sugar and a phosphate.

27. The method of claim 25, wherein said protecting group is removed by chemical or photochemical means.

28. The method of claim 27, further comprising using laser assisted deprotection.

29. The method of claim 15, further comprising analysis of said sample with MALDI-TOF MS.

30. The method of claim 15, further comprising synthesizing a second oligonucleotide, wherein the synthesis of two oligonucleotides occur in parallel.

31. The method of claim 15, further comprising synthesizing a second oligonucleotide, wherein the synthesis of two oligonucleotides occur sequentially.

32. The method of claim 15, wherein said solid-phase comprises dielectrically engineered beads.

33. The method of claim 32, wherein said beads are 2-50 μ

m in diameter.

34. The method of claim 32, wherein said beads are manipulated by dielectrophoresis.

35. The method of claim 32, wherein said beads are gold coated polystyrene beads.

36. The method of claim 32, wherein said beads are coated with a phospholipid.

37. The method of claim 32, wherein said beads are coated with a polyethylene glycol.

38. The method of claim 15, wherein said analyzing comprises gene discovery, SNP analysis, disease diagnosis, drug discovery, toxicological research, detection of chemical and biological warfare agents, analysis of terrorism agents, pathogen detection, pollution monitoring, water monitoring, fertilizer analysis, food pathogen detection, quality control and blending, massively parallel molecular biological protocols, genetic engineering, oncogene detection, or pharmaceutical development and testing.

39. The method of claim 15, wherein analyzing said sample comprises determining the interaction of said sample with said oligonucleotide.

40. The method of claim 15, wherein said oligonucleotide is synthesized immediately before analysis.

41. The method of claim 15, further comprising proofreading said oligonucleotide.

42. The method of claim 15, further comprising analyzing said sample a second time.

43. The method of claim 42, wherein said second analysis occurs in an analysis or diagnostic subunit.

44. The method of claim 42, wherein said second analysis occurs after removing said sample from said analysis or diagnostic subunit.

45. The method of claim 15, further comprising analyzing a second sample.

46. The method of claim 45, wherein synthesizing an oligonucleotide in a solid-phase oligonucleotide synthesis subunit for analysis of said second sample occurs before said analyzing the first sample in an analysis or diagnostic subunit is completed.

47. The method of claim 45, wherein said second sample is analyzed simultaneously with the first sample.

48. An apparatus for performing the method of claim 15.