Systems and methods for automated reusable parallel biological reactions

• US 9,533,305 B2
• Filed: 08/25/2015
• Issued: 01/03/2017
• Est. Priority Date: 10/04/2010
• Status: Active Grant

• Current Assignee: Sequencing Health Incorporated
• Original Assignee: GenapSys, Inc.
• Inventors: Esfandyarpour, Hesaam, Oldham, Mark
• Primary Examiner(s): Woolwine, Samuel
• Assistant Examiner(s): Zhang, Kaijiang
• Application Number:
  US14/835,070
• Publication Number:
  US 20150368707A1
• Time in Patent Office: 497 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: B01L 2200/0652 Sorting or classification of particles or molecules
• CPC Class Codes: B01L 2200/0668 Trapping microscopic beads
• CPC Class Codes: B01L 2200/0689 Sealing
• 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 2300/0645 Electrodes
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0887 Laminated structure
• CPC Class Codes: B01L 2300/089 Virtual walls for guiding liquids
• CPC Class Codes: B01L 2300/12 Specific details about materials
• CPC Class Codes: B01L 2300/123 Flexible; Elastomeric
• CPC Class Codes: B01L 2400/0415 electrical forces, e.g. electrokinetic
• CPC Class Codes: B01L 2400/0418 electro-osmotic flow [EOF]
• CPC Class Codes: B01L 2400/0421 electrophoretic flow
• 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 2400/0478 pistons
• CPC Class Codes: B01L 2400/0655 pinch valves
• CPC Class Codes: B01L 3/502738 characterised by integrated valves microvalves F16K99/0001
• 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 7/52 : with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples amplification or hybridisation processes per se C12Q1/68; controlling sequential reactions for synthesis B01J19/0046
• CPC Class Codes: B03C 1/286 : disposed at the inner circumference of a recipient, e.g. magnetic drain bolt
• CPC Class Codes: B03C 1/288 : disposed at the outer circumference of a recipient
• CPC Class Codes: B03C 1/30 : Combinations with other devices, not otherwise provided for
• CPC Class Codes: B03C 2201/26 : for use in medical applications
• CPC Class Codes: B03C 5/005 : Dielectrophoresis, i.e. dielectric particles migrating towards the region of highest field strength B03C5/02 takes precedence; electrophoresis B01D57/02
• CPC Class Codes: B03C 5/022 : Non-uniform field separators
• CPC Class Codes: B03C 5/026 : using open-gradient differential dielectric separation, i.e. using electrodes of special shapes for non-uniform field creation, e.g. Fluid Integrated Circuit [FIC]
• CPC Class Codes: C12Q 1/6848 : characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
• CPC Class Codes: C12Q 1/6853 : using modified primers or templates
• CPC Class Codes: C12Q 1/6869 : Methods for sequencing
• CPC Class Codes: C12Q 1/6874 : involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2523/307 : Denaturation or renaturation by electric current/voltage
• CPC Class Codes: C12Q 2563/116 : electrical properties of nucleic acids, e.g. impedance, conductivity or resistance
• CPC Class Codes: C12Q 2563/143 : Magnetism, e.g. magnetic label
• CPC Class Codes: C12Q 2565/543 : characterised by the use of two or more capture oligonucleotide primers in concert, e.g. bridge amplification
• CPC Class Codes: C12Q 2565/607 : being a sensor, e.g. electrode
• CPC Class Codes: C40B 60/10 : for identifying library members
• CPC Class Codes: G01N 1/40 : Concentrating samples
• CPC Class Codes: G01N 2001/4038 : electric methods, e.g. electromigration, electrophoresis, ionisation
• CPC Class Codes: G01N 27/4145 : specially adapted for biomolecules, e.g. gate electrode with immobilised receptors
• CPC Class Codes: G01N 27/4146 : involving nanosized elements, e.g. nanotubes, nanowires
• CPC Class Codes: G01N 33/5438 : Electrodes
• CPC Class Codes: H01L 29/00 : Semiconductor devices specially adapted for rectifying, amplifying, oscillating or switching and having potential barriers; Capacitors or resistors having potential barriers, e.g. a PN-junction depletion layer or carrier concentration layer; Details of semiconductor bodies or of electrodes thereof ; Multistep manufacturing processes therefor H01L31/00 - H01L33/00, H10K10/00, H10N take precedence; details other than of semiconductor bodies or of electrodes thereof H01L23/00; devices consisting of a plurality of solid state components formed in or on a common substrate H01L27/00

Abstract

A method comprises magnetically holding a bead carrying biological material (e.g., nucleic acid, which may be in the form of DNA fragments or amplified DNA) in a specific location of a substrate, and applying an electric field local to the bead to isolate the biological material or products or byproducts of reactions of the biological material. For example, the bead is isolated from other beads having associated biological material. The electric field in various embodiments concentrates reagents for an amplification or sequencing reaction, and/or concentrates and isolates detectable reaction by-products. For example, by isolating nucleic acids around individual beads, the electric field can allow for clonal amplification, as an alternative to emulsion PCR. In other embodiments, the electric field isolates a nanosensor proximate to the bead, to facilitate detection of at least one of local pH change, local conductivity change, local charge concentration change and local heat. The beads may be trapped in the form of an array of localized magnetic field regions.

Claims

1. A system for detecting a biological material or a reaction associated with said biological material, comprising:

a support;

a sensor array comprising a sensor that includes a plurality of electrodes that provides an electrical current flow path for detecting signals indicative of a change of impedance only within a Debye length associated with said support, said support comprising said biological material coupled thereto, wherein said plurality of electrodes detects said signals (i) while said biological material is coupled to said support or (ii) during said reaction associated with said biological material, and wherein during use, said plurality of electrodes is exposed to a solution comprising said biological material coupled to said support; and

a detection module that detects said biological material or said reaction associated with said biological material based on said signals detected by said plurality of electrodes, which signals are indicative of said change of impedance within said Debye length associated with said support.

2. The system of claim 1, wherein said detection module comprises said plurality of electrodes.

3. The system of claim 1, further comprising read-out circuitry that receives said signals from said plurality of electrodes.

4. The system of claim 3, wherein said detection module comprises said read-out circuitry.

5. The system of claim 1, wherein during use, said plurality of electrodes is within said Debye length associated with said support.

6. The system of claim 1, wherein said support is a particle, and wherein during use, said biological material is coupled to said particle.

7. The system of claim 6, wherein said plurality of electrodes includes individual electrodes that are electrically separated in the absence of said particle in proximity to said plurality of electrodes.

8. The system of claim 6, wherein during use, said particle is immobilized in proximity to said plurality of electrodes.

9. The system of claim 8, wherein during use, said particle is immobilized in proximity to said plurality of electrodes via a magnetic force.

10. The system of claim 6, wherein said sensor array comprises a well structure that aids in limiting motion of said particle while detecting said biological material or said reaction associated with said biological material.

11. The system of claim 1, wherein said plurality of electrodes detects said signals while said biological material is coupled to said support and during said reaction associated with said biological material.

12. The system of claim 1, wherein during use, said plurality of electrodes detects said change of impedance within said Debye length associated with said support.

13. The system of claim 1, wherein said biological material comprises a nucleic acid molecule.

14. The system of claim 1, wherein said biological material comprises a protein or antibody.

15. The system of claim 1, wherein said reaction is a sequencing reaction.

16. The system of claim 1, wherein said plurality of electrodes includes electrodes that are separated by a dielectric.

17. The system of claim 1, wherein said sensor array comprises an electrode that at least partially encircles said support.

18. The system of claim 1, wherein said plurality of electrodes provides said electrical current flow path for detecting signals indicative of said change of impedance without the use of a redox sensitive material.

19. A method for detecting a biological material or a reaction associated with said biological material, comprising:

(a) exposing a plurality of electrodes to a solution comprising said biological material coupled to a support, wherein said plurality of electrodes provides an electrical current flow path for detecting signals indicative of a change of impedance only within a Debye length associated with said support comprising said biological material coupled thereto, wherein said plurality of electrodes is part of a sensor in a sensor array;

(b) using said plurality of electrodes to detect said signals, wherein said plurality of electrodes detects said signals (i) while said biological material is coupled to said support or (ii) during said reaction associated with said biological material; and

(c) detecting said biological material or said reaction associated with said biological material based on said signals detected by said plurality of electrodes in (b), which signals are indicative of said change of impedance within said Debye length associated with said support.

20. The method of claim 19, wherein said signals are directed from said plurality of electrodes to read-out circuitry.

21. The method of claim 19, wherein said plurality of electrodes is within said Debye length associated with said support.

22. The method of claim 19, wherein said support is a particle, and wherein said biological material is coupled to said particle.

23. The method of claim 22, wherein said plurality of electrodes includes individual electrodes that are electrically separated in the absence of said particle in proximity to said plurality of electrodes.

24. The method of claim 22, wherein said particle is immobilized in proximity to said plurality of electrodes.

25. The method of claim 24, wherein during use, said particle is immobilized in proximity to said plurality of electrodes via a magnetic force.

26. The method of claim 22, wherein said sensor array comprises a well structure that aids in limiting motion of said particle while detecting said biological material or said reaction associated with said biological material.

27. The method of claim 19, wherein said plurality of electrodes detects said signals while said biological material is coupled to said support and during said reaction associated with said biological material.

28. The method of claim 19, wherein said plurality of electrodes detects said change of impedance within said Debye length associated with said support.

29. The method of claim 19, wherein said biological material comprises a nucleic acid molecule.

30. The method of claim 19, wherein said biological material comprises a protein or antibody.

31. The method of claim 19, wherein said reaction is a sequencing reaction.

32. The method of claim 19, wherein said plurality of electrodes provides said electrical current flow path for detecting signals indicative of said change of impedance without the use of a redox sensitive material.

33. A system for detecting a biological material or a reaction associated with said biological material, comprising:

a particle;

a sensor array comprising a sensor that includes a plurality of electrodes that provides an electrical current flow path for detecting signals indicative of a change of impedance within a Debye length associated with said particle, said particle comprising said biological material coupled thereto, wherein said plurality of electrodes detects said signals (i) while said biological material is coupled to said particle or (ii) during said reaction associated with said biological material, and wherein during use, said plurality of electrodes is exposed to a solution comprising said biological material coupled to said particle; and

a detection module that detects said biological material or said reaction associated with said biological material based on said signals detected by said plurality of electrodes, which signals are indicative of said change of impedance within said Debye length associated with said particle.

34. A method for detecting a biological material or a reaction associated with said biological material, comprising:

(a) exposing a plurality of electrodes to a solution comprising said biological material coupled to a particle, wherein said plurality of electrodes provides an electrical current flow path for detecting signals indicative of a change of impedance within a Debye length associated with said particle comprising said biological material coupled thereto, wherein said plurality of electrodes is part of a sensor in a sensor array;

(b) using said plurality of electrodes to detect said signals, wherein said plurality of electrodes detects said signals (i) while said biological material is coupled to said particle or (ii) during said reaction associated with said biological material; and

(c) detecting said biological material or said reaction associated with said biological material based on said signals detected by said plurality of electrodes in (b), which signals are indicative of said change of impedance within said Debye length associated with said particle.