Systems and methods for automated reusable parallel biological reactions

• US 10,472,674 B2
• Filed: 11/23/2016
• Issued: 11/12/2019
• 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): Zhang, Kaijiang
• Application Number:
  US15/360,369
• Publication Number:
  US 20170073750A1
• Time in Patent Office: 1,084 Days
• Field of Search: None
• 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 or biological applications
• CPC Class Codes: B03C 5/005 : Dielectrophoresis, i.e. dielectric particles migrating towards the region of highest field strength
• 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 identifying at least a portion of a biological material, comprising:

a container configured to retain a solution containing or suspected of containing said biological material;

a sensor adjacent to said container, wherein said sensor comprises at least two electrodes configured to (i) couple to a double layer associated with said biological material and (ii) detect one or more signals indicative of a change of charge or conductivity within said double layer, wherein during use, said at least two electrodes are exposed to said solution containing or suspected of containing said biological material; and

a detection module operatively coupled to said sensor, wherein said detection module is configured to use said one or more signals detected by said sensor to identify said at least said portion of said biological material.

2. The system of claim 1, wherein said sensor comprises more than two electrodes.

3. The system of claim 1, wherein said at least two electrodes are separated by a dielectric.

4. The system of claim 1, wherein said sensor is configured to detect said one or more signals within said double layer associated with said biological material when said biological material is coupled to a support adjacent to said sensor.

5. The system of claim 4, wherein said at least two electrodes are electrically isolated in the absence of said support.

6. The system of claim 4, 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, during use, said particle is positioned adjacent to said sensor such that said double layer is in electrical communication with said particle and said sensor.

8. The system of claim 6, wherein said container is a well that aids in limiting motion of said particle while detecting said at least said portion of said biological material.

9. The system of claim 6, further comprising a magnet that, during use, provides a magnetic force that immobilizes said particle adjacent to said sensor.

10. The system of claim 1, further comprising a confinement unit that is configured to attract said biological material or one or more reagents to said container, which one or more reagents are for conducting one or more reactions on said biological material.

11. The system of claim 10, wherein said confinement unit is configured to selectively attract charged species in said solution to reduce contamination of said biological material or said one or more reagents in said container.

12. The system of claim 10, wherein said confinement unit comprises a plurality of electrodes that is configured to direct said biological material or said one or more reagents to said container.

13. The system of claim 1, further comprising read-out circuitry that receives said one or more signals from said sensor.

14. The system of claim 1, wherein said biological material is a nucleic acid molecule.

15. The system of claim 14, wherein said detection module is configured to identify at least a portion of a sequence of said nucleic acid molecule.

16. The system of claim 1, wherein said biological material is a protein.

17. The system of claim 1, further comprising a plurality of sensors, which plurality of sensors comprises said sensor.

18. The system of claim 17, wherein said container encloses said plurality of sensors.

19. The system of claim 1, wherein said biological material is coupled to a surface of said sensor.

20. The system of claim 19, wherein said surface of said sensor is substantially planar.

21. The system of claim 1, wherein said one or more signals are indicative of said change of conductivity.