Systems and methods for automated reusable parallel biological reactions

• US 10,100,356 B2
• Filed: 09/21/2015
• Issued: 10/16/2018
• Est. Priority Date: 10/04/2010
• Status: Active Grant

• Current Assignee: Sequencing Health Incorporated
• Original Assignee: GenapSys, Inc.
• Inventors: Esfandyarpour, Hesaam, Oldham, Mark F., Parizi, Kosar Baghbani, Nordman, Eric S.
• Primary Examiner(s): Merkling, Sally A
• Application Number:
  US14/859,725
• Publication Number:
  US 20160076097A1
• Time in Patent Office: 1,121 Days
• 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 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, comprising:

at least one electrode that applies an electric field that concentrates or isolates molecules to each of a plurality of particles, wherein said plurality of particles are coupled to a biological species; and

a substantially planar sensor array adjacent to or downstream of said at least one electrode, wherein said substantially planar sensor array comprises a plurality of sensors comprising electrodes that are each (i) separate from said at least one electrode and (ii) in contact with a solution comprising said plurality of particles, wherein said plurality of sensors senses biological interaction events between said molecules and said biological species, and wherein said plurality of sensors senses said biological interaction events between said molecules and said biological species within Debye lengths of said plurality of particles or said plurality of sensors when said plurality of particles is disposed adjacent to said plurality of sensors.

2. The system of claim 1, wherein said biological species are nucleic acid molecules and said biological interaction events are nucleic acid incorporation events, and wherein in (b), said plurality of sensors sense said nucleic acid incorporation events during sequencing of said nucleic acid molecules.

3. The system of claim 2, further comprising a separation module upstream of said substantially planar sensor array, wherein said separation module separates particles among the plurality of particles that have nucleic acid molecules bound to or associated with the particles from particles that do not have nucleic acid molecules bound to or associated with the particles.

4. The system of claim 2, further comprising a fragmentation module upstream of said substantially planar sensor array, wherein said fragmentation module (i) fragments nucleic acid molecules to generate nucleic acid fragments and (ii) binds or associates the nucleic acid fragments with the plurality of particles.

5. The system of claim 1, wherein said biological species are proteins or antibodies.

6. The system of claim 1, wherein said substantially planar sensor array is downstream of said at least one electrode.

7. The system of claim 1, further comprising a magnetic array that is part of or adjacent to said planar sensor array, wherein said magnetic array provides a magnetic field to position an individual particle among said plurality of particles at a given position on the magnetic array.

8. The system of claim 1, wherein the substantially planar sensor array does not contain wells.

9. The system of claim 1, wherein an individual sensor of said substantially planar sensor array comprises two electrodes that measure an impedance of an individual particle among said plurality of particles during said biological interaction events.

10. The system of claim 1, wherein the plurality of sensors measure changes in at least one of (i) a charge associated with, or a change in, the Debye length of a surface of an individual sensor among said plurality of sensors, (ii) a charge associated with the Debye length or a change in the Debye length of an individual particle among said plurality of particles, (iii) and a charge associated with the Debye length or a change in the Debye length of nucleic acid molecules carried on said individual particle.

11. The system of claim 7, wherein said at least one electrode is a part of said magnetic array.

12. The system of claim 11, wherein said at least one electrode is positioned such that said electric field is disposed around said magnetic field at said given position on said magnetic array.

13. The system of claim 7, wherein said given position on said magnetic array comprises an individual sensor of said plurality of sensors.

14. The system of claim 1, further comprising a plurality of signal amplifiers coupled to said plurality of sensors.

15. The system of claim 1, wherein said at least one electrode is coupled to a microfluidic channel.

16. The system of claim 9, wherein said two electrodes of said individual sensor are separated by a dielectric.

17. The system of claim 1, wherein said at least one electrode is a pair of electrodes that apply said electric field.

18. The system of claim 1, wherein said plurality of sensors is in contact with a solution having said plurality of particles coupled to said biological species.

19. The system of claim 1, wherein said substantially planar sensor array is a two-dimensional array.

20. The system of claim 1, wherein said at least one electrode comprises a corrosion resistant metal, noble metal, noble metal alloy, or carbon.