Chamber free nanoreactor system

• US 9,399,217 B2
• Filed: 05/27/2012
• Issued: 07/26/2016
• Est. Priority Date: 10/04/2010
• Status: Active Grant

• Current Assignee: Sequencing Health Incorporated
• Original Assignee: GenapSys, Inc.
• Inventors: Esfandyarpour, Hesaam, Parizi, Kosar B., Oldham, Mark F.
• Primary Examiner(s): Woolwine, Samuel
• Assistant Examiner(s): Oyeyemi, Olayinka
• Application Number:
  US13/481,858
• Publication Number:
  US 20130034880A1
• Time in Patent Office: 1,521 Days
• Field of Search: 435/6.12, 435/91.2, 204/557, 204/660
• 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 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

Aspects of the invention include methods for improving the accuracy and read length of sequencing reactions by utilizing unlabeled unincorporable nucleotides, or by rephasing colony based sequencing reactions. Other aspects include systems and devices for improved measurement of biological reactions associated with bead which may be removed, utilizing current measurement methods through the counter ions associated with said beads due to the presence of reactants bound or associated with said bead, wherein electrodes for generating and measuring said current may be within the Debye length of said bead. Other aspects of the invention include methods for determining concentrations of input samples, means for reuse of an array, methods and apparatus for separating beads with different charge levels from each other.

Claims

1. A system for sensing a biological reaction in a solution, comprising:

a bead in said solution bound or attached to at least one biological reactant, wherein said biological reactant comprises a nucleic acid template;

a pair of electrodes in contact with said solution and positioned such that, during sensing by said pair of electrodes, said pair of electrodes are each within the Debye layer of said bead when said bead is immobilized in proximity to said pair of electrodes;

a bead capture feature that immobilizes said bead in proximity to said pair of electrodes; and

a device that (i) receives electrical signals from said pair of electrodes when said pair of electrodes is within the Debye layer of said bead, and (ii) using said electrical signals, determines change(s) in impedance resulting from a biological reaction with said nucleic acid template.

2. The system of claim 1, wherein one electrode of said pair of electrodes is on a device substrate, a dielectric layer is on said device electrode, and a second electrode of said pair of electrodes is on said dielectric layer.

3. The system of claim 1, wherein said pair of electrodes is part of an array of electrode pairs.

4. The system of claim 3, wherein said array comprises a 2D array of electrode pairs.

5. The system of claim 1, wherein said solution is an aqueous solution.

6. The system of claim 5, wherein said aqueous solution has an ionic concentration of less than 10⁻

8 molar.

7. The system of claim 1, wherein said solution is a miscible mixture of an aqueous solution and an organic solution.

8. The system of claim 7, wherein said miscible solution has an ionic concentration less than 10⁻

7 molar.

9. The system of claim 1, wherein one or more of the electrodes of said pair of electrodes is shaped to conform to the shape of said bead.

10. The system of claim 9, wherein said one or more electrodes of said pair of electrodes are shaped at least in part in an arc with a diameter similar to the diameter of said bead.

11. The system of claim 1, wherein at least one of said pair of electrodes is within at least 0.1 Debye lengths of said bead.

12. The system of claim 1, wherein said pair of electrodes comprises a first electrode and a second electrode separated by a dielectric layer, and wherein said device further comprises a substrate adjacent to said first electrode.

13. The system of claim 12, wherein said first electrode is below a center line of said bead, and said second electrode is above a center line of said bead.

14. The system of claim 1, wherein said electrodes are planar.

15. The system of claim 1, wherein an individual electrode of said pair of electrodes has a Debye layer.

16. The system of claim 1, wherein said device receives electrical signals from said pair of electrodes when said bead is immobilized in proximity to said pair of electrodes.

17. The system of claim 1, wherein said bead capture feature immobilizes said bead in proximity to said pair of electrodes by an immobilizing force.

18. The system of claim 17, wherein said immobilizing force is selected from the group consisting of a magnetic force and an electrical force.

19. The system of claim 17, wherein said bead capture feature comprises a magnet, and wherein said immobilizing force includes a magnetic force.

20. The system of claim 1, wherein said bead capture feature is selected from the group consisting of a magnetic structure and a depression.

21. The system of claim 1, wherein said bead capture feature is part of a magnetic array.