Methods of bead manipulation and forming bead arrays

• US 10,351,907 B2
• Filed: 10/16/2014
• Issued: 07/16/2019
• Est. Priority Date: 08/31/2009
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Fry, George A., Inman, Christina E., Bridgham, John, Hunkapiller, Timothy, Vann, Charles S.
• Primary Examiner(s): Dines, Karla A
• Application Number:
  US14/515,741
• Publication Number:
  US 20150065356A1
• Time in Patent Office: 1,734 Days
• Field of Search: 506 7
• CPC Class Codes: B01F 33/30 Micromixers
• CPC Class Codes: B01F 33/403 for mixing liquids B01F33/402, B01F33/405, B01F33/406 take precedence
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 19/0093 Microreactors, e.g. miniaturised or microfabricated reactors laboratory containers with capillary fluid transport in microfabricated channels or chambers B01L3/5027
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00351 Means for dispensing and evacuation of reagents
• CPC Class Codes: B01J 2219/00466 in a slurry
• CPC Class Codes: B01J 2219/00511 Walls of reactor vessels
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00691 using robots
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00869 Microreactors placed in parallel, on the same or on different supports
• CPC Class Codes: B01L 2200/025 Align devices or objects to ensure defined positions relative to each other
• CPC Class Codes: B01L 2200/027 for microfluidic devices
• CPC Class Codes: B01L 2200/0647 Handling flowable solids, e.g. microscopic beads, cells, particles
• CPC Class Codes: B01L 2200/0684 Venting, avoiding backpressure, avoid gas bubbles
• CPC Class Codes: B01L 2200/16 : Reagents, handling or storing thereof
• CPC Class Codes: B01L 2300/0819 : Microarrays; Biochips
• CPC Class Codes: B01L 2300/0822 : Slides
• CPC Class Codes: B01L 2300/0851 : Bottom walls
• CPC Class Codes: B01L 2300/0867 : Multiple inlets and one sample wells, e.g. mixing, dilution
• CPC Class Codes: B01L 2300/0877 : Flow chambers
• CPC Class Codes: B01L 2300/0887 : Laminated structure
• CPC Class Codes: B01L 2300/1822 : using Peltier elements
• CPC Class Codes: B01L 2400/0427 : Electrowetting
• CPC Class Codes: B01L 3/5025 : for parallel transport of multiple samples
• CPC Class Codes: B01L 3/502707 : characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B01L 3/502715 : characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 3/50273 : characterised by the means or forces applied to move the fluids micropumps F04B19/006, of the membrane type F04B43/043
• 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: G01N 2035/00148 : Test cards, e.g. Biomerieux or McDonnel multiwell test cards
• CPC Class Codes: G01N 2035/00237 : Handling microquantities of analyte, e.g. microvalves, capillary networks
• CPC Class Codes: G01N 2035/1034 : Transferring microquantities of liquid
• CPC Class Codes: G01N 21/05 : Flow-through cuvettes G01N21/09 takes precedence; handling fluid samples G01N1/10
• CPC Class Codes: G01N 21/11 : Filling or emptying of cuvettes
• CPC Class Codes: G01N 35/00069 : whereby the sample substrate is of the bio-disk type, i.e. having the format of an optical disk
• CPC Class Codes: G01N 35/0099 : comprising robots or similar manipulators robots per se B25J
• CPC Class Codes: G01N 35/1002 : Reagent dispensers
• CPC Class Codes: G01N 35/1011 : Control of the position or alignment of the transfer device
• CPC Class Codes: G01N 35/1097 : characterised by the valves valves in general F16K
• CPC Class Codes: G02B 21/34 : Microscope slides, e.g. mounting specimens on microscope slides
• CPC Class Codes: Y10T 436/11 : Automated chemical analysis
• CPC Class Codes: Y10T 436/143333 : Saccharide [e.g., DNA, etc.]

Abstract

According to various embodiments, a method is provided that comprises washing an array of DNA-coated beads on a substrate, with a wash solution to remove stacked beads from the substrate. The wash solution can include inert solid beads in a carrier. The DNA-coated beads can have an average diameter and the solid beads in the wash solution can have an average diameter that is at least twice the diameter of the DNA-coated beads. The washing can form dislodged DNA-coated beads and a monolayer of DNA-coated beads. In some embodiments, first beads for forming an array are contacted with a poly(ethylene glycol) (PEG) solution comprising a PEG having a molecular weight of about 350 Da or less. In some embodiments, slides for forming bead arrays are provided as are systems for imaging the same.

Claims

1. A method of depositing beads into an array substrate, the method comprising:

contacting a plurality of beads with a solution comprising poly ethylene glycol to form a bead mixture, wherein the plurality of beads includes a plurality of polynucleotide beads, wherein the poly ethylene glycol has an average molecular weight of not greater than 350 Daltons;

depositing the bead mixture on a surface of the array substrate, the surface defining a plurality of bead receiving areas including microwells or posts, beads of the plurality of beads depositing into the plurality of bead receiving areas, each bead receiving area configured to receive a single bead of the plurality of beads;

removing the solution from the array substrate; and

performing a sequencing process following removing the solution.

2. The method of claim 1, wherein the average molecular weight is in a range of 100 Daltons to 300 Daltons.

3. The method of claim 2, wherein the average molecular weight is in a range of 150 Daltons to 250 Daltons.

4. The method of claim 3, wherein the average molecular weight is about 200 Daltons.

5. The method of claim 1, wherein the solution includes sodium chloride.

6. The method of claim 5, wherein the solution includes the sodium chloride in a concentration of about 100 mM.

7. The method of claim 1, wherein depositing the bead mixture includes centrifuging the array substrate in the presence of the bead mixture.

8. The method of claim 1, further comprising detecting deposited polynucleotide beads following removing the solution.

9. A method of depositing beads into an array substrate, the method comprising:

contacting a plurality of polynucleotide beads with a solution comprising poly ethylene glycol to form a bead mixture, wherein an average molecular weight of the poly ethylene glycol is in a range of 100 Daltons to 300 Daltons;

centrifuging the bead mixture on a surface of the array substrate, the surface defining a plurality of receptacles, a receptacle of the plurality of receptacles including a microwell or post, polynucleotide beads of the plurality of polynucleotide beads depositing into the plurality of receptacles, each receptacle configured to receive a single polynucleotide bead of the plurality of polynucleotide beads; and

removing the solution from the array substrate.

10. The method of claim 9, wherein the average molecular weight of the poly ethylene glycol is in a range of 150 Daltons to 250 Daltons.

11. The method of claim 10, wherein the average molecular weight of the poly ethylene glycol is about 200 Daltons.

12. The method of claim 9, wherein the solution includes sodium chloride.

13. The method of claim 12, wherein the solution includes the sodium chloride in a concentration of about 100 mM.

14. The method of claim 9, further comprising detecting deposited polynucleotide beads following removing the solution.

15. The method of claim 9, further comprising performing a sequencing process following removing the solution.