Devices and systems for creation of DNA cluster arrays

• US 9,415,368 B2
• Filed: 11/24/2014
• Issued: 08/16/2016
• Est. Priority Date: 06/23/2006
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Reed, Mark T., Sabot, Andrea
• Primary Examiner(s): HOBBS, MICHAEL L
• Application Number:
  US14/551,232
• Publication Number:
  US 20150298088A1
• Time in Patent Office: 631 Days
• US Class Current: 1/1
• 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 2219/00286 Reactor vessels with top and bottom openings
• CPC Class Codes: B01J 2219/00333 Closures attached to the reactor vessels
• CPC Class Codes: B01J 2219/00353 Pumps
• CPC Class Codes: B01J 2219/00355 peristaltic
• CPC Class Codes: B01J 2219/00391 Rotary valves
• CPC Class Codes: B01J 2219/00418 using pressure
• CPC Class Codes: B01J 2219/00495 Means for heating or cooling the reaction vessels
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• 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 2565/629 : being a microfluidic device

Abstract

The present invention comprises systems and devices for isothermal amplification of polynucleotide sequences to produce DNA cluster arrays.

Claims

1. An assembly for creating nucleic acid cluster arrays, the assembly comprising:

a flow cell having a bottom side and a top side that face in opposite directions, the flow cell including an inlet hole and an outlet hole along the top side and a flow channel that fluidicly couples the inlet and outlet holes, the flow channel being defined by a surface that includes a plurality of oligonucleotides immobilized thereto for nucleic acid cluster generation; and

a disposable manifold that is separable from the flow cell, the manifold including a main body configured to be mounted onto the flow cell, the main body comprising an outer side and an under side that face in opposite directions, the under side including an input port and an output port that align with the inlet hole and the outlet hole of the flow cell, respectively, when the under side is mounted onto the top side of the flow cell during the nucleic acid cluster generation, the manifold also including an input tube and an output tube that are coupled to the main body and in flow communication with the input and output ports, respectively, wherein fluid flows from the input tube, through the flow channel, and through the outlet tube during the nucleic acid cluster generation.

2. The assembly of claim 1, wherein the flow cell has a uniform thickness measured between the top side and the bottom side.

3. The assembly of claim 1, wherein the flow cell includes at least four of the flow channels, the flow channels having essentially equal lengths.

4. The assembly of claim 1, wherein the input tube and the output tube are coupled to the outer side of the main body, the input tube and the output tube being separated from each other along the outer side by a distance that is essentially equal to a length of the flow channel.

5. The assembly of claim 1, wherein the flow cell includes a plurality of the flow channels, wherein the number of input tubes and the number of output tubes is equal to the number of flow channels.

6. The assembly of claim 5, wherein each of the output tubes includes a tube end, the tube ends being coupled to a common manifold plug that is configured to removably couple to a system.

7. The assembly of claim 1, wherein the input tube and the output tube have respective tube ends that are configured to removably couple to respective ports of a system.

8. The assembly of claim 7, wherein at least one of the tube ends is coupled to a manifold plug that is configured to removably couple to the system.

9. The assembly of claim 1, wherein the main body includes first and second positioning holes that open to the under side and are configured to receive alignment posts of a system, the flow cell being located between the positioning holes when the main body is mounted onto the flow cell.

10. The assembly of claim 1, wherein the flow cell has an elongated structure such that a length of the flow cell is greater than a width of the flow cell.

11. The assembly of claim 1, wherein the plurality of oligonucleotides comprise primer oligonucleotides being located at an approximately uniform density over an area of the surface of the flow channel with one or more single stranded polynucleotide molecules being immobilized individually at intervals within the primer oligonucleotides.

12. A system for creating nucleic acid cluster arrays, the system comprising:

a system body having a placement area configured to receive a flow cell;

a temperature control device configured to regulate a temperature of the flow cell, the temperature control device including, or being in thermal communication with, the placement area;

a fluid flow system including at least one pump, the fluid flow system configured to direct fluid through the flow cell during nucleic acid cluster generation;

a computer control component functionally connected to the temperature control device and the fluid flow system, the computer control component configured to control the temperature control device and the fluid flow system to conduct the nucleic acid cluster generation; and

a flow cell holder that is configured to move between open and closed positions, the flow cell holder permitting access to the placement area when in the open position for placing the flow cell on the placement area and placing a manifold onto the flow cell, the flow cell holder configured to press the manifold against the flow cell when in the closed position so that the manifold presses the flow cell toward the flow cell placement area.

13. The system of claim 12, wherein the flow cell holder includes a clamp that is coupled to the system body, the system further comprising a handle coupled to the system body, the clamp extending over the placement area when the flow cell holder is in the closed position, the handle coupling to the clamp to hold the clamp against the manifold.

14. The system of claim 12, wherein the system body includes a manifold attachment area include a plurality of ports, the ports being spaced apart from the placement area.

15. The system of claim 14, wherein the manifold attachment area is a first manifold attachment area, the system body including a second manifold attachment area having a plurality of ports that are spaced apart from the placement area and the first manifold attachment area.

16. The system of claim 12, wherein the flow cell holder includes a compression bar, the compression bar configured to exert a force toward the placement area when the flow cell holder is in the closed position.

17. The system of claim 12, wherein the temperature control device is a thermoelectric controller (TEC).

18. The system of claim 12, wherein the system body includes alignment posts that are positioned on opposite sides of the flow cell when the flow cell is positioned within the placement area.

19. The system of claim 12, wherein the placement area includes an edge that is sized and shaped to surround and hold the flow cell.

20. The system of claim 12, wherein the computer control component controls the temperature control device and the fluid flow system to generate the nucleic acid clusters through isothermal amplification.

21. The system of claim 12, further comprising the manifold and the flow cell.