Devices and systems for creation of DNA cluster arrays

• US 8,921,073 B2
• Filed: 06/22/2007
• Issued: 12/30/2014
• Est. Priority Date: 06/23/2006
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Reed, Mark, Sabot, Andrea
• Primary Examiner(s): HOBBS, MICHAEL L
• Application Number:
  US12/305,347
• Publication Number:
  US 20100009871A1
• Time in Patent Office: 2,748 Days
• Field of Search: 435/6, 435/91.2, 435/464, 435/304.1, 435/307.1, 435/285.1, 506/26, 506/40
• US Class Current: 435/91.2
• 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. A system for creation of samples in a flow cell, the system comprising:

a system chassis and a flow cell placement area that is supported by the system chassis, the placement area being configured to receive the flow cell;

at least one manifold having a manifold body configured to be placed onto the flow cell;

at least one reagent reservoir;

at least one temperature control component; and

at least one computer control component;

wherein the reagent reservoir, the manifold, the temperature control component, and the computer control component are functionally connected to one another;

wherein the reagent reservoir and the manifold are capable of being directly or indirectly fluidly connected to one another when connected to said flow cell;

wherein the reagent reservoir, the manifold body, and the flow cell are arranged such that one or more fluids are capable of flow under control of the computer control component from the reagent reservoir, through the manifold body, and into said flow cell, allowing creation of the sample;

wherein the manifold body includes a manifold port that is configured to removably engage a flow cell port of the flow cell to fluidly connect the reagent reservoir to the flow cell, the manifold body configured to move with respect to the placement area to removably engage the manifold port and flow cell port; and

wherein the system further comprises a flow cell holder that is configured to move between open and closed positions to permit access to the flow cell placement area for placing the flow cell on the flow cell placement area and for placing the manifold body onto the flow cell, the manifold body configured to move with respect to the flow cell holder when the flow cell holder is stationary in the open position, the flow cell holder pressing the manifold body against the flow cell when in the closed position so that the manifold body presses the flow cell toward the flow cell placement area.

2. The system of claim 1, wherein the system further comprises said flow cell, said flow cell being directly or indirectly fluidly connected to the reagent reservoir and the manifold.

3. The system of claim 2, wherein the flow cell includes a flow channel having a channel surface, the channel surface having nucleic acid strands immobilized thereon.

4. The system of claim 3, wherein the nucleic acid strands comprise a plurality of single strand nucleic acid molecules, a portion of whose sequences vary between different members of the plurality, and wherein substantially all members of the plurality comprise one or more universal 20-30 base sequences capable of hybridization to one or more a nucleic acid primers.

5. The system of claim 4, wherein said flow cell comprises an additional one or more immobilized primers who sequences are complementary to universal sequences on the nucleic acid strands.

6. The system of claim 1, wherein the reagent reservoir comprises a plurality of reservoirs.

7. The system of claim 6, wherein one or more or all of the members of the plurality of reservoirs are not structurally connected to the system chassis, but are fluidly connected to the manifold, and/or flow cell.

8. The system of claim 1, wherein the temperature control component comprises a heating component, the heating component regulating the temperature of the flow cell.

9. The system of claim 8, wherein the heating component holds the flow cell at a substantially isothermal temperature for a determinable period of time.

10. The system of claim 1, wherein the reagent reservoir, the manifold, the temperature control component, and the computer control component are configured to keep the flow cell under substantially isothermal conditions during creation of the samples.

11. The system of claim 1, wherein the manifold port includes an input manifold port and an output manifold port, the input manifold port configured to direct the fluid into the flow cell and the output manifold port configured to receive the fluid from the flow cell.

12. The system of claim 11, wherein the manifold body has a mounting side that interfaces with a side of the flow cell, the input and output manifold ports being located on the mounting side and opening toward the flow cell in a common direction.

13. The system of claim 11, wherein the input manifold port comprises a plurality of input manifold ports and the output manifold port comprises a plurality of output manifold ports.

14. The system of claim 1, wherein the temperature control component is located proximate to the flow cell placement area such that the temperature control component interfaces with the flow cell when the flow cell is positioned thereon.

15. The system of claim 13, wherein each of the input manifold ports is coupled to a corresponding input flexible tube and each of the output manifold ports is coupled to a corresponding output flexible tube.

16. The system of claim 15, wherein the manifold body has a mounting side that interfaces with a side of the flow cell and a top side that engages the flow cell holder, the input and output flexible tubes projecting away from the top side, the flow cell holder being located between the input flexible tubes and the output flexible tubes.

17. The system of claim 13, wherein the manifold body is elongated and extends between opposite ends, the input manifold ports being located proximate to one of the ends and the output manifold ports being located proximate to the other end.

18. The system of claim 17, wherein the manifold body has a mounting side that interfaces with a side of the flow cell and a top side that engages the flow cell holder, the flow cell holder engaging the top side between the input manifold ports and the output manifold ports.

19. The system of claim 13, wherein the manifold includes a manifold plug, each of the output flexible tubes includes a body end that is coupled to the manifold body and a plug end that is coupled to the manifold plug, the output flexible tubes extending between the manifold body and the manifold plug, the manifold plug configured to be secured to an attachment area of the system chassis.

20. A method of creating nucleic acid cluster arrays through isothermal nucleic acid amplification, the method comprising:

a.) providing a cluster station system, the system comprising at least one manifold having a manifold body;

at least one reagent reservoir;

at least one temperature control component; and

at least one computer control component, the system also including a system chassis and a flow cell placement area that is supported by the system chassis, the placement area being configured to receive a flow cell, the manifold body configured to be placed onto the flow cell;

wherein the reagent reservoir, the manifold, the temperature control component, and the computer control component are functionally connected to one another;

wherein the reagent reservoir and the manifold body are directly or indirectly fluidly connected to one another when connected to a flow cell;

wherein the reagent reservoir, the manifold body, and the flow cell are arranged such that one or more fluids are capable of flow under control of the computer control component from the reagent reservoir, through the manifold body, and onto a surface of the flow cell; and

wherein the manifold body includes a manifold port that is configured to removably engage a flow cell port of the flow cell to fluidly connect the reagent reservoir to the flow cell, the manifold body movable with respect to the placement area to removably engage the manifold port and flow cell port;

wherein the system further comprises a flow cell holder that is configured to move between open and closed positions to permit access to the flow cell placement area for placing the flow cell on the flow cell placement area and for placing the manifold body onto the flow cell, the manifold body configured to move with respect to the flow cell holder when the flow cell holder is stationary in the open position, the flow cell holder pressing the manifold body against the flow cell when in the closed position so that the manifold body presses the flow cell toward the flow cell placement area;

b.) providing amplification reagents, a chemical denaturant, and template nucleic acid; and

c.) flowing cycles of the amplification reagents and denaturant under control of the cluster station device through the flow cell, the flow cell comprising the nucleic acid template, wherein the flow cell is kept under substantially isothermal conditions by the cluster station system, and wherein the nucleic acid template is amplified within the flow cell thus creating nucleic acid cluster arrays.