DEVICES AND SYSTEMS FOR CREATION OF DNA CLUSTER ARRAYS

• US 20100009871A1
• Filed: 06/22/2007
• Published: 01/14/2010
• Est. Priority Date: 06/23/2006
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Reed, Mark, Sabot, Andrea
• Granted Patent: US 8,921,073 B2
• Time in Patent Office: Days
• US Class Current: 506/26
• 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 or device for creation of nucleic acid cluster arrays through isothermal amplification of nucleic acid strands in a flow cell, the system or device comprising:

a body chassis;

at least one manifold;

at least one fluidic valve;

at least one fluidic pump;

at least one reagent reservoir;

at least one temperature control component; and

, at least one computer control component;

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

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

,

wherein one or more fluids are capable of flow under control of the computer from the reagent reservoir into said flow cell, thus, allowing nucleic acid amplification and creation of nucleic acid cluster arrays.

2. The system or device of claim 1, wherein the system or device further comprises at least one flow cell directly or indirectly fluidly connected to the reservoir, valve, pump, and manifold.

3. The system or device of claim 2, wherein the surface of the flow cell comprises immobilized nucleic acid strands.

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

6. The system or device of claim 1, wherein the reagent and/or waste reservoir comprises a plurality of reservoirs.

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

8. The system or device of claim 6, wherein one or more of the plurality of reservoirs comprises a waste storage reservoir.

9. The system or device of claim 1, wherein the first temperature control component comprises a heating component, which heating component regulates the temperature of the flow cell.

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

11. The system or device of claim 9, wherein the first temperature control does not comprise an active cooling component.

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

a.) providing a cluster station system or device, which system or device comprises a body chassis;

at least one manifold;

at least one fluidic valve;

at least one fluidic pump;

at least one reagent and/or waste storage reservoir;

at least one temperature control component; and

, at least one computer control component;

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

wherein the reservoir, valve, pump, and manifold, are directly or indirectly fluidly connected to one another; and

, wherein one or more fluids are capable of flow under control of the computer from the reagent reservoir onto a surface of a flow cell;

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

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