Apparatus and methods for parallel processing of micro-volume liquid reactions

• US 7,604,983 B2
• Filed: 02/09/2005
• Issued: 10/20/2009
• Est. Priority Date: 02/18/2000
• Status: Expired due to Fees

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Inventors: Foreman, Pamela K., O'Keefe, Matthew
• Primary Examiner(s): Beisner; William H
• Application Number:
  US11/054,184
• Publication Number:
  US 20050148066A1
• Time in Patent Office: 1,714 Days
• Field of Search: 435/6, 435/91, 435/2, 435/287.2, 435/287.9, 435/288.4, 435/288.7, 435/303.1, 435/305.2, 435/305.3, 435/309.4, 435/810, 435/288.5, 422/68.1, 422/100, 422/102, 356/244, 356/246
• US Class Current: 435/287.2
• CPC Class Codes: B01F 2215/0431 Numerical size values, e.g. diameter of a hole or conduit, area, volume, length, width, or ratios thereof
• CPC Class Codes: B01F 33/30 Micromixers
• CPC Class Codes: B01F 33/3021 the components to be mixed being combined in a single independent droplet, e.g. these droplets being divided by a non-miscible fluid or consisting of independent droplets
• CPC Class Codes: B01F 33/30351 using hydrophilic/hydrophobic surfaces
• CPC Class Codes: B01F 35/712 for feeding fluids
• CPC Class Codes: B01F 35/7172 using capillary forces
• CPC Class Codes: B01J 2219/00286 Reactor vessels with top and bottom openings
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/0074 Biological products
• CPC Class Codes: B01L 2200/0642 Filling fluids into wells by specific techniques
• CPC Class Codes: B01L 2300/0819 Microarrays; Biochips
• CPC Class Codes: B01L 2300/0829 Multi-well plates; Microtitration plates
• CPC Class Codes: B01L 2300/087 Multiple sequential chambers
• CPC Class Codes: B01L 2300/10 Means to control humidity and/or other gases
• CPC Class Codes: B01L 2300/165 Specific details about hydrophobic, oleophobic surfaces
• CPC Class Codes: B01L 2400/0688 surface tension valves, capillary stop, capillary break
• CPC Class Codes: B01L 3/5025 for parallel transport of multiple samples
• CPC Class Codes: B01L 3/50857 using arrays or bundles of open capillaries for holding samples
• CPC Class Codes: B01L 3/5088 : confining liquids at a location by surface tension, e.g. virtual wells on plates, wires B01L3/50857 takes precedence
• CPC Class Codes: C12Q 1/686 : Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6883 : for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 : Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 : Primer sets for multiplex assays
• CPC Class Codes: C12Q 2600/172 : Haplotypes
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: H01J 49/0418 : for laser desorption, e.g. matrix-assisted laser desorption/ionisation [MALDI] plates or surface enhanced laser desorption/ionisation [SELDI] plates
• CPC Class Codes: Y02P 20/582 : Recycling of unreacted starting or intermediate materials

Abstract

Disclosed herein are apparatuses and methods for conducting multiple simultaneous micro-volume chemical and biochemical reactions in an array format. In one embodiment, the format comprises an array of microholes in a substrate. Besides serving as an ordered array of sample chambers allowing the performance of multiple parallel reactions, the arrays can be used for reagent storage and transfer, library display, reagent synthesis, assembly of multiple identical reactions, dilution and desalting. Use of the arrays facilitates optical analysis of reactions, and allows optical analysis to be conducted in real time. Included within the invention are kits comprising a microhole apparatus and a reaction component of the method(s) to be carried out in the apparatus.

Claims

1. An apparatus for containing multiple micro-volume liquid samples comprising a substrate, wherein the substrate defines a plurality of sample chambers, wherein each sample chamber:

(a) extends through the substrate;

(b) comprises one or more walls and an opening at each end; and

(c) comprises a hydrophobic annular ring on the wall of the chamber, separating two hydrophilic regions; and

(d) holds a sample in the form of a thin film such that a liquid sample present in the sample chamber does not intermix with a liquid sample present in another sample chamber.

2. An apparatus according to claim 1, wherein the sample chamber has a height to width ratio less than or equal to 2:

1 when the height of the sample chamber is measured from one face of the substrate to the other.

3. An apparatus according to claim 1 wherein the substrate comprises hydrophobic regions located on the substrate such that a liquid sample present in one sample chamber does not intermix with a liquid sample present in another sample chamber.

4. An apparatus according to claim 3, wherein the substrate comprises an upper face and a lower face.

5. An apparatus according to claim 4, wherein the through axes of the sample chambers are perpendicular to both faces of the substrate.

6. An apparatus according to claim 5, wherein the sample chamber has the shape of a right circular cylinder.

7. An apparatus according to claim 5, wherein the sample chamber has the shape of a right polygonal prism.

8. An apparatus according to claim 3, wherein the hydrophobic regions are located on the upper and lower faces of the substrate such that the openings of at least one sample chamber is separated from at least one adjacent sample chamber by a hydrophobic region.

9. An apparatus according to claim 1, wherein additional hydrophobic regions are located on the walls of the sample chambers.

10. An apparatus according to claim 1, wherein each sample chamber further comprises a second hydrophobic annular ring along the wall of the sample chamber.

11. An apparatus according to claim 10, wherein the hydrophobic annular ring and the second hydrophobic annular ring define one or more annular non-hydrophobic rings therebetween.

12. An apparatus according to claim 1, further comprising at least one component of a reaction to be carried out in the apparatus.

13. An apparatus according to claim 12, wherein the component is a reagent used in a nucleotide sequencing reaction, a hybridization reaction, or a polynucleotide amplification reaction.

14. An apparatus according to claim 1, wherein a reaction component is affixed to the substrate.

15. An apparatus according to claim 1, wherein the apparatus is substantially free from contaminating amplifiable polynucleotides.

16. An apparatus according to claim 1, wherein the substrate comprises top and bottom surfaces that each contain raised features which form closed curves circumscribing the openings to said sample chambers.