Systems and methods for preparing and analyzing low volume analyte array elements

• US 6,569,385 B1
• Filed: 10/28/1999
• Issued: 05/27/2003
• Est. Priority Date: 01/23/1997
• Status: Expired due to Term

• Current Assignee: Agena Bioscience Inc. (Mesa Laboratories Inc.)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Köster, Hubert, Little, Daniel P.
• Primary Examiner(s): Warden, Jill
• Assistant Examiner(s): HANDY, DWAYNE K
• Application Number:
  US09/429,683
• Time in Patent Office: 1,307 Days
• Field of Search: 422/55, 422/61, 422/68.1, 422/99, 422/100-104, 422/81, 422/82, 436/174, 436/177, 436/178, 436/179, 436/180, 435/287, 435/310, 435/292, 738/63, 738/630.1, 738/633.1, 738/633.2, 738/64
• US Class Current: 422/502
• 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 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00387 Applications using probes
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00504 Pins
• CPC Class Codes: B01J 2219/00511 Walls of reactor vessels
• CPC Class Codes: B01J 2219/0052 in the shape of elongated tubes
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• 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 2219/0072 Organic compounds
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01L 3/0262 : using touch-off at substrate or container
• CPC Class Codes: B01L 3/0268 : using pulse dispensing or spraying, eg. inkjet type, piezo actuated ejection of droplets from capillaries
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07F 9/2408 : of hydroxyalkyl compounds
• CPC Class Codes: C07F 9/2429 : of arylalkanols
• CPC Class Codes: C07H 21/00 : Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 2035/00237 : Handling microquantities of analyte, e.g. microvalves, capillary networks
• CPC Class Codes: G01N 2035/1037 : Using surface tension, e.g. pins or wires
• CPC Class Codes: G01N 2035/1069 : by adjusting the spacing between multiple probes of a single transferring head
• CPC Class Codes: G01N 35/1067 : for transfer to or from containers having different spacing
• CPC Class Codes: G01N 35/1074 : arranged in a two-dimensional array
• CPC Class Codes: Y10T 436/25 : including sample preparation
• CPC Class Codes: Y10T 436/25125 : Digestion or removing interfering materials
• CPC Class Codes: Y10T 436/2575 : Volumetric liquid transfer

Abstract

Serial and parallel dispensing tools that can deliver defined and controlled volumes of fluid to generate multi-element arrays of sample material on a substrate surface are provided. The substrates surfaces can be flat or geometrically altered to include wells of receiving material. Also provided are tools that allow the parallel development of a sample array. To this end, the tool can be understood as an assembly of vesicle elements, or pins, where each of the pins can include a narrow interior chamber suitable for holding nanoliter volumes of fluid. Each of the pins can fit inside a housing that forms an interior chamber. The interior chamber can be connected to a pressure source that will control the pressure within the interior chamber to regulate the flow of fluid within the interior chamber of the pins. The prepared sample arrays can then be passed to a plate assembly that disposes the sample arrays for analysis by mass spectrometry.

Claims

1. A fluid dispensing apparatus for dispensing a fluid in chemical or biological procedures into one or more wells of a multi-well substrate, comprising:

a housing having a plurality of sides and a bottom portion having formed therein a plurality of apertures, said walls and bottom portion defining an interior volume;

a plurality of fluid transmitting vesicles, mounted within said apertures having a fluid holding chamber disposed in communication with said interior volume of said housing;

a fluid selection and dispensing means in communication with said interior volume of said housing for variably selecting an amount of the fluid loaded with said fluid holding chambers of said vesicles to be dispensed from a single set of plurality of fluid transmitting vesicles; and

whereby said dispensing means dispenses a selected amount of the fluid into the wells of the multi-well substrate when the apparatus is disposed over and in registration with the substrate, where in the selected amount of fluid is about 10<sup>−

10</sup> to 10<sup>−

6</sup> liters.

2. A fluid dispensing apparatus for dispensing fluid in chemical or biological procedures into one or more wells of a multi-well substrate, said apparatus comprising:

a housing having a plurality of sides and top and bottom portions of said bottom portion having formed therein a plurality of apertures, said walls and top and bottom portions of said housing defining an interior volume;

a plurality of fluid transmitting vesicles, mounted within said apertures having a fluid holding chamber sized to hold nanovolumes of the fluid, said fluid holding chamber being disposed in fluid communication with said volume of said housing, wherein the nanovolumes are about 10<sup>−

10</sup> to 10<sup>−

6</sup> liters; and

mechanical biasing means for mechanically biasing said plurality of said transmitting vesicles into sealing contact with said housing bottom portion.

3. A system for dispensing uniform nanoliter volumes onto the surface of a substrate, comprising:

a robotic arm assembly;

a data processing system for controlling operation of the robotic arm assembly;

a nanoliter dispensing apparatus operably connected to the robotic arm assembly for dispensing a nanoliter volume to a substrate, whereby the nanoliter volume dispensed is from 10<sup>−

10</sup> to 10<sup>−

6</sup> liters or 0.2 nL to 20 nL to produce an array of spots on the substrate such that spot-to-spot characteristics are reproducible in the array; and

a substrate for receiving the nanoliter volumes, wherein;

the substrate comprises sample material deposited at discrete locations on the surface of the substrate in an array of spots on the substrate such that spot-to-spot characteristics are reproducible in the array; and

the sample comprises matrix for performing matrix-assisted laser desorption (MALDI) mass spectrometry.

4. The system of claim 3, wherein the sample further comprises nucleic acid.

5. A system for dispensing uniform nanoliter volumes onto the surface of a substrate;

comprising;

a robotic arm assembly;

a data processing system for controlling operation of the robotic arm assembly;

a nanoliter dispensing apparatus operably connected to the robotic arm assembly for dispensing a nanoliter volume to a substrate, whereby the volume dispensed is 0.2-20 nL to produce an array of spots on the substrate such that spot-to-spot characteristics are reproducible in the array;

a substrate for receiving the nanoliter volumes; and

a mass spectrometer.

6. A dispensing apparatus for dispensing nanovolumes of fluid in chemical or biological procedures onto the surface of a substrate, comprising:

a housing having a plurality of sides and a bottom portion having formed therein a plurality of apertures, said walls and bottom portion of said housing defining an interior volume;

one or more fluid transmitting vesicles, mounted within said apertures, having a nanovolume-sized fluid holding chamber for holding nanovolumes of fluid, said fluid holding chamber being disposed in fluid communication with said interior volume of said housing; and

dispensing means in communication with said interior volume of said housing for selectively dispensing nanovolumes of fluid from said nanovolume-sized fluid transmitting vesicles when the fluid is loaded with said fluid holding chambers of said vesicles, whereby said dispensing means dispenses nanovolumes of the fluid onto the surface of the substrate when the apparatus is disposed over and in registration with the substrate, whereby the volume dispensed is about 0.2-20 nL.

7. A system for dispensing nanoliter volumes onto the surface of a substrate comprising:

a robotic arm assembly;

a data processing system for controlling operation of the robotic arm assembly;

a nanoliter dispensing apparatus operably connected to the robotic arm assembly for dispensing a nanoliter volume to a substrate, whereby the nanoliter volume dispensed is from 10<sup>−

10</sup> to 10<sup>−

6</sup> liters to produce an array of spots on the substrate such that spot-to-spot characteristics are reproducible in the array;

a substrate for receiving the nanoliter volumes; and

a mass spectrometer.

8. The system of claim 7, wherein the dispensing apparatus delivers defined and controlled volumes of fluid to generate multi-element arrays of sample material on the substrate surface.

9. A system of claim 7, wherein the substrate comprises an array of pins, wherein the matrix material is deposited on the end of the pin.

10. The system of claim 7, wherein the substrate comprises sample material deposited at discrete locations on the surface of the substrate, wherein each,sample comprises an amount resulting from delivery of a nanoliter volume.

11. The system claim 10, wherein the sample comprises nucleic acid.

12. A system of claim 11, wherein the surface of the substrate is flat.

13. A system of claim 10, wherein the substrate comprises wells disposed on the surface;

and sample material is deposited in the wells.

14. A system of claim 13, wherein the wells have a rough interior surface.

15. A system of claim 10, wherein the surface of the substrate is pitted.

16. A system of claim 15, wherein the substrate comprises pits with beads therein.

17. A system of claim 11, wherein the substrate comprises a material selected from the group consisting of silica gel, controlled pore glass, magnetic, cross-linked dextrans, agarose, cellulose, glass, metal, and plastic.

18. A system of claim 17, wherein the metal is selected from the group consisting of steel, gold, silver, aluminum, and copper.

19. A system of claim 10, wherein the substrate is selected from the group consisting of capillaries, a capillary, a flat support and a membrane.

20. A system of claim 19, wherein the membrane comprises polyethylene, polypropylene, polyamide or polyvinylidenedifluoride.

21. A system of claim 10, wherein the substrate comprises silicon.

22. A system of claim 21, wherein the substrate is a silicon wafer.

23. The system of claim 21, wherein the substrate is a pitted silicon chip.

24. A system of claim 10, wherein the surface of the substrate comprises a material selected from the group consisting of metal, plastic, a membrane, polymeric material and a metal-grafted polymer.

25. A system of claim 10, wherein the surface of the substrate is functionalized chemically, functionalized with beads or functionalized with dendrite trees of captured material.

26. The system of claim 10, wherein the discrete locations comprise an array.

27. The system of claim 10, wherein the discrete locations are approximately 500 μ

m apart.

28. The system of claim 11, wherein the surface of the substrate comprises hydrophilic portions.

29. The system of claim 28, wherein the substrate comprises silicon.

30. The system of claim 29, wherein the substrate comprises a silicon wafer with hydrophilic portions on the surface.

31. A dispensing apparatus for dispensing nanovolumes of fluid in chemical or biological procedures onto the surface of a substrate, comprising:

a housing having a plurality of sides and a bottom portion having formed therein a plurality of apertures, said walls and bottom portion of said housing defining an interior volume;

one or more fluid transmitting vesicles, mounted within said apertures, having a nanovolume-sized fluid holding chamber for holding nanovolumes of fluid, said fluid holding chamber being disposed in fluid communication with said interior volume of said housing; and

dispensing means in communication with said interior volume of said housing for selectively dispensing nanovolumes of fluid from said nanovolume-sized fluid transmitting vesicles when the fluid is loaded with said fluid holding chambers of said vesicles, whereby said dispensing means dispenses nanovolumes of the fluid onto the surface of the substrate when the apparatus is disposed over and in registration with the substrate, wherein the volume dispensed is about 10<sup>−

10</sup> to 10<sup>−

6</sup> liters.