Method and apparatus for creating biopolymer arrays on a solid support surface

• US 5,429,807 A
• Filed: 10/28/1993
• Issued: 07/04/1995
• Est. Priority Date: 10/28/1993
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Beckman Instruments, Inc. (Danaher Corporation)
• Inventors: Southern, Edwin M., Coassin, Peter J., Rampal, Jang B., Matson, Robert S.
• Primary Examiner(s): Warden, Robert J.
• Assistant Examiner(s): Kim, Christopher Y.
• Application Number:
  US08/144,954
• Time in Patent Office: 614 Days
• Field of Search: 422/101, 422/102, 422/116, 422/131, 422/134, 422/132, 422/133, 422/135, 435/6, 435/287, 435/289, 435/299, 435/300, 435/301, 436/518, 935/88
• US Class Current: 506/32
• 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 2219/00427 using masks
• CPC Class Codes: B01J 2219/0043 for direct application of reagents, e.g. through openings in a shutter
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/0059 Sequential 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 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00686 Automatic
• CPC Class Codes: B01J 2219/00722 Nucleotides
• 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: C07K 1/045 using devices to improve synthesis, e.g. reactors, special vessels
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• 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: G01N 35/1072 with provision for selective pipetting of individual channels

Abstract

An automated method and apparatus for performing biopolymer synthesis on a two-dimensional support surface whereby a two-dimensional matrix or array of biopolymers are obtained on the surface. An applicator in the form of a thick plate having in a surface at least one cavity in the form of an open chamber or channel is used for applying reagents to the surface of a solid phase support material. The applicator is positioned over the solid support material with the surface having the cavity sealed against the material surface. For each cavity, reagents for synthesis are introduced sequentially into one end of the cavity and collected from the other end of the cavity. A one-dimensional array of biopolymers are thus formed on the support material, where each element of the array contains a population of biopolymers having identical sequence. Further synthesis of additional biopolymers is performed by linearly moving or rotating the applicator relative to the support material and carrying out synthesis procedure so that another one-dimensional matrix or array of biopolymers are formed at an offset position to the previous array. At each overlapping region of the two arrays, a cell of biopolymers are formed which each comprises a strand from the first array and a strand from the second array. The result is a two-dimensional array of biopolymers of different sequences at each discrete cell. The arrays of discrete cell containing different biopolymers may be used to conduct hybridization reaction analysis of a biological sample.

Claims

1. A device for synthesizing biopolymer comprising:

a fixed polypropylene support having a surface activated for attaching bipolymers;

an applicator for applying reagents to said activated surface, the applicator contacting said activated surface;

positioning means for positioning the applicator with respect to the activated surface in first and second positions;

reagent supply means for distributing reagents to said activated surface to synthesize a first one-dimensional array of biopolymers in said first position and a second one-dimensional array of biopolymers in said second position, the positioning means positioning the first and second positions such that said second one-dimensional array overlaps the first one-dimensional array to form a two-dimensional array of cells at overlapping regions on said surface in each of which a third biopolymer is obtained which includes corresponding biopolymer strands from said first and second arrays.

2. A device as in claim 1 wherein said applicator includes a face having therein at least one cavity for flowing reagents for synthesis of the biopolymer.

3. A device as in claim 2 wherein the means for positioning includes means for sealing said cavity against said activated surface and flowing reagents for synthesis through the cavity such as to contact the activated surface with the reagents to allow reactions associated with synthesis to take place.

4. A device as in claim 3 wherein the cavity has a circular opening.

5. A device as in claim 3 wherein the cavity is in the shape of an elongated channel.

6. A device as in claim 2 wherein said applicator includes a face having a plurality of elongated channels having one end communicated to the reagent supply means, whereby the first and second arrays of biopolymers synthesize along regions on the activated surface corresponding to said channels.

7. A device as in claim 1 wherein said applicator includes a face having a plurality of elongated channels having one end communicated to the reagent supply means whereby the first and second arrays of biopolymers synthesize along regions on the activated surface corresponding to said channels, and the positioning means includes means for rotating the applicator relative to the activated surface.

8. A device as in claim 7 wherein the positioning means rotates the applicator by 90°

relative to the activated surface such that the second one-dimensional array is orthogonal to the first one-dimensional array.

9. A device as in claim 1 wherein the positioning means includes means for moving the applicator linearly relative to the activated surface.

10. A device as in claim 1 wherein the positioning means includes means for rotating the applicator relative to the activated surface.

11. A method for synthesizing biopolymer comprising the steps of:

providing a fixed polypropylene support having a surface activated for attaching biopolymers;

providing an applicator in contact with said activated surface for applying reagents to said activated surface;

positioning the applicator with respect to the activated surface and applying reagents to said activated surface to synthesize a first one-dimensional array of biopolymers;

repositioning the applicator and applying reagents to said activated surface to synthesize a second one-dimensional array of biopolymers in a manner where said second one-dimensional array overlaps the first one-dimensional array to form a two-dimensional array of cells at overlapping regions on the activated surface in each of which a third biopolymer is obtained which includes a corresponding biopolymer from said first and second arrays of biopolymers.

12. A method as in claim 11 wherein said applicator provided includes a face having therein at least one cavity for flowing reagents for synthesis of the biopolymer, and the positioning and repositioning steps include the steps of:

sealing said cavity against said activated surface; and

flowing reagents for synthesis through the cavity such as to contact the activated surface with the reagents to allow reactions associated with synthesis to take place.

13. A method as in claim 12 wherein the cavity has a circular opening.

14. A method as in claim 12 wherein the cavity is in the shape of an elongated channel.

15. A method as in claim 12 wherein said applicator includes a face having a plurality of elongated channels having one end communicated to the reagent supply means, whereby the first and second arrays of biopolymers synthesize along regions on the activated surface corresponding to said channels.

16. A method as in claim 11 wherein said applicator includes a face having a plurality of elongated channels having one end communicated to the reagent supply means whereby the first and second arrays of biopolymers synthesize along regions on the activated surface corresponding to said channels, and the positioning step includes the step of rotating the applicator relative to the activated surface.

17. A method as in claim 16 wherein the applicator is rotated by 90°

relative to the activated surface such that the second one-dimensional array is orthogonal to the first one-dimensional array.

18. A method as in claim 11 wherein the positioning step includes the step of moving the applicator linearly relative to the activated surface.

19. A method as in claim 11 wherein the positioning step includes the step of rotating the applicator relative to the activated surface.

20. A method for synthesizing polynucleotides comprising the steps of:

providing a fixed polypropylene support having a surface activated for attaching polynucleotides;

providing an applicator in contact with said activated surface for applying reagents suitable for polynucleotide synthesis to said activated surface;

positioning the applicator with respect to the activated surface and applying reagents to said activated surface to synthesize a first one-dimensional array of polynucleotides;

repositioning the applicator and applying reagents to said activated surface to synthesize a second one-dimensional array of polynucleotides in a manner where said second one-dimensional array overlaps the first one-dimensional array to form a two-dimensional array of cells at overlapping regions on the activated surface in each of which a third polynucleotide is obtained which includes corresponding polynucleotide strands from said first and second arrays.

21. A device for synthesizing biopolymer comprising:

a support material having a surface activated for attaching biopolymers;

an applicator for applying reagents to said activated surface, the applicator contacting said activated surface;

reagent supply means for distributing reagents to said activated surface to synthesize a first one-dimensional array of biopolymers in a first position and a second one-dimensional array of biopolymers in a second position, the reagent supply means including;

a primary rotary valve with a plurality of ports,

a plurality of secondary rotary valves each with a plurality of ports, each secondary rotary valve connected in parallel with respect to the other secondary rotary valves and the primary and secondary rotary valves connected in series, the ports of the primary and secondary rotary valves being capable of variable alignment, and

a controller for selective operation of the primary and secondary rotary valves resulting in selective reagent distribution to the applicator in a sequence-specific manner, and

positioning means for positioning the applicator with respect to the activated surface in the first and the second positions, the positioning means positioning the first and second positions such that said second one-dimensional array overlaps the first one-dimensional array to form a two-dimensional array of cells at overlapping regions on said surface in each of which a third biopolymer is obtained which includes corresponding biopolymer strands from said first and second arrays.