Method and system for synthesizing oligonucleotides using nucleotide-specific dispensing bars

• US 5,733,509 A
• Filed: 04/17/1996
• Issued: 03/31/1998
• Est. Priority Date: 04/17/1996
• Status: Expired due to Fees

• Current Assignee: Amersham Biosciences (GE Healthcare Technologies, Inc.)
• Original Assignee: Motorola, Inc. (Motorola Solutions, Inc.)
• Inventors: Shieh, Chan-Long, Ackley, Donald E., Harvey, Thomas B. III
• Primary Examiner(s): MCMAHON, TIMOTHY M
• Application Number:
  US08/634,082
• Time in Patent Office: 713 Days
• Field of Search: 536/25.3, 422/131, 422/134
• US Class Current: 422/131
• 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 2219/00306 Reactor vessels in a multiple arrangement
• CPC Class Codes: B01J 2219/00351 Means for dispensing and evacuation of reagents
• CPC Class Codes: B01J 2219/00369 in multiple or parallel arrangements
• CPC Class Codes: B01J 2219/00376 in multiple or parallel arrangements
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/0054 Means for coding or tagging the apparatus or the reagents
• CPC Class Codes: B01J 2219/00563 Magnetic means
• CPC Class Codes: B01J 2219/00565 Electromagnetic means
• CPC Class Codes: B01J 2219/00585 Parallel processes
• 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 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00686 Automatic
• 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: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: C40B 70/00 : Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G01N 2035/1037 : Using surface tension, e.g. pins or wires

Abstract

A plurality of oligonucleotides are synthesized at a plurality of locations on a substrate using a plurality of dispensing bars. Each of the plurality of dispensing bars has a respective plurality of dispensing heads arranged along a respective axis. Each of the plurality of dispensing bars is operative to selectively deposit a volume of a respective one of a plurality of nucleotide bases in any of a row of locations. A positioning mechanism positions the substrate with respect to the plurality of dispensing bars. A controller controls the plurality of dispensing bars and the positioning mechanism so that, at each of the plurality of locations, a respective sequence of nucleotide bases is deposited to form a respective oligonucleotide.

Claims

1. A system for synthesizing a plurality of oligonucleotides at a plurality of locations on a substrate, the plurality of locations arranged as a plurality of rows on the substrate, the system comprising:

a plurality of dispensing bars each having a respective plurality of dispensing heads arranged along a respective axis, each of the plurality of dispensing bars operative to selectively deposit from the plurality of dispensing heads a volume of a respective one of a plurality of nucleotide bases in any of a plurality of locations along a respective row;

a positioning mechanism which positions the substrate with respect to the plurality of dispensing bars; and

a controller which controls the plurality of dispensing bars the plurality of dispensing heads and the positioning mechanism so that, at each of the plurality of locations, a respective sequence of nucleotide bases is deposited to form a respective oligonucleotide.

2. The system of claim 1 wherein the plurality of dispensing bars includes a first dispensing bar for dispensing a first nucleotide type, a second dispensing bar for dispensing a second nucleotide type, a third dispensing bar for dispensing a third nucleotide type, and a fourth dispensing bar for dispensing a fourth nucleotide type.

3. The system of claim 2 wherein the first nucleotide type contains adenine, the second nucleotide type contains cytosine, the third nucleotide type contains thymine, and the fourth nucleotide type contains guanine.

4. The system of claim 2 wherein the first nucleotide type contains adenine, the second nucleotide type contains cytosine, the third nucleotide type contains uracil, and the fourth nucleotide type contains guanine.

5. The system of claim 1 wherein the positioning mechanism translates the substrate along an axis transverse to each respective axis of the plurality of dispensing bars.

6. The system of claim 1 wherein the positioning mechanism translates the plurality of dispensing bars along an axis transverse to each respective axis of the plurality of dispensing bars.

7. The system of claim 1 wherein the controller controls the plurality of dispensing bars and the positioning mechanism to deposit a volume of a single respective nucleotide at each of the plurality of locations during a single pass of the substrate through the plurality of dispensing bars.

8. The system of claim 7 wherein each single respective nucleotide has a protection group bound thereto, the system further comprising a deprotection device to remove the protection group from each respective nucleotide deposited on the substrate prior to a subsequent deposition of a subsequent nucleotide.

9. The system of claim 8 wherein the deprotection device removes the protection group at each of the plurality of locations prior to a subsequent pass of the substrate through the plurality of dispensing bars.

10. The system of claim 8 wherein the positioning mechanism transports the substrate to the deprotection device.

11. The system of claim 7 further comprising a coupling station which provides at least one condition for attaching a first layer of nucleotides to a surface of the substrate.

12. The system of claim 11 wherein the at least one condition includes providing a solution for achieving proper attachment of the first layer of nucleotides to the surface.

13. The system of claim 11 wherein the at least one condition includes housing the substrate at the coupling station for a predetermined time duration.

14. The system of claim 11 wherein the positioning mechanism transports the substrate to the coupling station.

15. The system of claim 1 wherein the plurality of dispensing bars are fixedly positioned relative to one another.

16. The system of claim 1 wherein each plurality of dispensing heads is fixedly positioned on its respective dispensing bar.