Apparatus for synthesizing oligonucleotides and methods of use

• US 9,034,272 B2
• Filed: 05/28/2010
• Issued: 05/19/2015
• Est. Priority Date: 06/05/2009
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Cedillo, Isaiah E., Moore, Max N., Ring, Francis J.
• Primary Examiner(s): Griffin, Walter D
• Assistant Examiner(s): Nguyen, Huy-Tram
• Application Number:
  US13/375,697
• Publication Number:
  US 20120107181A1
• Time in Patent Office: 1,817 Days
• Field of Search: 422/201, 435/289.1
• US Class Current: 422/201
• 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 2219/0029 with pistons or plungers
• CPC Class Codes: B01J 2219/00418 using pressure
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00698 Measurement and control of process parameters
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 8/02 with stationary particles, e.g. in fixed beds
• CPC Class Codes: C12M 1/00 Apparatus for enzymology or microbiology

Abstract

The present invention relates to apparatus and methods for synthesizing oligonucleotides wherein a reaction zone has a variable volume based on the position of a piston, and the piston is adjusted to control the amount of headspace above solid support in the reaction zone. Methods and apparatus that limit the size or existence of the headspace are described.

Claims

1. A reactor for synthesizing oligonucleotides comprising:

a vessel configured to contain a solid support, the vessel having an inlet and an outlet;

a piston operatively arranged to reciprocate with the vessel;

an actuator coupled to the piston;

a monitor configured to at least periodically adjust the actuator during a synthesis process to maintain the piston substantially in contact with the solid support; and

at least one sensor located upstream of the vessel outlet and in communication with the vessel, each sensor configured to generate an output to the monitor;

wherein the monitor adjusts the actuator according to the output from the at least one sensor or alternatively the monitor adjusts the actuator according to archival sensor output from a previous synthesis process.

2. The reactor of claim 1 wherein the vessel comprises a cylinder having a sidewall, top and bottom.

3. The reactor of claim 1 wherein the actuator comprises a hydraulic cylinder.

4. The reactor of claim 1 comprising a pressure sensor.

5. The reactor of claim 1 wherein the monitor further is configured to sense the output of a pressure sensor and adjust the actuator responsive to the output of the pressure sensor.

6. The reactor of claim 1 comprising a pressure sensor wherein the synthesis process comprises a series of steps, and the monitor is programmed to periodically adjust the actuator by discrete displacements corresponding to selected ones of the series of steps, archival sensor output and output from a pressure sensor.

7. The reactor of claim 1 wherein the synthesis process comprises a series of steps, and the monitor is programmed to adjust the actuator responsive to the output of each sensor wherein at least one sensor is selected from the group consisting of optical sensors, acoustic sensors, magnetic sensors, energy ray sensors, mechanical sensors and fiber-optic sensors and provides output corresponding to the detection of headspace adjacent to the solid support.

8. The reactor of claim 1 wherein each sensor is selected from the group consisting of optical sensors, acoustic sensors, magnetic sensors, energy ray sensors, mechanical sensors;

and fiber-optic sensors.

9. A synthesizer comprising:

a vessel configured to contain a granular polymeric material, the vessel having an inlet and an outlet, the vessel further configured to receive a fluid through the inlet;

a piston operatively arranged to reciprocate with the vessel;

an actuator coupled to the piston;

a monitor configured to at least periodically adjust the actuator during a synthesis process to maintain the piston within a predetermined distance from the granular polymeric material; and

at least one sensor located upstream of the vessel outlet and in communication with the vessel, each sensor configured to generate an output to the monitor;

wherein the monitor adjusts the actuator according to the output from the at least one sensor or alternatively the monitor adjusts the actuator according to archival sensor output from a previous synthesis process.

10. The synthesizer of claim 9 wherein the vessel comprises a cylinder having a sidewall and a bottom.

11. The synthesizer of claim 9 wherein the actuator comprises a hydraulic cylinder.

12. The synthesizer of claim 9 comprising a pressure sensor.

13. The synthesizer of claim 9 wherein the monitor further is configured to sense the output of the pressure sensor and adjust the actuator responsive to the output of the pressure sensor.

14. The synthesizer of claim 9 comprising a pressure sensor wherein the synthesis process comprises a series of steps, and the monitor is programmed to periodically adjust the actuator by discrete displacements corresponding to selected ones of the series of steps, archival sensor output and output from a pressure sensor.

15. The synthesizer of claim 9 wherein the synthesis process comprises a series of steps, and the monitor is programmed to adjust the actuator responsive to the output of each sensor wherein at least one sensor is selected from the group consisting of optical sensors, acoustic sensors, magnetic sensors, energy ray sensors, mechanical sensors and fiber-optic sensors and provides output corresponding to the detection of headspace adjacent to the solid support.

16. The synthesizer of claim 9 wherein the sensor is selected from the group consisting of optical sensors, acoustic sensors, magnetic sensors, energy ray sensors, mechanical sensors and fiber-optic sensors.