Chemical reaction monitor

• US 8,592,214 B2
• Filed: 02/11/2011
• Issued: 11/26/2013
• Est. Priority Date: 01/21/2003
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Heiner, David Louis, Fambro, Steven P., Kotseroglou, Theo, Lebl, Michal
• Primary Examiner(s): Hyun, Paul
• Application Number:
  US13/026,086
• Publication Number:
  US 20110136684A1
• Time in Patent Office: 1,019 Days
• Field of Search: 436/50, 435/6.12, 422/62, 422/68.1, 422/82.05, 506/23, 536/25.3
• US Class Current: 436/50
• 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 2219/0036 Nozzles
• CPC Class Codes: B01J 2219/00414 using suction
• CPC Class Codes: B01J 2219/00421 using centrifugation
• CPC Class Codes: B01J 2219/00423 using filtration, e.g. through porous frits
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00587 High throughput processes
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00693 Means for quality control
• CPC Class Codes: B01J 2219/00698 Measurement and control of process parameters
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• 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 50/14 Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: Y10T 436/115831 : Condition or time responsive

Abstract

Disclosed herein are systems for monitoring chemical reactions. The systems can comprise a lighting device, a camera device for obtaining an image of the chemical reaction mixtures and an analyzer program to process data obtained from the image. Also disclosed are methods of monitoring the progress of chemical reactions using these systems.

Claims

1. A method for synthesizing a plurality of polymers comprising:

(a) providing a plurality of wells, each well comprising a polymer;

(b) dispensing a reagent comprising a reaction component to said plurality of wells under conditions sufficient for said reaction component to be incorporated into said polymer, wherein incorporation of the reaction component into said polymer increases the length of said polymer and yields an optical signal indicative of the increased length of said polymer;

(c) obtaining an image of said plurality of wells and saving said image data to computer memory;

(d) accessing said image data in computer memory and determining a specific value corresponding to the extent of polymer synthesis within each well based on the optical signal at the time the image was obtained;

(e) determining whether a difference between a value expected if the chemical reaction is successful and the specific value indicates failure of the chemical reaction within a well;

(f) determining a batch quality for the plurality of polymers; and

(g) repeating steps (b) through (f),

wherein said dispensing is to at least one well where failure of the chemical reaction is not indicated, while discontinuing dispensing to one or more wells where failure of the chemical reaction is indicated,

wherein said repeating is discontinued if the batch quality is less than a threshold batch quality.

2. The method of claim 1, wherein step (e) further comprises communicating a representation of said specific values to a graphical user interface.

3. The method of claim 2, wherein step g further comprises receiving a command from said graphical user interface to repeat steps (a) through f.

4. The method of claim 1, wherein step (c) further comprises removing said reagent from said plurality of wells after obtaining said image.

5. The method of claim 4, wherein removing said reagent comprises a centrifugation or aspiration.

6. The method of claim 1, wherein said polymer comprises a polynucleotide.

7. The method of claim 1, wherein said plurality of wells comprises a multi-well plate.

8. The method of claim 1, wherein step (c) further comprises illuminating said plurality of wells with a light emitting diode (LED) array.

9. The method of claim 1, wherein said image is obtained with a charge couple device (CCD) capable of imaging the plurality of wells simultaneously.

10. A method for synthesizing a plurality of polymers comprising:

(a) providing a substrate comprising a plurality of fixed locations, each location comprising a polymer associated therewith;

(b) dispensing a reagent comprising a reaction component to said plurality of locations under conditions sufficient for incorporation of said reaction component into said polymer, wherein incorporation of the reaction component into said polymer increases the length of said polymer and yields an optical signal indicative of the incorporation of the reaction component into said polymer;

(c) obtaining an image of said plurality of locations;

(d) determining a specific value corresponding to the extent of incorporation of the reaction component into the polymer at each location at the time the image was obtained;

(e) determining whether a difference between a value expected if incorporation of a reaction component into the polymer is successful and said specific value indicates failure of the polymer synthesis at a location;

(f) determining a batch quality for the plurality of polymers; and

(g) repeating steps (b) through (f),

wherein said dispensing is to locations where failure of the incorporation of a reaction component into the polymer is not indicated, while discontinuing said dispensing to one or more locations where failure of the incorporation of a reaction component into the polymer is indicated,

wherein said repeating is discontinued if the batch quality is less than a threshold batch quality.

11. The method of claim 10, wherein step g further comprises resuming said dispensing to said one or more locations if the value of the synthesis is greater than the cost of the synthesis.

12. The method of claim 10, wherein the reaction component is selected from the group consisting of monomeric reaction components and polymeric reaction components.

13. The method of claim 10, wherein the synthesis comprises polynucleotide synthesis.

14. The method of claim 13, wherein the specific value is determined by determining the amount of a blocking group released from the polymer.

15. The method of claim 14, wherein the blocking group comprises dimethyltrityl.

16. The method of claim 10, wherein the plurality of fixed locations comprises a plurality of wells.

17. The method of claim 10, wherein the substrate comprises a multiwell plate.

18. The method of claim 10, wherein the one or more locations comprises a subset of locations where failure is indicated.

19. The method of claim 10, wherein the value expected if the incorporation of the reaction component into the polymer is successful and said specific value each comprises a plurality of measurements.

20. A method for synthesizing a plurality of polymers comprising:

(a) providing a substrate comprising a plurality of fixed locations, each location comprising a polymer associated therewith;

(b) dispensing a reagent comprising a reaction component to said plurality of locations under conditions sufficient for incorporation of said reaction component into said polymer, wherein incorporation of the reaction component into said polymer increases the length of said polymer and yields an optical signal indicative of the incorporation of the reaction component into said polymer;

(c) obtaining an image of said plurality of locations;

(d) determining a specific value corresponding to the extent of incorporation of the reaction component into the polymer at each location at the time the image was obtained;

(e) determining whether a difference between a value expected if incorporation of a reaction component into the polymer is successful and said specific value indicates failure of the polymer synthesis at a location; and

(f) repeating steps (b) through (e),

wherein said dispensing is to locations where failure of the incorporation of a reaction component into the polymer is not indicated, while discontinuing said dispensing to one or more locations where failure of the incorporation of a reaction component into the polymer is indicated,

wherein step (f) further comprises resuming said dispensing to said one or more locations if one or more criteria are met.