Feature Quality in Array Fabrication

• US 20070218484A1
• Filed: 02/20/2007
• Published: 09/20/2007
• Est. Priority Date: 01/26/2000
• Status: Abandoned Application

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Bass, Jay
• Application Number:
  US11/677,016
• Publication Number:
  US 20070218484A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00549 2-dimensional
• 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 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00693 Means for quality control
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2565/507 characterised by the density of the capture oligonucleotide
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• 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: C40B 70/00 : Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G01N 33/54353 : with ligand attached to the carrier via a chemical coupling agent coatings G01N33/54393

Abstract

A method, and apparatus and computer program products for executing the method. The method includes obtaining a set of multiple images of a target feature location on an array of multiple features, each image of the set representing the target feature location following deposition of a corresponding sub-set of multiple droplets for that feature. An overlay composite may be generated from the image set. The overlay composite may be used as a quality control tool, or in interrogating the array or processing results of the interrogation.

Claims

1. A method of fabricating an array of features, comprising:

depositing multiple reagent droplets for each of multiple target feature locations so as to form the array of features;

obtaining a set of multiple images of a target feature location, each image of the set representing the target feature location following deposition of a corresponding sub-set of multiple droplets for that feature; and

storing the set on a storage medium.

2. A method according to claim 1 wherein the multiple droplets are deposited from a pulsejet.

3. A method according to claim 1 wherein the set is stored on a storage medium and forwarded to a remote user of the array.

4. A method according to claim 1 additionally comprising:

exposing the array to a sample;

interrogating the array following the exposure and optionally processing results of the interrogation;

wherein either the interrogation or processing is based at least in part on the overlay composite.

5. A method according to claim 4 wherein a result of the interrogation or processing is forwarded to a remote location.

6. A method comprising transmitting data representing a result of the interrogation or processing from the method of claim 5.

7. The method of claim 1, wherein each droplet is a reagent droplet deposited in a cycle of in situ synthesis of a biopolymer at the target feature location on the array.

8. The method of claim 1, wherein each droplet is ejected from a pulse-jet.

9. The method of claim 1, wherein each droplet is a phosphoramidite droplet.

10. A method of providing information of a target feature of a biopolymer array, the method comprising:

a) depositing at least one reagent droplet on a target feature location of the array;

b) obtaining an image of the target feature location,

c) repeating steps a) and b) to compile a set of two or more images representing the target feature location following deposition of droplets; and

d) generating an overlay composite from the set of images, wherein the overlay composite provides information on the target feature.

11. The method of claim 10, wherein steps a) and b) represent at least one cycle of in situ synthesis of a target feature.

12. The method of claim 10, wherein compiling a set of two or more images representing the target feature location further comprises collecting an image following deposition of 1 to 5 droplets.

13. The method of claim 10, wherein compiling a set of two or more images representing the target feature location further comprises collecting an image following deposition of 1 to 10 droplets.

14. A method according to claim 10, wherein the reagent droplet is deposited by a pulse-jet.

15. A method according to claim 10 wherein the overlay composite comprises a region of overlap of the droplets.

16. The method according to claim 10, wherein the method is performed simultaneously for multiple target feature locations.

17. A method according to claim 10, wherein the array is a polynucleotide array, and wherein each image represents the target feature location following deposition of at least one droplet of a nucleotide monomer.

18. The method according to claim 10, additionally comprising altering the deposition of additional droplets for the target feature based at least in part on the overlay composite.

19. The method of claim 10, wherein the information is size, shape, or location of the target feature.

20. The method of claim 19, additionally comprising:

exposing the array to a sample; and

interrogating the array following the exposure and optionally processing results of the interrogation;

wherein the overlay composite controls interrogation at the target feature of the array.