Polynucleotide array fabrication

• US 20040203047A1
• Filed: 04/27/2004
• Published: 10/14/2004
• Est. Priority Date: 04/30/1999
• Status: Abandoned Application

• Current Assignee: Herbert F. Cattell, Jay K. Bass, Michael P. Caren, Peter G. Webb, Richard P. Tella
• Original Assignee: Herbert F. Cattell, Jay K. Bass, Michael P. Caren, Peter G. Webb, Richard P. Tella
• Inventors: Caren, Michael P., Tella, Richard P., Bass, Jay K., Webb, Peter G., Cattell, Herbert F.
• Application Number:
  US10/833,594
• Publication Number:
  US 20040203047A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2219/0036 Nozzles
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• 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 2219/00585 Parallel 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 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00619 using hydrophilic or hydrophobic regions
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition 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 2219/00695 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: B01L 3/0241 : Drop counters; Drop formers making arrays for combinatorial libraries B01J19/0046; automation of dispensing for analysis G01N35/10
• 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 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: G06T 7/0012 : Biomedical image inspection

Abstract

A method and apparatus for fabricating an array of polynucleotides on a substrate. A polynucleotide deposition system is operated to deposit an array of polynucleotide containing fluid droplets on the substrate and which, when dry, will yield polynucleotide containing spots of respective target locations and dimensions. Droplets deposited by the system are allowed to dry to yield actual spots. An image is captured of the substrate with dried actual spots. Dried actual spot locations or dimensions from the image, are compared with target locations or dimensions of polynucleotide containing spots. A signal indicative of the result of the comparison may be generated.

Claims

1. A method of using an array of biopolymers on a substrate, which array is associated with a medium carrying an identification, the method comprising retrieving a map of array features using the identification, exposing the array to a biological sample, determining an observed binding pattern of the exposed array, and modifying the determination or altering the results of the determination based on the retrieved map.

2. A method according to claim 1, wherein the array comprises an array of polynucleotides.

3. A method according to claim 1, wherein the array comprises an array of amino acid containing polymers.

4. A method according to claim 1, wherein the map is retrieved from a memory.

5. A method according to claim 1, wherein the retrieval of the map comprises communicating the identification to a remote server on which is stored the identification and the map, and receiving in response the map from the remote server.

6. A method according to claim 1, wherein the map is retrieved from a portable storage medium.

7. A method according to claim 6, additionally comprising receiving the portable storage medium in a same package along with the array.

8. A method according to claim 1, wherein the map comprises an indication that an array feature is mis-positioned, an actual location of a feature, or an area of a feature.

9. A method according to claim 1, wherein the map is retrieved from the identification.

10. A method according to claim 1, wherein the identification comprises a bar code.

11. A method according to claim 10, wherein the bar code is attached to the substrate.

12. A method according to claim 1, wherein the map comprises an indication of one or more errors in the array.

13. A kit comprising:

a substrate carrying an array of biopolymers;

a machine readable medium carrying an error indication describing one or more errors in the array or an identification of the error indication.

14. A kit according to claim 13, wherein the array comprises an array of polynucleotides.

15. A kit according to claim 13, wherein the array comprises an array of amino acid containing polymers.