Methods for manufacturing molecular arrays

• US 8,987,174 B2
• Filed: 10/28/2011
• Issued: 03/24/2015
• Est. Priority Date: 10/28/2011
• Status: Active Grant

• Current Assignee: Prognosys Biosciences Inc.
• Original Assignee: Prognosys Biosciences Inc.
• Inventors: Routenberg, David A.
• Primary Examiner(s): Babic, Christopher M
• Assistant Examiner(s): Flinders, Jeremy C
• Application Number:
  US13/283,906
• Publication Number:
  US 20130109595A1
• Time in Patent Office: 1,243 Days
• Field of Search: None
• US Class Current: 506/32
• 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 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00382 Stamping
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00619 using hydrophilic or hydrophobic regions
• 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 2565/515 characterised by the interaction between or sequential use of two or more arrays
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/06 Biochemical methods, e.g. using enzymes or whole viable microorganisms
• CPC Class Codes: C40B 50/18 using a particular method of attachment to the solid support
• CPC Class Codes: C40B 60/12 for screening libraries

Abstract

The methods of the present invention provide methods for manufacturing a master substrate and methods for manufacturing replica arrays from the master substrate. The methods may be used, for example, directly to manufacture or “print” peptide arrays from a DNA array; however, the methods are applicable to a wide range of manufacturing applications for use any time multiple copies of an array needs to be printed.

Claims

1. A method of manufacturing an array of products on a substrate comprising:

delivering a continuous volume of a liquid reagent or reaction mix on the surface of a substrate by laminar flow;

providing partitioned reaction volumes of the liquid reagent or reaction mix on the substrate, wherein the partitioned reaction volumes are partitioned by surface energetic barriers provided by adjacent hydrophobic regions and hydrophilic regions on the substrate;

generating products by one or more enzymatic processes in the partitioned reaction volumes of the liquid reagent or reaction mix; and

immobilizing the products from the partitioned reaction volumes on capture moieties on the substrate, wherein partitioning of the reaction volumes prevents diffusion of products between them.

2. The method of claim 1, wherein there are at least 100 partitioned reaction volumes per square centimeter on the substrate.

3. The method of claim 2, wherein there are at least 10,000 partitioned reaction volumes per square centimeter on the substrate.

4. The method of claim 1, wherein at least 1000 different products from separate partitioned reaction volumes are arrayed on the substrate at a density of at least 1000 different products per square centimeter.

5. The method of claim 1, wherein at least one component of at least one of the enzymatic processes is attached to the substrate.

6. The method of claim 1, further comprising before the providing step, a step of introducing a second substrate in proximity to the first substrate, wherein the partitioned reaction volumes are partitioned by surface energetic barriers provided on the second substrate, or are partitioned by a combination of surface energetic barriers provided on the first and second substrates.

7. The method of claim 1, wherein the one or more enzymatic processes comprise one or more of replication, transcription, and translation.

8. The method of claim 1, wherein the one or more enzymatic processes comprise transcription and translation.

9. The method of claim 1, wherein the surface energetic barriers are provided by adjacent superhydrophobic regions and hydrophilic regions on the substrate.

10. The method of claim 1, wherein physical barriers are provided to partition the reaction volumes, wherein the physical barriers are provided on the substrate or on a second substrate in proximity to the first substrate, or by a combination of the first and second substrates.

11. The method of claim 1, wherein the partitioned reaction volumes in the providing step contain one or more enzymes.

12. The method of claim 1, wherein excess liquid reagent or reaction mix during partitioning in the providing step is removed by wiping or spinning the substrate, by evaporation, or by using air pressure or vacuum.

13. The method of claim 1, wherein the surface energetic barriers are provided by adjacent superhydrophobic regions and superhydrophilic regions on the substrate.

14. A method of manufacturing an array of products on a substrate comprising:

introducing a first substrate in proximity to a second substrate;

delivering a continuous volume of a liquid reagent or reaction mix on the surface of the first and/or second substrate by flowing the liquid reagent or reaction mix between the proximal first and second substrates;

providing partitioned reaction volumes of the liquid reagent or reaction mix on the first and/or second substrate, wherein the partitioned reaction volumes are partitioned by surface energetic barriers provided by adjacent hydrophobic regions and hydrophilic regions on the first and/or second substrate;

generating products by one or more enzymatic processes in the partitioned reaction volumes of the liquid reagent or reaction mix; and

immobilizing the products from the partitioned reaction volumes on capture moieties on the first and/or second substrate, wherein partitioning of the reaction volumes prevents diffusion of products between them.

15. The method of claim 14, wherein the surface energetic barriers are provided on the first substrate or on the second substrate.

16. The method of claim 14, wherein the surface energetic barriers are provided by adjacent superhydrophobic regions and hydrophilic regions on the first substrate, and/or adjacent superhydrophobic regions and hydrophilic regions on the second substrate.

17. The method of claim 14, wherein the surface energetic barriers are provided by adjacent superhydrophobic regions and superhydrophilic regions on the first substrate, and/or adjacent superhydrophobic regions and superhydrophilic regions on the second substrate.

18. The method of claim 14, wherein the partitioned reaction volumes in the providing step contain one or more enzymes.

19. The method of claim 14, wherein at least one component of at least one of the enzymatic processes is attached to the first or second substrate.

20. The method of claim 14, wherein the one or more enzymatic processes comprise one or more of replication, transcription, and translation.