Method for producing polymers

• US 7,790,369 B2
• Filed: 06/06/2003
• Issued: 09/07/2010
• Est. Priority Date: 02/19/1999
• Status: Expired due to Term

• Current Assignee: Codex DNA, Inc.
• Original Assignee: Febit Holding GmbH (FEBIT)
• Inventors: Müller, Manfred, Stähler, Peer F., Stähler, Cord F.
• Primary Examiner(s): Strzelecka; Teresa E
• Application Number:
  US10/455,369
• Publication Number:
  US 20030198948A1
• Time in Patent Office: 2,650 Days
• Field of Search: None
• US Class Current: 435/6.16
• 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 19/0093 Microreactors, e.g. miniaturised or microfabricated reactors laboratory containers with capillary fluid transport in microfabricated channels or chambers B01L3/5027
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00436 Maskless processes
• CPC Class Codes: B01J 2219/00439 using micromirror arrays
• CPC Class Codes: B01J 2219/00441 using lasers
• CPC Class Codes: B01J 2219/00448 using microlens arrays
• CPC Class Codes: B01J 2219/00479 Means for mixing reactants or products in the reaction vessels
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00511 Walls of reactor vessels
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00603 Making arrays on substantially continuous surfaces
• 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 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00648 : by the use of solid beads
• 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 2219/00702 : Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00704 : integrated with the reactor apparatus
• CPC Class Codes: B01J 2219/00711 : Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01L 2300/0654 : Lenses; Optical fibres
• CPC Class Codes: B01L 2300/069 : Absorbents; Gels to retain a fluid
• CPC Class Codes: B01L 2300/0864 : comprising only one inlet and multiple receiving wells, e.g. for separation, splitting
• CPC Class Codes: B01L 3/502707 : characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B01L 3/5085 : for multiple samples, e.g. microtitration plates
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12N 15/10 : Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12N 15/66 : General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
• CPC Class Codes: C12P 19/34 : Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• 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: G03F 7/70216 : Mask projection systems
• CPC Class Codes: G16B 30/00 : ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 50/00 : ICT programming tools or database systems specially adapted for bioinformatics

Abstract

The invention relates to a method for producing polymers, in particular synthetic nucleic acid double strands of optional sequence, comprising the steps: (a) providing a support having a surface area which contains a plurality of individual reaction areas, (b) location-resolved synthesizing nucleic acid fragments each having different base sequences in several of the individual reaction areas, and (c) detaching the nucleic acid fragments from individual reaction areas.

Claims

1. A method for synthesizing a nucleic acid polymer, the method comprising:

synthesizing in parallel a plurality of different oligomeric nucleic acid building blocks, wherein each of the plurality of different oligomeric nucleic acid building blocks is synthesized in situ bound to a reaction area on a single support, wherein the oligomeric nucleic acid building blocks are partially complementary oligonucleotide building blocks, wherein the plurality of oligomeric building blocks is synthesized on a plurality of reaction areas, wherein the single support comprises multiple channels, wherein each channel comprises one or more reaction spaces for synthesis of oligomeric nucleic acid building blocks and one or more reaction chambers for contacting oligomeric nucleic acid building blocks, wherein each reaction space comprises multiple reaction areas, and wherein each reaction area is on a surface of the channel in the reaction space,

detaching the plurality of oligomeric nucleic acid building blocks from the one or more reaction areas on the single support and

contacting the detached plurality of oligomeric nucleic acid building blocks with one another in multiple reaction chambers to synthesize the nucleic acid polymer, wherein the contacting comprises forming multiple partial nucleic acid polymers that are subsequently combined to form the nucleic acid polymer.

2. The method according to claim 1, wherein the nucleic acid polymer is a double-stranded nucleic acid polymer of at least 300 bp in length.

3. The method according to claim 1, wherein the nucleic acid polymer is a nucleic acid selected from the group consisting of a gene or a section thereof, a gene cluster or a section thereof, a chromosome or a section thereof, a viral genome or a section thereof and a bacterial genome or a section thereof.

4. The method according to claim 1, wherein the oligomeric nucleic acid building blocks are from 5 to 150 monomer units in length.

5. The method according to claim 1, wherein the the detached partially complementary oligonucleotide building blocks are brought into contact with one another or with an intermediate polymer under hybridization conditions.

6. The method according to claim 1 for producing synthetic nucleic acid double strands of optional sequence, comprising the steps:

(a) providing a support comprising multiple channels comprising a plurality of individual reaction areas in a plurality of reaction spaces,

(b) location-resolved synthesizing nucleic acid fragments each having different base sequences in situ bound to several of the individual reaction areas, and

(c) detaching the nucleic acid fragments from the individual reaction areas.

7. The method according to claim 6, wherein the base sequences of the nucleic acid fragments synthesized in individual reaction areas are chosen such that they can assemble to form a nucleic acid double strand hybrid.

8. The method according to claim 6, wherein the nucleic acid fragments according to step (c) are detached in one or more steps under conditions such that a plurality of the detached nucleic acid fragments assemble to form a nucleic acid double strand hybrid.

9. The method according to claim 8, wherein several nucleic acid fragments which form one strand of the nucleic acid double strand hybrid are linked covalently to one another.

10. The method according to claim 9, wherein the covalent linking includes treatment with ligase or/and filling in gaps in the strands using DNA polymerase.

11. The method according to claim 6, wherein the sequence comprises at one or more positions recognition sequences for specific interaction with molecules selected from the group consisting of proteins, nucleic acids, peptides, pharmaceuticals, saccharides, lipids, hormones, and organic compounds.

12. The method according to claim 6, wherein the sequence of the nucleic acid double strands is selected from the group consisting of a naturally occurring sequence, a non-naturally occurring sequence or a combination of these two.

13. The method according to claim 6, wherein the sequence is taken from a database, a sequencing experiment or a device for the integrated synthesis and analysis of polymers.

14. The method according to claim 1, wherein the oligomeric nucleic acid building blocks are synthesized by location- or/and time-resolved illumination by means of a programmable light source matrix.

15. The method according to claim 1, wherein a location- or/and time-resolved synthesis of the oligomeric nucleic acid building blocks takes place on the reaction areas in the reaction spaces and wherein the single support is a microfluidic reaction support.

16. The method according to claim 1, wherein the oligomeric building blocks contain nucleotides occurring in nature, modified nucleotides or mixtures thereof.

17. The method according to claim 1, wherein modified nucleotides are used for labeling and subsequent detection of assembled nucleic acid double strands.

18. The method according to claim 17, wherein the labeling groups are molecules which are detected in a light-dependent manner.

19. A method for producing a gene product comprising transcribing and translating a nucleic acid polymer obtained by the method according to claim 1, wherein the nucleic acid polymer is a gene.

20. The method of claim 1, wherein the nucleic acid polymer is a gene and wherein the method further comprises transcribing and translating the nucleic acid polymer to synthesize a gene product polymer.

21. The method according to claim 1, wherein the nucleic acid polymer is a double-stranded nucleic acid polymer of at least 1000 by in length.

22. The method according to claim 1, wherein the nucleic acid oligomeric building blocks are from 5 to 30 monomer units in length.

23. The method according to claim 1, wherein the one or more reaction spaces are at least partially in fluid communication.

24. The method according to claim 1, wherein the contacting comprises one or more steps, and wherein at least a portion of the detaching and at least a portion of the contacting are performed within a common channel.

25. The method according to claim 1, wherein the contacting comprises one or more steps performed in the multiple channels.

26. The method according to claim 1, wherein multiple channels are at least partially in fluid communication and wherein the contacting comprises one or more steps performed in the multiple channels.

27. The method according to claim 1, wherein the contacting comprises one or more steps, and wherein at least a portion of the detaching and at least a portion of the contacting are performed within a common channel and wherein the contacting comprises one or more steps performed in the multiple channels.