Method for parallel synthesis and transfer of molecules to a substrates

• US 20040203085A1
• Filed: 04/29/2004
• Published: 10/14/2004
• Est. Priority Date: 04/26/2001
• Status: Abandoned Application

• Current Assignee: Indigon GmbH
• Original Assignee: Indigon GmbH
• Inventors: Dubel, Stefan, Bernard, Andre
• Application Number:
  US10/475,801
• Publication Number:
  US 20040203085A1
• Time in Patent Office: Days
• US Class Current: 435/7.94
• 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 2219/00382 Stamping
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00527 Sheets
• 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 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• 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 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00686 Automatic
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00713 Electrochemical synthesis
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01J 2219/00729 : Peptide nucleic acids [PNA]
• CPC Class Codes: B01J 2219/00731 : Saccharides
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07K 1/047 : Simultaneous synthesis of different peptide species; Peptide libraries
• 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 40/12 : Libraries containing saccharides or polysaccharides, 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: G01N 33/54306 : Solid-phase reaction mechanisms
• CPC Class Codes: G01N 33/54393 : Improving reaction conditions or stability, e.g. by coating or irradiation of surface, by reduction of non-specific binding, by promotion of specific binding

Abstract

The invention relates to a method for highly parallel production of complex molecule libraries on the surface of a substrate with the aid of regeneratable matrix dies. According to prior art, the production of molecule libraries on a support is expensive, and requires a lot of time and a large amount of apparatus. By using regeneratable matrix dies it is possible to simplify and accelerate the production of molecule libraries, especially DNA and protein libraries, in a significant manner. The matrix-10 die is made of an elastic material such as polydimethylsiloxane and includes locally-bound matrix molecules on the surface thereof, said molecules being used as a model for the synthesis of copy molecules. The copy molcules are transferred to the target surface by means of a contact printing method. The matrix molecules remain on the die for further synthesis and print cycles which can repeated several times. The inventive method is suitable for copying and reproducing differently produced molecule arrays.

Claims

1. A method for preparing molecule libraries arranged in a defined pattern on a substrate, characterized by

preparation of at least one template die comprising a defined arrangement of template molecules,

true-to-location biochemical or chemical in situ synthesis of copy molecules on said template molecules located on the surface of said template die and serving as templates,

transfer of the synthesized copy molecules to a solid or polymeric substrate by means of contact printing, retaining the spatial arrangement of said copy molecules on the substrate,

reproducibility of the synthetic steps and transfer steps.

2. The method as claimed in claim 1, characterized in that the template molecules on the template die and the copy molecules on the substrate surface are arranged in the form of a dot matrix, a circular, helical, strip-shaped, linear or other geometric or stochastic structure.

3. The method as claimed in either of claims 1 and 2, characterized in that the molecule libraries synthesized on the substrate surface may be used for carrying out parallel binding reactions.

4. The method as claimed in any of claims 1 to 3, characterized in that the die comprises at least partially an elastic material, preferably polydimethylsiloxane.

5. The method as claimed in any of claims 1 to 4, characterized in that two or more different dies are used for preparing an array.

6. The method as claimed in any of claims 1 to 5, characterized in that the template molecules on the die are prepared by in situ synthesis on the molecules of a molecule array prepared in a different manner, which serve as templates.

7. The method as claimed in any of claims 1 to 5, characterized in that the template molecules on the die are prepared by chemical in situ synthesis or by in situ synthesis controlled by electric fields or light.

8. The method as claimed in any of claims 1 to 5, characterized in that the template molecules are applied to the die by application in drop form.

9. The method as claimed in any of claims 1 to 5, characterized in that the die is made of a material transparent for a particular wavelength and thus enables, via location-selective light conduction, photochemical reactions or near-field optical processes for binding or synthesizing the template molecules on the die surface to be carried out.

10. The method as claimed in any of claims 1 to 9, characterized in that the die is made of a material transparent for a particular wavelength and thus makes it possible to control relative positioning of said die on the substrate surface via location-selective light conduction.

11. The method as claimed in any of claims 1 to 10, characterized in that the template molecules are DNA, RNA or their nuclease-resistant derivatives such as PNA or thioRNA.

12. The method as claimed in any of claims 1 to 10, characterized in that the copy molecules are DNA, RNA or aptamers or their, in particular nuclease-resistant, derivatives such as PNA or thioRNA.

13. The method as claimed in any of claims 1 to 10, characterized in that the copy molecules are peptides, proteins, antibodies or antibody fragments, in particular scFv fragments, or molecules functionally equivalent thereto, in particular anticalins, fibronectin subdomains or individual antibody domains.

14. The method as claimed in any of claims 1 to 10, characterized in that the copy molecules are carbohydrates or combinatorially synthesized compounds.

15. The method as claimed in any of claims 1 to 14, characterized in that the copy molecules are modified after synthesis, in particular by means of proteolysis, phosphorylation, alkylation, glycosylation, methylation or chemical treatment.

16. The method as claimed in claim 15, characterized in that the copy molecules are modified in one or more stamping processes.

17. The method as claimed in any of claims 1 to 16, characterized in that the copy molecules comprise covalently or noncovalently bound anchors or chemical groups which mediate binding to the substrate surface to be printed.

18. The method as claimed in claim 17, characterized in that the substrate surface to be printed comprises the corresponding molecular counterpart to binding of the anchor or the substance reacting with the chemical group of said anchor.

19. The method as claimed in claim 18, characterized in that the anchor and its molecular counterpart on the substrate surface to be printed comprise, for example, in each case complementary nucleotide sequences or an antibody fragment and an antigen, or an S peptide and an S protein, or a biotin and a streptavidin, or a ligand and a receptor, or in each case vice versa.

20. The method as claimed in any of claims 1 to 19, characterized in that the surface of the die has topological structures in the form of a relief.

21. The method as claimed in claim 20, characterized in that the structured die comprises topological structures whose dimensions are smaller than those of the molecule spots applied to the die by means of a standard method, in particular application in drop form, and are preferably smaller than 10 μ

m, in particular smaller than 2 μ

m.

22. The method as claimed in claim 21, characterized in that molecule spots generated on the substrate are smaller than those generated on the structured die by means of a standard method, in particular application in drop form, and are preferably smaller than 10 μ

m, in particular smaller than 2 μ

m.

23. The method as claimed in either of claims 21 and 22, characterized in that repeated staggered contact printing produces an array having a higher spot density than the spot density generated on the structured die by means of a standard method, in particular application in drop form.

24. The method as claimed in claim 20, characterized in that the structured die comprises topological structures whose dimensions are smaller than the molecule spots on the molecule array prepared in a different manner and serving as template for molecule synthesis, and are preferably smaller than 10 μ

m, in particular smaller than 2 μ

m.

25. The method as claimed in claim 24, characterized in that molecule spots generated on the substrate are smaller than the spots on the molecule array prepared in a different manner and serving as template for molecule synthesis, and are preferably smaller than 10 μ

m, in particular smaller than 2 μ

m.

26. The method as claimed in either of claims 24 and 25, characterized in that repeated staggered contact printing generates an array having a higher density than on the molecule array prepared in a different manner and serving as template for molecule synthesis.

27. The method as claimed in any of claims 1 to 26, characterized in that it may be use for improving the quality and simplifying the preparation of protein and, in particular, of antibody arrays or of arrays of functionally equivalent molecules, in particular anticalins, fibronectin subdomains, antibody single chains or antibody fragments.

28. The method as claimed in claim 27, characterized in that the protein or antibody arrays or arrays of functionally equivalent molecules are used in the diagnostics of various pathogens.

29. An apparatus for preparing the dies and the molecule arrays according to a method as defined in claims 1 to 28, characterized in that individual steps are carried out semi-automatically or automatically.

30. A kit, comprising the essential substances for preparation of molecule arrays according to a method as defined in claims 1 to 28.

31. A kit, comprising the essential substances for carrying out binding assays on arrays prepared as claimed in any of claims 1 to 30.

32. A die, in particular template die, in particular for carrying out the method as claimed in any of claims 1 to 28.

33. The die as claimed in claim 32, characterized by at least one feature of the characterizing clauses of claims 1 to 28.