Method and apparatus for combinatorial chemistry

• US 7,550,410 B2
• Filed: 11/14/2006
• Issued: 06/23/2009
• Est. Priority Date: 05/05/1999
• Status: Expired due to Term

• Current Assignee: Robert S. Foote
• Original Assignee: Robert S. Foote
• Inventors: Foote, Robert S.
• Primary Examiner(s): Low; Christopher
• Assistant Examiner(s): Lundgren; Jeffrey S.
• Application Number:
  US11/559,549
• Publication Number:
  US 20070087367A1
• Time in Patent Office: 952 Days
• Field of Search: None
• US Class Current: 506/23
• 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 2219/00286 Reactor vessels with top and bottom openings
• CPC Class Codes: B01J 2219/00306 Reactor vessels in a multiple arrangement
• CPC Class Codes: B01J 2219/00369 in multiple or parallel arrangements
• CPC Class Codes: B01J 2219/00427 using masks
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00511 Walls of reactor vessels
• CPC Class Codes: B01J 2219/0052 in the shape of elongated tubes
• CPC Class Codes: B01J 2219/00522 in a multiple parallel arrangement
• CPC Class Codes: B01J 2219/00524 in the shape of fiber bundles
• 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 2219/00617 by chemical means
• 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 2219/00664 : Three-dimensional arrays
• CPC Class Codes: B01J 2219/00675 : In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00711 : Light-directed 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 2219/00731 : Saccharides
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07H 19/06 : Pyrimidine radicals
• CPC Class Codes: C07H 21/00 : Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• 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 60/14 : for creating libraries

Abstract

A method and apparatus are provided for performing light-directed reactions in spatially addressable channels within a plurality of channels. One aspect of the invention employs photoactivatable reagents in solutions disposed into spatially addressable flow streams to control the parallel synthesis of molecules immobilized within the channels. The reagents may be photoactivated within a subset of channels at the site of immobilized substrate molecules or at a light-addressable site upstream from the substrate molecules. The method and apparatus of the invention find particularly utility in the synthesis of biopolymer arrays, e.g., oligonucleotides, peptides and carbohydrates, and in the combinatorial synthesis of small molecule arrays for drug discovery.

Claims

1. An apparatus comprising:

a plurality of substantially parallel channels disposed within a unitary synthesis block, each of said channels having a first end and a second end;

a fluid chamber continuous with the first ends of said plurality of channels, said fluid chamber effective for flowing a photoactivatable reagent through said plurality of channels from the first end to the second end thereof; and

a light source for selectively illuminating at least a portion of said plurality of channels from the first end thereof to activate the flowing photoactivatable reagent for effecting a photochemical reaction between the photoactivatable reagent and immobilized molecules within said selectively illuminated channels.

2. The apparatus of claim 1, wherein said channels are comprised of a material at least partly comprised of a glass or polymeric material.

3. The apparatus of claim 1, wherein said channels have inner diameters in the range of about 1μ

m to about 500 μ

m

4. The apparatus of claim 1, wherein said channels have inner diameters in the range of about 1 μ

m to about 100 μ

m.

5. The apparatus of claim 1, wherein said channels have inner diameters in the range of about 1 μ

m to about 10 μ

m.

6. The apparatus of claim 1, wherein said fluid chamber has one or more valves for controlling the flow of fluids into or out of said fluid chamber.

7. The apparatus of claim 1, further comprising a second fluid chamber continuous with the second ends of said plurality of channels.

8. The apparatus of claim 1, wherein said second fluid chamber is comprised of one or more valves for controlling the flow of fluids into or out of said second fluid chamber.

9. The apparatus of claim 1, wherein said plurality of channels have one or more immobilized molecules attached to inner surfaces of the plurality of channels.

10. The apparatus of claim 9, wherein said immobilized molecules have terminal subunits, said terminal subunits having protecting groups coupled thereto.

11. The apparatus of claim 10, wherein said immobilized molecules are selected from the group consisting of peptides and oligonucleotides.

12. The apparatus of claim 11, wherein said immobilized molecules are oligonucleotides and said terminal subunits of said oligonucleotides have protecting groups selected from the group consisting of dimethoxytrityl, monomethoxytrityl, 3-(irnidazole-1-ylrnethyl)bis(4′

,4″

-dimethoxyphenyl)methyl and 9-(9-phenyl)xanthenyl.

13. The apparatus of claim 11, wherein said immobilized molecules are peptides and said protecting groups are selected from the group consisting of 9-fluorenylmethoxycarbonyl and t-butyloxycarbonyl.

14. The apparatus of claim 1, wherein said channels contain a solid synthesis substrate, said substrate having immobilized molecules bound on surfaces thereof.

15. The apparatus of claim 14, wherein said immobilized molecules have terminal subunits, said terminal subunits having protecting groups coupled thereto.

16. The apparatus of claim 15, wherein said immobilized molecules are selected from the group consisting ofpeptides and oligonucleotides.

17. The apparatus of claim 16, wherein said immobilized molecules are oligonucleotides and said terminal subunits of said oligonucleotides have protecting groups selected from the group consisting of dimethoxytrityl, monomethoxytrityl, 3-(irnidazole-1-ylrnethyl)-bis-(4′

,4″

-dimethoxyphenyl)methyl and 9-(9-phenyl)xanthenyl.

18. The apparatus of claim 16, wherein said immobilized molecules are peptides and said protecting groups are selected from the group consisting of 9-fluorenylmethoxycarbonyl and t-butyloxycarbonyl.

22. The apparatus of claim 1, wherein said channels have inner diameters in the range of about 1 μ

m to about 1000 μ

m.

19. A method for the synthesis of an array of molecules comprising:

(a) providing housing containing a unitary synthesis block, said unitary synthesis block including a plurality of elongated channels containing immobilized oligomeric or polymeric molecules wherein the molecules have protecting groups coupled to termini of the molecules;

(b) flowing a photoactivatable reagent through the plurality of elongated channels from a first end to a second end of the channels while selectively illuminating at least a portion of the channels from an end thereof, to provide flowing photoactivated reagent in the selectively illuminated channels;

(c) removing protecting groups from the termini of immobilized molecules using the flowing photoactivated reagent thereby forming deprotected molecules in the selectively illuminated channels;

(d) reacting the deprotected molecules with one or more monomers under conditions effective for coupling the monomers with the deprotected molecules; and

(e) repeating steps (b) to (d) until a desired molecular array is formed within the channels.

20. The method of claim 19 wherein photoactivatable reagent comprises a reagent selected from the group consisting of an acid precursor, triarylsulfonium hexafluoroantimonates, triarylsulfonium hexafluorophosphates, 2,1,4-diazonaphthoquinone sulfonates, perhalogenated triazines, and a trihaloacetic acid having a photocleavable carboxyl-protecting group selected from the group consisting of α

-and phenyl-substituted2-nitrobenzyl groups, phenacyl groups, benzoinyl groups, and 2,4-dinotrobenzenesulphenyl groups.

21. The method of claim 19 further comprising slicing the synthesis block containing the arrays into thin sections having a thickness ranging from about 1 micron to about 500 microns to provide a plurality of substantially planar sections of molecular arrays.