Chemical amplification for the synthesis of patterned arrays

• US 6,083,697 A
• Filed: 11/13/1997
• Issued: 07/04/2000
• Est. Priority Date: 11/14/1996
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: McGall, Glenn H., Goldberg, Martin J., Beecher, Jody E.
• Primary Examiner(s): Celsa, Bennett
• Assistant Examiner(s): Ricigliano, Joseph W.
• Application Number:
  US08/969,227
• Time in Patent Office: 964 Days
• Field of Search: 435/7.1, 435/6, 422/134, 422/129, 430/269, 430/270.1, 430/311
• US Class Current: 506/40
• 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 2219/00427 using masks
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00576 fluorophore
• 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 2219/00617 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 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• 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: C07B 61/00 : Other general methods
• 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: C07H 21/04 : with deoxyribosyl as saccharide radical
• CPC Class Codes: C07K 1/04 : on carriers C07K1/003, C07K1/006 take precedence
• CPC Class Codes: C07K 1/045 : using devices to improve synthesis, e.g. reactors, special vessels
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, 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: Y02P 20/55 : Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

Radiation-activated catalysts (RACs), autocatalytic reactions, and protective groups are employed to achieve a highly sensitive, high resolution, radiation directed combinatorial synthesis of pattern arrays of diverse polymers. When irradiated, RACs produce catalysts that can react with enhancers, such as those involved in autocatalytic reactions. The autocatalytic reactions produce at least one product that removes protecting groups from synthesis intermediates. This invention has a wide variety of applications and is particularly useful for the solid phase combinatorial synthesis of polymers.

Claims

1. An apparatus for solid phase chemical synthesis comprising:

i) a substrate having one or more synthesis intermediates bound thereon, the one or more synthesis intermediates including a reactive group protected from reaction by a removable protecting group attached by a chemical bond to the one or more synthesis intermediates;

ii) a radiation sensitive compound or group, said radiation sensitive compound or group producing a catalyst when irradiated, and

iii) an autocatalytic compound or group, said autocatalytic compound or group generating a protecting group removing product when said autocatalytic compound is activated by said catalyst,

wherein the radiation sensitive compound or group and the autocatalytic compound or group are included in a polymer layer on the substrate and further wherein the radiation sensitive compound or group and the autocatalytic compound or group are nonidentical and wherein the catalyst and autocatalytic compound or group are nonidentical.

2. The apparatus recited in claim 1 wherein said radiation sensitive compound is a photosensitive compound.

3. The apparatus recited in claim 1 wherein said autocatalytic compound is a masked acid.

4. The apparatus recited in claim 1 wherein said synthesis intermediate is a linker molecule.

5. The apparatus recited in claim 1 wherein said synthesis intermediate is a nucleotide.

6. The apparatus recited in claim 1 wherein said synthesis intermediate is an polynucleotide.

7. The apparatus recited in claim 1 wherein said synthesis intermediate is an amino acid.

8. The apparatus recited in claim 1 wherein said synthesis intermediate is an polypeptide.

9. The apparatus recited in claim 1 wherein said removable protecting group is an acid removable group.

10. The apparatus recited in claim 1 wherein said autocatalytic compound is pentafluorobenoic acid.

11. The apparatus recited in claim 1 wherein said acid removable protecting group is 5'"'"' dimethoxytrityl.

12. The apparatus of claim 1 wherein the protecting group is selected from the group consisting of dimethoxytrityl (DMT), tert-butylcarbamate (tBoc), trifluoroacetyl (Tfa), 9-fluorenylmethoxycarbonyl (Fmoc), isobutyrl (iBu), benzoyl (Bz), phenoxyacetyl (pac), acetamidomethyl, acetyl, tert-amyloxycarbonyl, benzyl, benzyloxycarbonyl, 2-(4-biphenylyl)-2-propyloxycarbonyl, 2-bromobenzyloxycarbonyl, tert-butyl, tert-butyloxycarbonyl, 1-carbobenzoxamido-2,2,2-trifluoroethyl, 2,6-dichlorobenzyl, 2-(3,5-dimethoxyphenyl)-2-propyloxycarbonyl, 2,4-dinitrophenyl, dithiasuccinyl, formyl, 4-methoxybenzenesulfonyl, 4-methoxybenzyl, 4-methylbenzyl, o-nitrophenylsulfenyl, 2-phenyl-2-propyloxycarbonyl, α

-2,4,5-tetramethylbenzyloxycarbonyl, p-toluenesulfonyl, xanthenyl, benzyl ester, N-hydroxysuccinimide ester, p-nitrobenzyl ester, p-nitrophenyl ester, phenyl ester, p-nitrocarbonate, p-nitrobenzylcarbonate, trimethylsilyl and pentachlorophenyl ester.

13. The apparatus recited in claim 2 wherein said photosensitive compound is a photoactivated acid catalyst.

14. The apparatus recited in claim 2 wherein said photosensitive compound is a photoactivated catalyst.

15. The apparatus recited in claim 14 wherein said photoactivated catalyst is toluenesulfonic acid.

16. The apparatus of claim 14 wherein the photoactivated catalyst is a member selected from the group consisting of naphthoquinone diazide sulfonic acids, 2,1,4-diazonaphthoquinone sulfonic acid esters, 2,1,5-diazonaphthoquinone sulfonic acid esters, nitrobenzyl esters, s-triazine derivatives of nitrobenzyl esters, 1,1-bis(p-chorophenyl)-2,2,2-trichloroethane (DDT), 1,1-bis(p-methoxyphenyl)-2,2,2-trichloroethane, 1,2,5,6,9,10-hexabromocyclododecane, 1,10-dibromodecane, 1,1-bis(p-chlorophenyl)-2,2-dichloroethane, 4,4 dichloro-2-(trichloromethyl) benzhydrol (Kelthane), hexachlorodimethyl sulfone, 2-chloro-6-(trichloromethyl)pyridine, o,o-diethyl-o-(3,5,6-trichloro-2-pyridyl) phosphorothionate, 1,2,3,4,5,6-hexachlorocyclohexane, N(1,1-bis(p-chlorophenyl)-2,2,2-trichloroethyl)acetamide, tris (2,3-dibromopropyl) isocyanurate, 2,2-bis(p-chlorophenyl-1,1-dichloroethylene, tris (trichloromethyl) striazine, 1,1-bis(chlorophenyl)-2,2,2-trichloroethanol, tris(1,2,3-methanesulfonyl) benzene, tris(trichloromethyl)trizine, onium salts, diaryl-diazonium salts, onium salts of group VI and VII of the Periodic Table, halonium salts, quaternary ammonium, phosphonium and arsonium salts, aromatic sulfonium salts, sulfoxonium salts, seleonium salts, sulfonated esters, sulfonyloxy ketones, benzoin tosylate, t-butylphenyl alpha-(ptoluenesulfonyloxy)-acetate, t-butyl alpha-(p-toluenesulfonyloxy)-acetate, di-tert-butylphenyl iodonium triflate (TBI-T), di-tertbutylphenliodonium camphorsulfonate (TBI-CAM), di-tert-butylphenyl iodonium dichloracetate (TBI-DCA), naphthalimidotriftete, phthalimidotosylate, o-nitrobenzyl esters of toluenesulfonic acid, 2-nitro-3,4-dimethoxybenzyl tosylate, ##STR9## wherein R is sulfonate, tosylate, mesolate, PF₆^- or BF₄^-.

17. A substrate for use in making a polymer array comprising:

a) a substrate having one or more synthesis intermediates bound thereon, the one or more synthesis intermediates having a reactive group protected from reaction by a protective group attached by a chemical bond to the one or more synthesis intermediates;

b) a catalyst system for catalyzing removal of the protective group, the catalyst system contacting the synthesis intermediates and

wherein the catalyst system is included in a polymer layer on the substrate and further wherein the catalyst system and the protective group are nonidentical.

18. A method of making a substrate for use in making a polymer array comprising:

a) providing a substrate surface having one or more synthesis intermediates bound thereon, the one or more synthesis intermediates having a reactive group protected from reaction by a protective group attached by a chemical bond to the one or more synthesis intermediates;

b) applying over the substrate surface a polymer layer having a catalyst system capable of catalyzing removal of the protective group.