Photocleavable protecting groups and methods for their use

• US 6,566,515 B1
• Filed: 03/14/2000
• Issued: 05/20/2003
• Est. Priority Date: 12/15/1995
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Nam, Ngo Q., McGall, Glenn H., Rava, Richard P.
• Primary Examiner(s): Wilson, James O.
• Application Number:
  US09/525,045
• Time in Patent Office: 1,162 Days
• Field of Search: 536/25.3, 536/25.31, 536/25.32, 536/25.33, 536/25.34, 536/25.6, 536/424, 435/6, 435/7, 435/92, 435/7.94, 435/7.95
• US Class Current: 506/30
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/20 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/207 the phosphoric or polyphosphoric acids being esterified by a further hydroxylic compound, e.g. flavine adenine dinucleotide or nicotinamide-adenine dinucleotide
• 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: C07K 1/061 using protecting groups
• CPC Class Codes: C40B 40/04 Libraries containing only organic compounds
• 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 33/54353 with ligand attached to the carrier via a chemical coupling agent coatings G01N33/54393
• CPC Class Codes: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

Novel compounds are provided which are useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Ar—C(R₁)(R₂)—O—C(O)— wherein:

Ar is an optionally substituted fused polycyclic aryl or heteroaromatic group or a vinylogous derivative thereof;

R₁ and R₂ are independently H, optionally substituted alkyl, alkenyl or alkynyl, optionally substituted aryl or optionally substituted heteroaromatic, or a vinylogous derivative of the foregoing; and

X is a leaving group, a chemical fragment linked to Ar—C(R₁)(R₂)—O—C(O)— via a heteroatom, or a solid support; provided that when Ar is 1-pyrenyl and R₁ and R₂ are H, X is not linked to Ar—C(R₁)(R₂)—O—C(O)— via a nitrogen atom. Preferred embodiments are those in which Ar is a fused polycyclic aromatic hydrocarbon and in which the substituents on Ar, R₁ and R₂ are electron donating groups. A particularly preferred protecting group is the “PYMOC” protecting group, pyrenylmethyloxycarbonyl, where Ar is pyrenyl and R₁ and R₂ are H.

Also provided is a method of forming, from component molecules, a plurality of compounds on a support, each compound occupying a separate predefined region of the support, using the protected compounds described above.

Claims

1. A method of performing photochemical reactions on a surface, comprising:

providing at least one first chemical reactant covalently coupled on said surface;

applying a solution or coating to said surface, wherein said solution or coating provides an environment that is favorable to reaction of said at least one first chemical reactant covalently coupled on said surface; and

irradiating said at least one first chemical reactant covalently coupled surface, wherein the extent or rate of reaction of said first chemical reactant is enhanced compared to a reactant covalently coupled to a surface free of said solution or coating.

7. The method of claim 1, wherein said coating is spin coated onto said substrate surface.

8. The method of claim 1, wherein said at least one chemical reactant is a photolabile protecting group.

9. The method of claim 8, wherein said photolabile protecting group is removed by irradiation.

10. The method of claim 8, wherein said solution or coating comprises a nucleophilic solvent.

11. The method of claim 10, wherein said nucleophilic solvent is selected from the group consisting of water, an alcohol, or a water:

alcohol mixture.

12. The method of claim 10, wherein said alcohol is selected from methanol or ethanol.

13. The method of claim 8, wherein said solution or coating comprises a nucleophilic scavenger.

14. The method of claim 8, wherein a coating is applied to said surface.

15. The method of claim 14, wherein said coating is applied to said surface by spin coating, immersion or spray coating.

16. The method of claim 1 wherein said at least one first chemical reactant covalently coupled on said surface has the formula Ar—

C(R₁)(R₂)—

O—

C(O)—

X, where Ar is 1-pyrenyl, R₁ and R₂ are H, and X is a molecule bound to the support.

17. The method of claim 1 wherein said irradiating results in the removal of a protecting group from the 3′

or 5′

oxygen of a nucleic acid or nucleic acid analog bound to said surface.

2. A method of activating a functional group on a surface of a substrate, wherein said functional group is protected by a protecting group having the formula Ar—

C(R₁)(R₂)—

O—

C(O)—

, wherein Ar is an optionally substituted fused polycyclic aryl or a vinylogous derivative thereof;

R₁ and R₂ are H, optionally substituted alkyl, alkenyl, alkynyl, aryl or heteroaromatic, or a vinylogous derivative of the foregoing; and

the functional group is a chemical fragment or the surface linked to Ar—

C(R₁)(R₂)—

O—

C(O)—

via a heteroatom;

provided that when Ar is 1-pyrenyl and R₁ and R₂ are H, the functional group is not linked to the protecting group via a nitrogen atom, the method comprising;

applying a nucleophilic coating to said surface; and

exposing said surface to light to remove said protecting group.

3. The method of claim 2, wherein said nucleophilic coating comprises a surfactant.

4. The method of claim 2, wherein said surfactant is present at a concentration of from about 0.01% to about 10% v/v.

5. The method of claim 2, wherein said coating comprises a poly-alcohol.

6. The method of claim 5, wherein said poly-alcohol is selected from glycerol, ethylene glycol, and propylene glycol.

18. The method of claim 2 wherein the method is accomplished at a neutral or basic pH.

19. The method of claim 2 wherein the functional group on the surface is on a polypeptide.