Photocleavable protecting groups and methods for their use

• US 6,881,836 B2
• Filed: 01/22/2003
• Issued: 04/19/2005
• Est. Priority Date: 12/15/1995
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: McGall, Glenn H., Rava, Richard P., Nam, Ngo Q.
• Primary Examiner(s): Wilson, James
• Assistant Examiner(s): Khare, Devesh
• Application Number:
  US10/348,917
• Publication Number:
  US 20030144499A1
• Time in Patent Office: 818 Days
• Field of Search: 536/25.3, 536/25.31, 536/25.32, 536/25.33, 536/25.34, 436/518, 514/19, 514/215, 514/278, 435/6, 435/7.92, 435/7.94
• US Class Current: 536/25.3
• 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 protecting and deprotecting a reactive group in a compound, comprising:

coupling the reactive group with a second compound of the formula Ar—

C(R₁)(R₂)—

O—

C(O)—

X, wherein;

Ar is an optionally substituted fused polycyclic aryl or heteroaromatic group or a vinylogously substituted species of the foregoing;

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

X is a leaving group;

provided that when Ar is 1-pyrenyl and R₁ and R₂ are H, the reactive group being protected is not an amine, to provide a protected compound with its reactive group protected by linkage to Ar—

C(R₁)(R₂)—

O—

C(O)—

; and

irradiating the protected compound to provide a deprotected compound.

2. The method of claim 1, wherein Ar is independently 1-pyrenyl or 9-anthracenyl, R₁ is hydrogen and R₂ is independently hydrogen, methyl, substituted phenyl, 9-anthracenyl or 1-pyrenyl.

3. A method of protecting and deprotecting a reactive group in a compound, comprising:

coupling the reactive group with a second compound of the formula Ar—

C(R₁)(R₂)—

X, wherein;

Ar is an optionally substituted fused polycyclic aryl or heteroaromatic group or a vinylogously substituted species of the foregoing;

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

X is a leaving group, to provide a protected compound with its reactive group protected by linkage to Ar—

C(R₁)(R₂)—

O—

C(O)—

; and

irradiating the protected compound to provide a deprotected compound.

4. The method of claim 3, wherein Ar is independently 1-pyrenyl or 9-anthracenyl, R₁ is hydrogen and R₂ is independently hydrogen, methyl, substituted phenyl, 9-anthracenyl or 1-pyrenyl.

5. The method of claim 4, wherein Ar is 1-pyrenyl and R₁ and R₂ are hydrogen.

6. The method of claim 4, wherein Ar is 9-anthracenyl, R₁ is hydrogen and R₂ is hydrogen.

7. The method of claim 3, wherein the compound is a ribonucleoside, deoxyribonucleoside or 2′

-O-methylribonucleoside.

8. The method of claim 7, wherein the deoxyribonucleoside is linked to the Ar—

C(R₁)(R₂)—

O—

C(O)—

group via a 3′

or 5′

-OH.

9. The method of claim 3, wherein the Ar—

C(R₁)(R₂)—

O—

C(O)—

group is removed by irradiation with light.

10. The method of claim 9, wherein the wavelength is greater than 340 nm.

11. The method of claim 10, wherein the wavelength is about 365 nm.