Precursors for two-step polynucleotide synthesis

• US 7,427,679 B2
• Filed: 08/30/2003
• Issued: 09/23/2008
• Est. Priority Date: 08/30/2003
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc., The Board of Regents of the University of Colorado (University of Colorado System)
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Caruthers, Marvin H., Dellinger, Douglas J., Sierzchala, Agnieszka B.
• Primary Examiner(s): Crane; L. E.
• Application Number:
  US10/652,048
• Publication Number:
  US 20050049407A1
• Time in Patent Office: 1,851 Days
• Field of Search: 536/26.7, 536/26.8, 536/27.6, 536/27.81, 536/28.5
• US Class Current: 536/26.7
• CPC Class Codes: C07H 19/00 Compounds containing a hetero ring sharing one ring hetero atom with a saccharide radical; Nucleosides; Mononucleotides; Anhydro-derivatives thereof
• 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: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

Precursors for use in the synthesis of polynucleotides are disclosed. The precursors include a heterocyclic base having an exocyclic amine group and a substituted or unsubstituted triaryl methyl protecting group bound to the exocyclic amine group. In particular embodiments, the precursor has the structure:

wherein:

• • O and H represent oxygen and hydrogen, respectively,
  • R1 is hydrido, hydroxyl, protected hydroxyl, lower alkyl, modified lower alkyl, or alkoxy,
  • one of R2 or R3 is a hydroxyl protecting group; and the other of R2 or R3 is a reactive group capable of reacting with a reactive site hydroxyl,
  • Base is a heterocyclic base having an exocyclic amine group, and
  • Tram is a triaryl methyl group having the structure (V)

wherein the broken line represents a bond to the amino nitrogen of the exocyclic amine group, and R4, R5 and R6 are independently selected from unsubstituted or substituted aryl groups, provided that at least one of R4, R5, and R6 is an aryl group other than phenyl and other than substituted phenyl.

Claims

1. A compound having the structure (III)

2. The compound of claim 1, wherein at least one of R₄, R₅, and R₆ is an optionally substituted aryl group independently selected from naphthanyl, pyridinyl, 2-thienyl, 3-thienyl, furanyl, annulenyl, quinolinyl, and anthracenyl.

3. The compound of claim 1, wherein R₄, R₅, and R₆ are aryl groups independently selected from phenyl, methoxyphenyl, dimethoxyphenyl, trimethoxyphenyl, and furanyl.

4. The compound of claim 1 wherein the phosphorous derivative reactive group has the structure (V):

(page 18, line

     4)

5. The compound of claim 4, wherein X is a secondary amino group having the structure —

NQ1Q2;

in which Q1 and Q2 are independently selected from the group consisting of alkyl, aryl, aralkyl, cycloalkyl, alkenyl, cycloalkenyl, alkynyl, cycloalkynyl, and substituted alkyl.

6. The compound of claim 4, wherein Y is selected from alkyl, lower alkyl, alkenyl, benzyl, substituted benzyl, aryl, aralkyl, cycloalkyl, β

-(electron-withdrawing group) substituted alkyl, β

-(electron-withdrawing group) substituted ethyl;

electron-withdrawing substituted phenyl; and

electron-withdrawing substituted phenylethyl.

7. The compound of claim 4, wherein X is a diisopropyl amino group and Y is selected from methyl, benzyl, substituted benzyl, β

-cyanoethyl, methyl-β

-cyanoethyl, dimethyl-β

-cyanoethyl, phenylsulfonylethyl, methyl-sulfonylethyl, p-nitrophenylsulfonylethyl, 2,2,2-trichloro-1,1-dimethylethyl, 2-(4-pyridyl)ethyl, 2-(2-pyridyl)ethyl, allyl, 4-methylene-1-acetylphenol, β

-thiobenzoylethyl, 1,1,1,3,3,3-hexafluoro-2-propyl 2,2,2-trichloroethyl, p-nitrophenylethyl, p-cyanophenyl-ethyl, 9-fluorenylmethyl, 1,3-dithionyl-2-methyl, 2-(trimethylsilyl)ethyl, 2-methylthioethyl, 2-(diphenylphosphino)-ethyl, 1-methyl-1-phenylethyl, 3-buten-1-yl, 4-(trimethylsilyl)-2-buten-1-yl, cinnamyl, α

-methylcinnamyl, and 8-quinolyl.

8. The compound of claim 4, wherein X is a diisopropyl amino group and Y is selected from a cyanoethyl, benzyl, and substituted benzyl group.

9. The compound of claim 8, wherein the hydroxyl protecting group is an optionally substituted aryl carbonate protecting group.