Protected monomer and method of final deprotection for RNA synthesis

Patent metadata

Field	Value
Publication number	US-9896472-B2
Application number	US-201514853790-A
Country	US
Kind code	B2
Filing date	Sep 14, 2015
Priority date	Sep 22, 2008
Publication date	Feb 20, 2018
Grant date	Feb 20, 2018

Abstract

A method of deprotecting a solid support bound polynucleotide includes the step of contacting the polynucleotide with a composition comprising a diamine under conditions sufficient to deprotect the 2′-protected ribonucleotide residue. The solid support bound polynucleotide has at least one 2′-protected ribonucleotide residue, which has the following structure:

wherein B P is a protected or unprotected heterocycle; R 12 is a protecting group selected from a hydrocarbyl, a substituted hydrocarbyl, an aryl, and a substituted aryl; X is O or S; and PG is a thionocarbamate protecting group.

First claim

What is claimed is:

1. A method of deprotecting a solid support bound polynucleotide comprising a nucleobase protecting group and a ribonucleotide residue comprising a thionocarbamate protecting group, said method comprising:
(a) contacting the polynucleotide with a composition comprising a diamine, under conditions sufficient to remove said protecting groups and cleave said polynucleotide from said solid support, and produce a cleaved polynucleotide; wherein said cleaved polynucleotide is retained on the solid support;
(b) washing the solid support and said cleaved polynucleotide; and
(c) eluting said cleaved polynucleotide from said solid support.

2. The method of claim 1 , wherein the diamine is selected from 1,2-diaminoethane, 1,2-diaminopropane, 1,3-diaminopropane, 1,4-diaminobutane, 2,2′diaminodiethylamine, and substituted versions thereof.

3. The method of claim 1 , wherein the thionocarbamate protecting group is selected from:
(i) one of the structures:

wherein R 3 , R 4 and R 5 are independently selected from a hydrocarbyl, a substituted hydrocarbyl, an aryl, and a substituted aryl, and wherein optionally R 4 and R 5 can be cyclically linked;
(ii) one of the structures:

or
(iii) the structure:

4. The method of claim 1 , wherein the ribonucleotide residue comprises the structure:

wherein:
B P is a protected or unprotected heterocycle;
R 12 is a protecting group selected from a hydrocarbyl, a substituted hydrocarbyl, an aryl, and a substituted aryl,
X is O or S; and
PG is the thionocarbamate protecting group.

5. The method of claim 1 , wherein the diamine comprises two primary amino groups connected by a linker of about 2 to 12 atoms in length, preferably about 2 to 6 atoms in length.

6. The method of claim 1 , wherein the third composition comprises at least 50% by volume 1,2-diaminoethane.

7. The method of claim 1 , wherein the third composition comprises 1,2-diaminoethane and a solvent.

Assignees

• Agilent Technologies Inc

Inventors

• Dellinger Douglas J
• Myerson Joel
• Sierzchala Agnieszka
• Dellinger Geraldine F
• Timar Zoltan

Classifications

• Y02P20/55

  Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups · CPC title

• C07H23/00

  Compounds containing boron, silicon or a metal, e.g. chelates or vitamin B12 (esters with inorganic acids C07H11/00) · CPC title

• C07H19/167

  with ribosyl as the saccharide radical · CPC title

• A61K31/712

  Nucleic acids or oligonucleotides having modified sugars, i.e. other than ribose or 2'-deoxyribose · CPC title

• C07H1/00

  Processes for the preparation of sugar derivatives · CPC title