Method for labeling the 3' terminus of a synthetic oligonucleotide using a unique multifunctional controlled pore glass (MF-CPG) reagent in solid phase oligonucleotide synthesis

• US 5,401,837 A
• Filed: 08/24/1992
• Issued: 03/28/1995
• Est. Priority Date: 08/28/1989
• Status: Expired due to Term

• Current Assignee: Clontech Laboratories Incorporated
• Original Assignee: Clontech Laboratories Incorporated
• Inventors: Nelson, Paul S.
• Primary Examiner(s): Rollins, John W.
• Assistant Examiner(s): Kunz, Gary L.
• Application Number:
  US07/934,582
• Time in Patent Office: 946 Days
• Field of Search: 536/27, 536/25.3, 536/25.32, 428/402, 560/155, 501/33, 526/336
• US Class Current: 536/25.32
• 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: Y10T 428/2982 Particulate matter [e.g., sphere, flake, etc.]

Abstract

A method for derivatizing and labeling the 3'"'"'-terminus of an oligonucleotide during solid phase synthesis comprising the use of a multifunctional reagent whose preferred structure is shown below. ##STR1## wherein CPG is controlled pore glass beads, Fmoc is 9-fluorenylmethyoxycarbonyl, and the alkylamine contains 1 to 50 carbon atoms.

Claims

1. In an improved automated nucleotide synthesis process yielding an unbound oligonucleotide having a protected primary amine, sulfhydryl, disulfide, or hydroxyl attached to the 3'"'"' terminus, wherein the improvement comprises:

using a multifunctional solid support reagent having the structure ##STR6## wherein;

C=carbon atom;

W=a solid support which is stable under all conditions of solid phase oligonucleotide synthesis selected from the group consisting of

alkylamine CPG, wherein alkyl is from 1 to 50 carbon atoms, inclusive, and isomeric forms thereof;

chemically modified CPG, with modifications selected from the group consisting of hydroxyl, carboxyl, sulfhydryl, and disulfide; and

copolymers of styrene and divinylbenzene;

X=a cleavable linking arm connecting carbon C to W characterized as a combination of atom groups that covalently connects to the solid phase through a cleavable linkage, is stable to all the conditions of solid phase oligonucleotide synthesis, and which is readily cleaved from the solid phase, selected from the group consisting of --(CH₂)_n --, where n is an integer from 1 to 50, --OCO--, --CO₂, --NHCO--, --CONH--, and --O--CO--CH₂ --CH₂ --CO--;

Y=a linking arm connecting carbon C to R₁ O-- that is at least one carbon atom long characterized as a combination of atom groups that covalently connects to OR₁ and is stable to all the conditions of solid phase oligonucleotide synthesis selected from the group consisting of --(CH₂)_n --, where n is an integer from 1 to 50, --OCO--, --CO₂, --NHCO--, --CONH--, and --O--CO--CH₂ --CH₂ --CO--;

Z=a molecule selected from the group consisting of --(CH₂)_n --, where n is an integer from 1 to 50, --OCO--, --CO₂, --NHCO--, and --CONH--, wherein said molecule is bonded between the variable A-- and carbon C, wherein the ester and amide bonds are directed toward the A or C substituent;

R₁ O=a protected hydroxide group wherein R₁ is a base-stable/acid-labile hydroxyl protecting group selected from the group consisting of monomethoxytrityl and dimethoxytrityl;

A=a functional group that is capable of attaching a reporter molecule or a detectable complex wherein A is selected from the group consisting of primary amine, sulfhydryl, disulfide, and hydroxyl;

R₂ =corresponding protecting group for A that is stable to all the conditions of solid phase oligonucleotide synthesis wherein said protecting group is 9-fluorenylmethyl (Fmoc) or trifluoroacetyl (TFA); and

X'"'"'=a molecule that is inert to solid phase oligonucleotide synthesis selected from the group consisting of H, alkyl from 1 to 50 carbon atoms, inclusive, and isomeric forms thereof, --Z--A--R₂, and --Y--OR₁.

2. The process, according to claim 1, wherein said multifunctional reagent has the following structure:

##STR7## wherein the alkyl of alkylamine is 1 to 50 carbon atoms, inclusive, and isomeric forms thereof.

3. The process, according to claim 1, wherein said process further comprises attaching a reporter molecule to said functional group.

4. The process, according to claim 1, wherein the modified 3'"'"' terminus of the synthesized oligonucleotide is cleaved from said support.

5. The process, according to claim 4, wherein said cleaving of the oligonucleotide from the solid support comprises the use of ammonium hydroxide.

6. The process, according to claim 1, wherein W is CPG.

7. The process, according to claim 1, wherein R₁ is dimethoxytrityl.

8. The process, according to claim 1, wherein R₂ is 9-fluorenylmethyl (Fmoc).

9. The process, according to claim 1, wherein A is --NH--.