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

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 --(CH.sub.2).sub.n --, where n is an integer from 1 to 50, --OCO--, --CO.sub.2, --NHCO--, --CONH--, and --O--CO--CH.sub.2 --CH.sub.2 --CO--;
• Y=a linking arm connecting carbon C to R.sub.1 O-- that is at least one carbon atom long characterized as a combination of atom groups that covalently connects to OR.sub.1 and is stable to all the conditions of solid phase oligonucleotide synthesis selected from the group consisting of --(CH.sub.2).sub.n --, where n is an integer from 1 to 50, --OCO--, --CO.sub.2, --NHCO--, --CONH--, and --O--CO--CH.sub.2 --CH.sub.2 --CO--;
• Z=a molecule selected from the group consisting of --(CH.sub.2).sub.n --, where n is an integer from 1 to 50, --OCO--, --CO.sub.2, --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;
• R.sub.1 O=a protected hydroxide group wherein R.sub.1 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;
• R.sub.2 =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--R.sub.2, and --Y--OR.sub.1.