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

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