Chromophoric silyl protecting groups and their use in the chemical synthesis of oligonucleotides

A compound of the formula:

• L1-O—Si(R1)(R2)—X,
• wherein L1 is a substituent selected from the group consisting of a moiety derived from an azido moiety, wherein the azido moiety is capable of 1,3-dipolar cycloaddition with an alkyne compound in the presence a copper (I) salt to yield a 1,2,3-triazole, and an alkynyl moiety, wherein the alkynyl moiety is capable of 1,3-dipolar cycloaddition with an azide compound;
• R1 and R2 are independently selected from the group consisting of C1-8 alkyl, cycloalkyl, aryl, C1-8 alkyloxy, cycloalkyloxy, trialkylsilyloxy and triarylsilyloxy;
• and
• X is an oligoribonucleotide-derived substituent moiety, a ribonucleotide-derived substituent moiety or a ribonucleoside-derived substituent moiety that is attached to the Si at a 5′-O-position.

A method of synthesizing a compound of formula Y-Q-O—Si(R1)(R2)—X comprising,

• wherein Y is a chromophore-derived substituent;
• -Q-O— is a 1,2,3-triazolyloxy moiety which is a silyl-to-chromophore linking group;
• R1 and R2 are independently selected from the group consisting of C1-8 alkyl, cycloalkyl, aryl, C1-8 alkyloxy, cycloalkyloxy, trialkylsilyloxy and triarylsilyloxy;
• and
• X is a ribonucleoside moiety that is attached to the Si at a 5′ position;
• the method comprising reacting a compound of formula L1-O—Si(R1)(R2)—X with a compound of formula Y-L2 in the presence of a catalytic amount of a Cu(I) compound under conditions that if X has a 3′OH group or a protecting group at a position other than the 5′ position, permit Y-L2 to covalently react with L1-O—Si(R1)(R2)—X without reacting with said 3′OH group or protecting group at said position other than the 5′ position,
• wherein L1 and L2 are independently substituents selected from the group consisting of an azido moiety and an alkynyl moiety;
• and whereby L1 and L2 react to form the moiety Q, wherein one of L1 and L2 is an azido moiety and the other one of L1 and L2 is an alkynyl moiety;
• and wherein the azido moiety and the alkynyl moiety undergo 1,3-dipolar cycloaddition in the presence a copper (I) salt to yield a 1,2,3-triazolyl linking moiety.

A method of synthesizing a substrate-bound oligonucleotide comprising:

• a. providing a substrate bound, appropriately protected ribonucleotide, ribonucleoside or oligoribonucleotide having a 5′-O-protecting group of the formula Y-Q-O—Si(R1)(R2);
• wherein Y is a chromophore-derived substituent;
• -Q-O— is a 1,2,3-triazolyloxy moiety which is a silyl-to-chromophore linking group;
• and
• R1 and R2 are independently selected from the group consisting of C1-8 alkyl, cycloalkyl, aryl, C1-8 alkyloxy, cycloalkyloxy, trialkylsilyloxy and triarylsilyloxy;
• b. removing the 5′-O-protecting group by contact with a solution comprising fluoride ion and thereby providing a free 5′-OH group;
• c. reacting an appropriately protected ribonucleoside monomer having a 3′-phosphoramidityl substituent with the substrate-bound ribonucleotide, ribonucleoside or oligoribonucleotide whereby the 3′-phosphoramidityl substituent is coupled to the 5′-OH of the substrate-bound ribonucleotide, ribonucleoside or oligoribonucleotide to form a phosphite triester;
• and
• d. reacting the phosphite triester formed in (c) with a suitable oxidizing agent to convert it to a phosphate triester.