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

1. A compound of the formula:

Y-Q-O—Si(R 1 )(R 2 )—X,

wherein Y is an aromatic or heteroaromatic diazo chromophore-derived substituent;

-Q-O— is a 1,2,3-triazolyloxy moiety which is a silyl-to-chromophore linking group;

R 1 and R 2 are independently selected from the group consisting of C 1-8 alkyl, cycloalkyl, aryl, C 1-8 alkyloxy, cycloalkyloxy, trialkylsilyloxy and triarylsilyloxy; and

X is a ribonucleotide-derived substituent moiety, a ribonucleoside-derived substituent moiety or an oligoribonucleotide-derived substituent moiety that is attached to the Si at a 5′-O-position and is protected at each of its 2′-O-positions.

2. The compound of claim 1 , wherein X has 2′ substituent(s) selected from the group consisting of O-acetoxyethyl (ACE); O-Me; F; and O-MP, wherein MP=

3. The compound of claim 1 , wherein R 1 and R 2 are independently selected from the group consisting of C 1-8 trialkyloxy and C 1-4 trialkylsilyloxy.

4. The compound of claim 1 , wherein the compound is selected from the group consisting of:

a 5′-DR-Q-O—Si(—O-iPr) 2 ribophosphoramidite,

a 5′-DR-Q-O—Si(—O-Me) 2 ribophosphoramidite, and

a 5′-DR-Q-O—Si(—O-TMS) 2 ribophosphoramidite,

wherein DR is selected from the structures:

5. A compound of the formula:

L 1 -O—Si(R 1 )(R 2 )—X,

wherein L 1 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;

R 1 and R 2 are independently selected from the group consisting of C 1-8 alkyl, cycloalkyl, aryl, C 1-8 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.

6. A method of synthesizing a compound of formula Y-Q-O—Si(R 1 )(R 2 )—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;

R 1 and R 2 are independently selected from the group consisting of C 1-8 alkyl, cycloalkyl, aryl, C 1-8 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 L 1 -O—Si(R 1 )(R 2 )—X with a compound of formula Y-L 2 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-L 2 to covalently react with L 1 -O—Si(R 1 )(R 2 )—X without reacting with said 3′OH group or protecting group at said position other than the 5′ position,

wherein L 1 and L 2 are independently substituents selected from the group consisting of an azido moiety and an alkynyl moiety; and whereby L 1 and L 2 react to form the moiety Q, wherein one of L 1 and L 2 is an azido moiety and the other one of L 1 and L 2 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.

7. The method of claim 6 further comprising

a. reacting a compound of formula L 1 -O—Si(R 1 )(R 2 )(Z) with a 5′,3′-dideprotected-2′-protected ribonucleoside represented by variable X; and

b. purifying via chromatography the resulting precursor

L 1 -O—Si(R 1 )(R 2 )—X;

wherein Z is halo, imidazolyl, triazolyl, tetrazolyl, trifluoromethylsulfonyl, alkylamino or dialkylamino.

8. The method of claim 6 further comprising

a. reacting a compound of formula L 1 -O—Si(R 1 )(R 2 )Cl with X; and

b. purifying via chromatography the resulting precursor

L 1 -O—Si(R 1 )(R 2 )—X.

9. The method of claim 6 further comprising

a. reacting a compound of formula L 1 -O—Si(R 1 )(R 2 )(Z) with an appropriately monodeprotected ribonucleoside moiety; and

b. purifying via chromatography the resulting precursor, L 1 -O—Si(R 1 )(R 2 )-ribonucleoside;

wherein Z is N, N-diisopropylamino.

10. The method of claim 6 , wherein L 1 is an alkynyl moiety and L 2 is an azido moiety, and the copper (I) catalyst catalyzes the cycloaddition of said moieties.

11. 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(R 1 )(R 2 );

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

R 1 and R 2 are independently selected from the group consisting of C 1-8 alkyl, cycloalkyl, aryl, C 1-8 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.

12. The method of claim 11 wherein steps a through d are repeated.

13. The method of claim 11 wherein the nucleoside monomer and substrate bound ribonucleotide, ribonucleoside or oligoribonucleotide further comprise a 2′-O-protecting group.

14. The method of claim 11 further comprising detecting the 5′-O-protected group removed in step b.