Patent ID: 6825338
Filing Date: 2004-11-30
Classification: C07H

Abstract:
A process for preparing an oligonucleotide having the formula: wherein:R1 is a group having the formula: Q0 is O or S; R4 is O, hydroxyl, or a protected hydroxyl; R2 is hydroxyl, a protected hydroxyl or a group having the formula: each R3 is H, a 2â€²-substituent group or a protected 2â€²-substituent group; each X is, independently, Oâˆ’, hydroxyl, protected hydroxyl, or â€”Sâ€”L3; each Bx is an optionally protected heterocyclic base moiety; n is from 3 to about 50; and L1, L2 and each of said L3 are, independently, a cholesterol, phospholipid, biotin, phenazine, phenanthridine, anthraquinone, acridine, fluorescein, rhodamine, or coumarin wherein said R1 and at least one of said R2 or said X comprise a cholesterol, phospholipid, biotin, phenazine, phenanthridine, anthraquinone, acridine, fluorescein, rhodamine, or coumarin; comprising the steps of: a) providing a derivatized solid support for oligonucleotide synthesis, said derivatized solid support being derivatized with a group having one of the structures; whereinT is a bifunctional linking moiety linked to the solid support; and Q1 is an acid labile hydroxyl protecting group; b) treating said derivatized solid support with an acidic reagent to deblock said acid labile hydroxyl protecting group to give a free hydroxyl group; c) reacting said free hydroxyl group with a phosphoramidite composition to form an extended compound, said phosphoramidite composition having the formula: whereinQ2 is a 5â€²-terminal acid labile hydroxyl protecting group; Q3 is a phosphorus protecting group; and Z6 and Z7 are, independently, C1-6 alkyl; or Z6 and Z7 are joined together to form a 4- to 7-membered heterocyclic ring system including the nitrogen atom to which Z6 and Z7 are attached, wherein said ring system optionally includes at least one additional heteroatom selected from O, N and S; d) oxidizing said extended compound to form an oxidized compound, or treating said extended compound with an acidic reagent to deblock said 5â€²-terminal acid labile hydroxyl protecting group of said extended compound to give a free hydroxyl group and repeating step c) at least one time followed by oxidizing said extended compound to form an oxidized compound; e) treating said oxidized compound with an acidic reagent to deblock said acid labile hydroxyl protecting group to give a free hydroxyl group and repeating steps c) and d) at least three times to form an extended oxidized compound; f) treating said extended oxidized compound with a reagent effective to deblock said protected hydroxyl group to give a free hydroxyl group and reacting said free hydroxyl group with a compound of formula: â€ƒthereby forming a 5â€²-functionalized compound; wherein Q5 is an acid labile hydroxyl protecting group; g) treating said 5â€²-functionalized compound for a time and under conditiong effective to remove at least one phosphorus protecting group giving at least one deblocked phosphorothioate linkage; and h) reacting said deblocked phosphorothioate linkage with a cholesterol, phospholipid, biotin, phenazine, phenanthridine, anthraquinone, acridine, fluorescein, rhodamine, or coumarin, that is reactive with and forms a covalent bond with said deblocked phosphorothioate linkage to give said oligonucleotide.