Method of preparing oligomeric compounds using modified coupling protocols
Provided herein are methods for the synthesis of oligomeric compounds wherein the standard coupling protocols are modified when coupling bicyclic nucleosides of Formula I. More particularly, the modified coupling protocols provide for a decrease in the ratio of phosphoramidite solution to activator solution in the coupling reagent with an increased contact time. The modified coupling protocols provide for oligomeric compounds having comparable yields to similar oligomeric compounds having modified nucleosides other than bicyclic nucleosides of Formula I.
1. A method of coupling solid support bound free hydroxyl groups to bicyclic nucleosides of Formula I:
wherein for each bicyclic nucleoside of Formula I:
Bx is an optionally protected heterocyclic base moiety;
T 1 is a hydroxyl protecting group;
T 2 is a reactive phosphorus group capable of forming an internucleoside linkage;
one of Q 1 and Q 2 is H and the other of Q 1 and Q 2 is C 1 -C 6 alkyl or substituted C 1 -C 6 alkyl where each substituted group is OJ 1 , SJ 1 , NJ 1 J 2 , N 3 or CN wherein each J 1 and J 2 is, independently, H or C 1 -C 6 alkyl;
comprising treatment of the free hydroxyl groups with a coupling reagent which is about 70% by volume activator solution consisting of 1.0 molar 4,5-dicyanoimidazole and about 0.1 molar N-methylimidazole in acetonitrile and about 30% by volume of a solution having about a 0.2 molar concentration of bicyclic nucleosides of Formula I disolved in acetonitrile or a mixture of acetonitrile and toluene and wherein the volume of coupling reagent added provides about 1.75 equivalents of bicyclic nucleosides of Formula I based on the initial loading of the solid support with free hydroxyl groups.
2. The method of claim 1 wherein the initial loading of the free hydroxyl groups on the solid support is greater than about 100 mmol.
3. The method of claim 1 wherein the initial loading of the free hydroxyl groups on the solid support is greater than about 200 mmol.
4. The method of claim 1 wherein the initial loading of the free hydroxyl groups on the solid support is from about 220 mmol to about 900 mmol.
5. The method of claim 1 wherein the initial loading of the free hydroxyl groups on the solid support is greater than about 200 mmol and the delivery of the coupling reagent to the solid support is at a flow rate that requires from about 4 to about 5 minutes to deliver the about 1.75 equivalents.
6. The method of claim 5 further comprising recirculation of the coupling reagent for a time of from about 4.5 to about 5.5 minutes.
7. The method of claim 1 wherein the free hydroxyl groups are bound to the solid support through linking moieties.
8. The method of claim 1 wherein each of the free hydroxyl groups are provided by solid support bound UNYLINKER™ groups having one of the formulas:
wherein L is a linking moiety and SS is a solid support.
9. The method of claim 1 wherein each reactive phosphorus group is a diisopropylcyanoethoxy phosphoramidite.
10. The method of claim 1 wherein each T 1 is 4,4′-dimethoxy-trityl.
11. The method of claim 1 wherein one of Q 1 and Q 2 is H and the other of Q 1 and Q 2 is CH 3 .
12. The method of claim 1 wherein each heterocyclic base moiety is, independently, uracil, thymine, cytosine, 4-N-benzoylcytosine, 4-N-benzoyl-5-methyl-cytosine, adenine, 6-N-benzoyladenine, guanine or 2-N-isobutyrylguanine.
13. The method of claim 1 wherein dichloroacetic acid in toluene is used to deblock blocked hydroxyl groups.
14. The method of claim 13 further comprising treatment with triethylamine in acetonitrile to remove phosphorus protecting groups thereby providing linkages between monomer subunits that are independently selected from phosphodiester and phosphorothioate.
15. The method of claim 14 further comprising treatment with ammonium hydroxide to remove further protecting groups and cleave the oligomeric compound from the solid support.