Oligonucleotide compositions and methods of making the same
The present disclosure provides a solid phase method of making oligonucleotides via sequential coupling cycles including at least one coupling of a dinucleotide dimer subunit to a free 3′-terminal group of a growing chain. The oligonucleotides include at least two nucleoside subunits joined by a N3′→P5′ phosphoramidate linkage. The method may include the steps of (a) deprotecting the protected 3′ amino group of a terminal nucleoside attached to a solid phase support, said deprotecting forming a free 3′ amino group; (b) contacting the free 3′ amino group with a 3′-protected amino-dinucleotide-5′-phosphoramidite dimer in the presence of a nucleophilic catalyst to form an internucleoside N3′→P5′ phosphoramidite linkage; and (c) oxidizing (e.g., sulfurizing) the linkage. The compositions produced by the subject methods may include a reduced amount of one or more (N−x) oligonucleotide products. Also provided are pharmaceutical compositions including the subject oligonucleotide compositions.
1. A dinucleotide thiophosphoramidate compound described by Formula (II):
wherein:
B 1 and B 2 are each independently a purine, a protected purine, a pyrimidine or a protected pyrimidine, or an analog thereof;
R 11 is a phosphoramidite group; and
R 12 and R 13 are each independently a protecting group; or a salt thereof.
2. The compound of claim 1 , wherein B 1 and B 2 are each independently selected from protected adenine, protected cytosine, protected guanine, thymine and uracil.
3. The compound of claim 2 , wherein B 1 and B 2 are each independently selected from A(Bz), A(DMF), C(Bz), G(isobutyryl), T and U.
4. The compound of claim 3 , wherein B 1 is A(Bz) or A(DMF) and B 2 is A(Bz) or A(DMF).
5. The compound of claim 3 , wherein B 1 is A(Bz) or A(DMF) and B 2 is C(Bz).
6. The compound of claim 3 , wherein B 1 is A(Bz) or A(DMF) and B 2 is G(isobutyryl).
7. The compound of claim 3 , wherein B 1 is A(Bz) or A(DMF) and B 2 is T.
8. The compound of claim 3 , wherein B 1 is A(Bz) or A(DMF) and B 2 is U.
9. The compound of claim 3 , wherein B 1 is C(Bz) and B 2 is A(Bz) or A(DMF).
10. The compound of claim 3 , wherein B 1 is C(Bz) and B 2 is C(Bz).
11. The compound of claim 3 , wherein B 1 is C(Bz) and B 2 is G(isobutyryl).
12. The compound of claim 3 , wherein B 1 is C(Bz) and B 2 is T.
13. The compound of claim 3 , wherein B 1 is C(Bz) and B 2 is U.
14. The compound of claim 3 , wherein B 1 is G(isobutyryl) and B 2 is A(Bz) or A(DMF).
15. The compound of claim 3 , wherein B 1 is G(isobutyryl) and B 2 is C(Bz).
16. The compound of claim 3 , wherein B 1 is G(isobutyryl) and B 2 is G(isobutyryl).
17. The compound of claim 3 , wherein B 1 is G(isobutyryl) and B 2 is T.
18. The compound of claim 3 , wherein B 1 is G(isobutyryl) and B 2 is U.
19. The compound of claim 3 , wherein B 1 is T or U and B 2 is A(Bz) or A(DMF).
20. The compound of claim 3 , wherein B 1 is T or U and B 2 is C(Bz).
21. The compound of claim 3 , wherein B 1 is T or U and B 2 is G(isobutyryl).
22. The compound of claim 3 , wherein B 1 is T or U and B 2 is T.
23. The compound of claim 3 , wherein B 1 is T or U and B 2 is U.