Oligomer-conjugate complexes and their use
Oligonucleotides, chemically-modified oligonucleotides, and oligonucleotide-conjugate complexes for use in research, diagnostics, and/or therapeutics are described herein. In some embodiments, oligonucleotides comprising a stabilized phosphate moiety covalently attached to the 5′-terminal nucleoside are provided.
1. A compound comprising an oligonucleotide consisting of 10-30 linked nucleosides and at least one conjugate group, wherein the 5′-terminal nucleoside of the oligonucleotide has Formula IV:
wherein:
T 1 is
wherein:
R a and R c are each, independently, OH, SH, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, amino or substituted amino; and
R b is O or S;
T 2 is an internucleoside linking group linking the compound of Formula IV to the remainder of the oligonucleotide;
Q 1 and Q 2 are each, independently, H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, substituted C 2 -C 6 alkynyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy or N(R 3 )(R 4 );
each R 3 and R 4 is, independently, H, C 1 -C 6 alkyl or substituted C 1 -C 6 alkyl;
Bx is a heterocyclic base moiety;
G is H, OH, halogen, a conjugate group, or O—[C(R 8 )(R 9 )] n —[(C═O) m —X 1 ] j —Z;
each R 8 and R 9 is, independently, H, halogen, C 1 -C 6 alkyl or substituted C 1 -C 6 alkyl;
X 1 is O, S or N(E 1 );
Z is H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, substituted C 2 -C 6 alkynyl or N(E 2 )(E 3 );
E 1 , E 2 and E 3 are each, independently, H, C 1 -C 6 alkyl or substituted C 1 -C 6 alkyl;
n is from 1 to about 6;
m is 0 or 1;
j is 0 or 1;
each substituted group comprises one or more optionally protected substituent groups independently selected from halogen, OJ 1 , N(J 1 )(J 2 ), ═NJ 1 , SJ 1 , N 3 , CN, OC(═X 2 )J 1 , OC(═X 2 )—N(J 1 )(J 2 ) and C(═X 2 )N(J 1 )(J 2 );
X 2 is O, S or NJ 3 ;
each J 1 , J 2 and J 3 is, independently, H or C 1 -C 6 alkyl; and
provided that when j is 1 then Z is other than halogen or N(E 2 )(E 3 ).
2. The compound of claim 1 , wherein the conjugate group is covalently attached to the oligonucleotide at a nucleoside at position 1, 2, 3, 4, 6, 7, 8, 9, 18, 19, 20, or 21 from the 5′-end of the oligonucleotide or at position 1, 2, 3, 12, 13, 4, 15, 17, 18, 19, 20, or 21 from the 3′-end of the oligonucleotide.
3. The compound of claim 2 , wherein the conjugate group is covalently attached to any of the 1 to 4 5′-most terminal nucleosides of the oligonucleotide.
4. The compound of claim 2 , wherein the conjugate group is covalently attached to the 5′-terminal nucleoside of the oligonucleotide.
5. The compound of claim 2 , wherein the conjugate group is covalently attached to the 8 th nucleoside from the 5′-terminal end of the oligonucleotide.
6. The compound of claim 2 , wherein the conjugate group is covalently attached to the 6 th nucleoside from the 5′-terminal end of the oligonucleotide.
7. The compound of claim 2 , wherein the conjugate group comprises C 20 alkyl.
8. The compound of claim 2 , wherein the conjugate group comprises C 16 alkyl.
9. The compound of claim 2 , wherein the conjugate group comprises C 10 alkyl.
10. The compound of claim 2 , wherein the conjugate group comprises a steroid.
11. The compound of claim 2 , wherein the conjugate group comprises cholesterol.
12. The compound of claim 2 , wherein the conjugate group comprises a carbohydrate.
13. The compound of claim 2 , wherein the conjugate group comprises N-acetylgalactosamine.
14. The compound of claim 2 , wherein each nucleoside is a modified nucleoside.
15. The compound of claim 2 , comprising at least one 2′-substituted nucleoside.
16. The compound of claim 2 , wherein the compound is single-stranded.
17. The compound of claim 2 , wherein each of the 6 to 9 3′-most terminal internucleoside linkages is a phosphorothioate linkage and each of the other internucleoside linkages is a phosphodiester linkage.
18. The compound of claim 2 , wherein each of the 6 to 9 3′-most terminal internucleoside linkages is a phosphorothioate linkage and each of the other internucleoside linkages is a phosphodiester or a phosphorothioate linkage.
19. The compound of claim 2 , wherein the conjugate group comprises C 10 to C 22 alkyl.
20. The compound of claim 2 , wherein the conjugate group comprises C 10 to C 22 alkenyl.
21. The compound of claim 2 , wherein the conjugate group comprises C 22 alkyl.