Single-stranded and double-stranded oligonucleotides comprising a 2-arylpropyl moiety
View Patent ↗The present invention provides single-stranded and double-stranded oligonucleotides comprising at least one aralkyl ligand that improves the pharmacokinetic properties of the oligonucleotides. The aralkyl ligands of the present invention include naproxen, ibuprofen and derivatives thereof. The present invention also provides methods for modulating gene expression using the modified oligonucleotide compounds and compositions comprising those modified oligonucleotides.
1. A double-stranded oligonucleotide comprising a first strand and a second strand, wherein said first strand and said second are represented independently by formula I:
wherein
X is H, —P(O)(OM) 2 , —P(O)(OM)—O—P(O)(OM) 2 , —P(O)(Oalkyl) 2 , —P(O)(Oalkyl)—O—P(O)(Oalkyl) 2 , or -A 6 -[A 7 -(A 5 ) w ] y , wherein in at least one of the strands, X is -A 6 -[A 7 -(A 5 ) w ] y ;
Z 1 represents independently for each occurrence O or S;
Z 2 represents independently for each occurrence —OH, —OM, —Oalkyl, —Oaryl, —Oaralkyl, —SH, —SM, —Salkyl, —Saryl, —Saralkyl, —N(R 3 )R 4 , —(C(R 11 ) 2 ) m N(R 11 ) 2 ,or alkyl;
R 1 and R 2 represent independently for each occurrence H, OH, F, —Oalkyl, —Oallyl, —O(C(R 11 ) 2 ) v OR 11 , —O(C(R 11 ) 2 ) v SR 11 , —O(C(R 11 ) 2 ) v N(R 11 ) 2 , —O(C(R 11 ) 2 ) v C(O)N(R 11 ) 2 , —N(R 11 ) 2 , —S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C(R 11 ) 2 ) v N((C 1 -C 6 )alkyl) 2 , —O(C(R 11 ) 2 ) v ON((C 1 -C 6 )alkyl) 2 , or —O-A 10 -[A 11 -(A 5 ) w ] y ;
R 3 and R 4 represent H or alkyl; or R 3 and R 4 taken together form a 3-, 4-, 5-, 6-, or 7-membered ring;
R 5 represents independently for each occurrence H, OH, F, —Oalkyl, —Oallyl, —O(C(R 11 ) 2 ) v OR 11 , —O(C(R 11 ) 2 ) v SR 11 , —O(C(R 11 ) 2 ) v N(R 11 ) 2 , —O(C(R 11 ) 2 ) v C(O)N(R 11 ) 2 , —N(R 11 ) 2 , —S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C(R 11 ) 2 ) v N((C 1 -C 6 )alkyl) 2 , or —O(C(R 11 ) 2 ) v ON((C 1 -C 6 )alkyl) 2 ;
R 6 represents independently for each occurrence H, alkyl, or —NHCH 2 CH═CH 2 ;
R 8 represents independently for each occurrence hydrogen, alkyl, aryl, aralkyl, acyl, or silyl;
R 11 represents independently for each occurrence hydrogen or alkyl;
n 1 and n 2 represent independently 0-21, inclusive;
m represents independently for each occurrence 1, 2, 3, 4, 5, 6, 7, or 8;
m 1 represents independently for each occurrence 0, 1, 2, 3, 4, 5, 6, 7, or 8;
v represents independently for each occurrence 1, 2, 3, or 4;
w represents independently for each occurrence 1, 2, or 3 in accord with the rules of valence;
y represents independently for each occurrence 1, 2, 3, 4, or 5 in accord with the rules of valence;
M represents independently for each occurrence an alkali metal or a transition metal with an overall charge of +1;
A 1 represents independently for each occurrence:
A 2 represents independently for each occurrence:
A 3 represents independently for each occurrence
A 4 represents independently for each occurrence a bond, alkyl diradical, heteroalkyl diradical, alkenyl diradical, alkynyl diradical, alkylalkynyl diradical, aminoalkyl diradical, thioether, —C(O)—, —S(O)—, —S(O) 2 —-, B 1 C(R) 2 B 2 , B 1 C(R)(B 2 ) 2 , B 1 C(B 2 ) 3 , B 1 N(R)(B 2 ), B 1 N(B 2 ) 2 , or has the formula:
B 1 is a bond between A 3 and A 4 ;
B 2 is a bond between A 4 and A 5 ;
R represents independently for each occurrence hydrogen or alkyl;
A 5 has the formula II:
wherein R 1-IIA , R 1-IIB , R 2-II , and R 3-II represent independently for each occurrence H, halogen, amino, hydroxyl, alkyl, alkoxyl, aminoalkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl, heteroaralkyl, thiol, thioalkyl, silyl, nitro, nitrile, acyl, acylamino, —COR, or —CO 2 R, where R is defined as above;
A 6 has the formula:
B 3 is a bond between A 6 and A 7 ;
B 4 is a bond between A 6 and A 1 ;
A 7 has the formula:
p represents independently for each occurrence 1, 2, 3, or 4;
B 5 is a bond between A 5 and A 7 ;
A 8 has the formula:
B 6 is a bond between A 8 and A 1 ;
B 7 is a bond between A 8 and A 9 ;
A 9 has the formula:
B 8 a bond between A 5 and A 9 ;
A 10 has the formula:
B 9 is a bond between A 10 and A 11 ;
B 10 is a bond between A 10 and O;
A 11 has the formula:
B 11 is a bond between A 5 and A 11 .
2. The double-stranded oligonucleotide of claim 1 , wherein R 1-IIA is alkyl.
3. The double-stranded oligonucleotide of claim 1 , wherein R 1-IIA is methyl, ethyl, propyl, isopropyl, butyl, sec-butyl, isobutyl, or tert-butyl.
4. The double-stranded oligonucleotide of claim 1 , wherein R 1-IIA is methyl.
5. The double-stranded oligonucleotide of claim 1 , wherein R 1-IIB is hydrogen.
6. The double-stranded oligonucleotide of claim 1 , wherein R 1-IIA is methyl; and R 1-IIB is hydrogen.
7. The double-stranded oligonucleotide of claim 1 , wherein R 2-II is hydrogen, alkyl, halogen, hydroxyl or amino.
8. The double-stranded oligonucleotide of claim 1 , wherein R 2-II is H.
9. The double-stranded oligonucleotide of claim 1 , wherein R 3-II is alkoxyl.
10. The double-stranded oligonucleotide of claim 1 , wherein R 3-II methoxy, ethoxy, propoxy, isopropoxy, butoxy, sec-butoxy, isobutoxy, or tert-butoxy.
11. The double-stranded oligonucleotide of claim 1 , wherein R 3-II methoxy.
12. The double-stranded oligonucleotide of claim 1 , wherein R 1-IIA is methyl, R 1-IIB is H, each R 2-II is H, and R 3-II is methoxy.
13. The double-stranded oligonucleotide of claim 1 , wherein said first strand and said second strand each contain at least one occurrence of A 5 .
14. The double-stranded oligonucleotide of claim 1 , wherein said first strand contains at least one occurrence of A 5 ; and said second strand does not.
15. A single-stranded oligonucleotide represented by formula IV:
wherein
X is -A 6 -[A 7 -(A 5 ) w ] y ;
X 1 is
Z 1 represents independently for each occurrence O or S;
Z 2 represents independently for each occurrence —OH, —OM, —Oalkyl, —Oaryl, —Oaralkyl, —SH, —SM, —Salkyl, —Saryl, —Saralkyl, —N(R 3 )R 4 , —(C(R 11 ) 2 ) m N(R 11 ) 2 , —N(R 11 )(C(R 11 ) 2 ) m N(R 11 ) 2 , or alkyl;
R 1 and R 2 represent independently for each occurrence H, OH, F, —Oalkyl, —Oallyl, —O(C(R 11 ) 2 ) v OR 11 , —O(C(R 11 ) 2 ) v SR 11 , —O(C(R 11 ) 2 ) v N(R 11 ) 2 , —O(C(R 11 ) 2 ) v C(O)N(R 11 ) 2 , —N(R 11 ) 2 , —S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C(R 11 ) 2 ) v N((C 1 -C 6 )alkyl) 2 , —O(C(R 11 ) 2 ) v ON((C 1 -C 6 )alkyl) 2 , or —O-A 10 -[A 11 -(A 5 ) w ] y ;
R 3 and R 4 represent H or alkyl; or R 3 and R 4 taken together form a 3-, 4-, 5-, 6-, or 7-membered ring;
R 5 represents independently for each occurrence H, OH, F, —Oalkyl, —Oallyl, —O(C(R 11 ) 2 ) v OR 11 , —O(C(R 11 ) 2 ) v SR 11 , —O(C(R 11 ) 2 ) v N( 11 ) 2 , —O(C(R 11 ) 2 ) v C(O)N(R 11 ) 2 , —N(R 11 ) 2 , —S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v S(C 1 -C 6 )alkyl —O(C(R 11 ) 2 ) v O(C(R 11 ) 2 ) v N((C 1 -C 6 )alkyl) 2 , or —O(C(R 11 ) 2 ) v ON((C 1 -C 6 )alkyl) 2 ;
R 6 represents independently for each occurrence H, alkyl, or —NHCH 2 CH═CH 2 ;
R 8 represents independently for each occurrence hydrogen, alkyl, aryl, aralkyl, acyl, orsilyl;
R 11 represents independently for each occurrence hydrogen or alkyl;
n 1 and n 2 represent independently 0-21, inclusive;
m represents independently for each occurrence 1, 2, 3, 4, 5, 6, 7, or 8;
m 1 represents independently for each occurrence 0, 1, 2, 3, 4, 5, 6, 7, or 8;
v represents independently for each occurrence 1, 2, 3, or 4;
w represents independently for each occurrence 1, 2, or 3 in accord with the rules of valence;
y represents independently for each occurrence 1, 2, 3, 4, or 5 in accord with the rules of valence;
M represents independently for each occurrence an alkali metal or a transition metal with an overall charge of +1;
A 1 represents independently for each occurrence:
A 2 represents independently for each occurrence:
A 3 represents independently for each occurrence
A 4 represents independently for each occurrence a bond, alkyl diradical, heteroalkyl diradical, alkenyl diradical, alkynyl diradical, alkylalkynyl diradical, aminoalkyl diradical, thioether, —C(O)—, —S(O)—, —S(O) 2 —, B 1 C(R) 2 B 2 , B 1 C(R)(B 2 ) 2 , B 1 C(B 2 ) 3 , B 1 N(R)(B 2 ), B 1 N(B 2 ) 2 , or has the formula:
B 1 is a bond between A 3 and A 4 ;
B 2 is a bond between A 4 and A 5 ;
R represents independently for each occurrence hydrogen or alkyl;
A 5 has the formula V:
wherein R 1-VA , R 1-VB , R 2-V , and R 3-V represent independently for each occurrence H, halogen, amino, hydroxyl, alkyl, alkoxyl, aminoalkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl, heteroaralkyl, thiol, thioalkyl, silyl, nitro, nitrile, acyl, acylamino, —COR, or —CO 2 R, where R is defined as above;
A 6 has the formula:
B 3 is a bond between A 6 and A 7 ;
B 4 is a bond between A 6 and A 1 ;
A 7 has the formula:
p represents independently for each occurrence 1, 2, 3, or 4;
B 5 is a bond between A 5 and A 7 ;
A 8 has the formula:
B 6 is a bond between A 8 and A 1 ;
B 7 is a bond between A 8 and A 9 ;
A 9 has the formula:
B 8 a bond between A 5 and A 9 ;
A 10 has the formula:
B 9 is a bond between A 10 and A 11 ;
B 10 is a bond between A 10 and O;
A 11 has the formula:
B 11 is a bond between A 5 and A 11 .
16. The single-stranded oligonucleotide of claim 15 , wherein R 1-VA is alkyl.
17. The single-stranded oligonucleotide of claim 15 , wherein R 1-VA is methyl, ethyl, propyl, isopropyl, butyl, sec-butyl, isobutyl, or tert-butyl.
18. The single-stranded oligonucleotide of claim 15 , wherein R 1-VA is methyl.
19. The single-stranded oligonucleotide of claim 15 , wherein R 1-VB is hydrogen.
20. The single-stranded oligonucleotide of claim 15 , wherein R 1-VA is methyl; and R 1-VB is hydrogen.
21. The single-stranded oligonucleotide of claim 15 , wherein R 2-V is hydrogen, alkyl, halogen, hydroxyl or amino.
22. The single-stranded oligonucleotide of claim 15 , wherein R 2-V is H.
23. The single-stranded oligonucleotide of claim 15 , wherein R 3-V is alkoxyl.
24. The single-stranded oligonucleotide of claim 15 , wherein R 3-V is methoxy, ethoxy, propoxy, isopropoxy, butoxy, sec-butoxy, isobutoxy, or tert-butoxy.
25. The single-stranded oligonucleotide of claim 15 , wherein R 3-V is methoxy.
26. The single-stranded oligonucleotide of claim 15 , wherein R 1-VA is methyl, R 1-VH is H, each R 2-V is H, and R 3-V is methoxy.
27. The single-stranded oligonucleotide of claim 15 , wherein A 5 occurs at least two times.
28. The single-stranded oligonucleotide of claim 15 , wherein A 5 occurs at least five times.
29. The double-stranded oligonucleotide of claim 1 , wherein,
A 7 independently represents for each occurrence
30. The double-stranded oligonucleotide of claim 29 , wherein A 7 is
wherein each R is H and m 1 is 6.
31. The single-stranded oligonucleotide of claim 15 , wherein,
A 7 independently represents for each occurrence
32. The single-stranded oligonucleotide of claim 31 , wherein A 7 is
wherein each R is H and m 1 is 6.
33. A double-stranded oligonucleotide comprising a first strand and a second strand,
wherein said first strand and said second are represented independently by formula I:
wherein
X is H, —P(O)(OM) 2 , —P(O)(OM)—O—P(O)(OM) 2 , —P(O)(Oalkyl) 2 , —P(O)(Oalkyl)—O—P(O)(Oalkyl) 2 , or -A 6 -[A 7 -(A 5 ) w ] y ;
X 1 is
Z 1 represents independently for each occurrence O or S;
Z 2 represents independently for each occurrence —OH, —OM, —Oalkyl, —Oaryl, —Oaralkyl, —SH, —SM, —Salkyl, —Saryl, —Saralkyl, —N(R 3 )R 4 , —(C(R 11 ) 2 ) m N(R 11 ) 2 , —N(R 11 )(C(R 11 ) 2 , or alkyl;
R 1 and R 2 represent independently for each occurrence H, OH, F, —Oalkyl, —Oallyl, —O(C(R 11 ) 2 ) v OR 11 , —O(C(R 11 ) 2 ) v SR 11 , —O(C(R 11 ) 2 )N(R 11 ) 2 , —O(C(R 11 ) 2 ) v C(O)N(R 11 ) 2 , —N(R 11 ) 2 , —S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C(R 11 ) 2 ) v N(C 1 -C 6 )alkyl) 2 , —O(C(R 11 ) 2 ) v ON((C 1 -C 6 ) 2 , or —O-A 10 -[A 11 -(A 5 ) w ] y , wherein either R 1 or R 2 is —O-A 10 -[A 11 -(A 5 ) w ] y ;
R 3 and R 4 represent H or alkyl; or R 3 and R 4 taken together form a 3-, 4-, 5-, 6-, or 7-membered ring;
R 5 represents independently for each occurrence H, OH, F, —Oalkyl, —Oallyl, —O(C(R 11 ) 2 ) v OR 11 , —O(C(R 11 ) 2 ) v SR 11 , —O(C(R 11 ) 2 ) v N(R 11 ) 2 , —O(C(R 11 ) 2 ) v C(O)N(R 11 ) 2 , —N(R 11 ) 2 , —S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C(R 11 ) 2 ) v N(C 1 -C 6 )alkyl) 2 , or —O(C(R 11 ) 2 ) v ON((C 1 -C 6 )alkyl) 2 ,
R 6 represents independently for each occurrence H, alkyl, or —NHCH 2 CH═CH 2 ;
R 8 represents independently for each occurrence hydrogen, alkyl, aryl, aralkyl, acyl, or silyl;
R 11 represents independently for each occurrence hydrogen or alkyl;
n 1 and n 2 represent independently 0-21, inclusive;
m represents independently for each occurrence 1, 2, 3, 4, 5, 6, 7, or 8;
m 1 represents independently for each occurrence 0, 1, 2, 3, 4, 5, 6, 7, or 8;
v represents independently for each occurrence 1, 2, 3, or 4;
w represents independently for each occurrence 1, 2, or 3 in accord with the rules of valence;
y represents independently for each occurrence 1, 2, 3, 4, or 5 in accord with the rules of valence;
M represents independently for each occurrence an alkali metal or a transition metal with an overall charge of +1;
A 1 represents independently for each occurrence:
A 2 represents independently for each occurrence:
A 3 represents independently for each occurrence
A 4 represents independently for each occurrence a bond, alkyl diradical, heteroalkyl diradical, alkenyl diradical, alkynyl diradical, alkylalkynyl diradical, aminoalkyl diradical, thioether, —C(O)—, —S(O)—, —S(O) 2 —, B 1 C(R) 2 B 2 , B 1 C(R)(B 2 ) 2 , B 1 C(B 2 ) 3 , B 1 N(R)(B 2 ), B 1 N(B 2 ) 2 , or has the formula:
B 1 is a bond between A 3 and A 4 ;
B 2 is a bond between A 4 and A 5 ;
R represents independently for each occurrence hydrogen or alkyl;
A 5 has the formula II:
wherein
R 1-IIA , R 1-IIB , R 2-II , and R 3-II represent independently for each occurrence H, halogen, amino, hydroxyl, alkyl, alkoxyl, aminoalkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl, heteroaralkyl, thiol, thioalkyl, silyl, nitro, nitrile, acyl, acylamino, —COR, or —CO 2 R, where R is defined as above;
A 6 has the formula:
B 3 is a bond between A 6 and A 7 ;
B 4 is a bond between A 6 and A 1 ;
A 7 has the formula:
p represents independently for each occurrence 1, 2, 3, or 4;
B 5 is a bond between A 5 and A 7 ;
A 8 has the formula:
B 6 is a bond between A 8 and A 1 ;
B 7 a bond between A 8 and A 9 ;
A 9 has the formula:
B 8 a bond between A 5 and A 9 ;
A 10 has the formula:
B 9 is a bond between A 10 and A 11 ;
B 10 is a bond between A 10 and O;
A 11 has the formula:
B 11 is a bond between A 5 and A 11 .
34. The double-stranded oligonucleotide of claim 33 , wherein R 1-IIA is alkyl.
35. The double-stranded oligonucleotide of claim 34 , wherein R 1-IIA is methyl.
36. The double-stranded oligonucleotide of claim 33 , wherein R 1-IIB is hydrogen.
37. The double-stranded oligonucleotide of claim 33 , wherein R 1-IIA is methyl; and R 1-IIB is hydrogen.
38. The double-stranded oligonucleotide of claim 33 , wherein R 2-II is hydrogen, alkyl, halogen, hydroxyl or amino.
39. The double-stranded oligonucleotide of claim 38 , wherein R 2-II is hydrogen.
40. The double-stranded oligonucleotide of claim 33 , wherein R 3-II alkoxyl.
41. The double-stranded oligonucleotide of claim 40 , wherein R 3-II methoxy.
42. The double-stranded oligonucleotide of claim 33 , wherein R 1-IIA is methyl, R 1-IIB is H, each R 2-II is H, and R 3-II is methoxy.
43. The double-stranded oligonucleotide of claim 33 , wherein said first strand and said second strand each contain at least one occurrence of A 5 .
44. The double-stranded oligonucleotide of claim 33 , wherein said first strand contains at least one occurrence of A 5 ; and said second strand does not.
45. A single-stranded oligonucleotide represented by formula IV:
wherein
X is H, —P(O)(OM) 2 , —P(O)(OM)—O—P(O)(OM) 2 , —P(O)(Oalkyl) 2 , —P(O)(Oalkyl)—O—P(O)(Oalkyl) 2 , or -A 6 -[A 7 -(A 5 ) w ] y ;
X 1 is
Z 1 represents independently for each occurrence O or S;
Z 2 represents independently for each occurrence —OH, —OM, —Oalkyl, —Oaryl, —Oaralkyl, —SH, —SM, —Salkyl, —Saryl, —Saralkyl, —N(R 3 )R 4 , —(C(R 11 ) 2 ) m N(R 11 ) 2 , —N(R 11 )(C(R 11 ) 2 ) m N(R 11 ) 2 , or alkyl;
R 1 and R 2 represent independently for each occurrence H, OH, F, —Oalkyl, —Oallyl, —O(C(R 11 ) 2 ) v OR 11 , —O(C(R 11 ) 2 ) v SR 11 , —O(C(R 11 ) 2 ) v N(R 11 ) 2 , —O(C(R 11 ) 2 ) v C(O)N(R 11 ) 2 , —N(R 11 ) 2 , —S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C(R 11 ) 2 ) v N((C 1 -C 6 )alkyl) 2 , —O(C(R 11 ) 2 ) v ON((C 1 -C 6 ) 2 , or —O-A 10 -[A 11 -(A 5 ) w ] y , wherein either R 1 or R 2 is —O-A 10 -[A 11 -(A 5 ) w ] y ,
R 3 and R 4 represent H or alkyl; or R 3 and R 4 taken together form a 3-, 4-, 5-, 6-, or 7-membered ring;
R 5 represents independently for each occurrence H, OH, F, —Oalkyl, —Oallyl, —O(C(R 11 ) 2 ) v OR 11 , —O(C(R 11 ) 2 ) v SR 11 , —O(C(R 11 ) 2 ) v N(R 11 ) 2 , —O(C(R 11 ) 2 ) v C(O)N(R 11 ) 2 , —N(R 11 ) 2 , —S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v S(C 1 -C 6 )alkyl, —O(C(R 11 ) 2 ) v O(C(R 11 ) 2 ) v N(C 1 -C 6 )alkyl) 2 , or —O(C(R 11 ) 2 ) v ON((C 1 -C 6 )alkyl) 2 ,
R 6 represents independently for each occurrence H, alkyl, or —NHCH 2 CH═CH 2 ;
R 8 represents independently for each occurrence hydrogen, alkyl, aryl, aralkyl, acyl, or silyl;
R 11 represents independently for each occurrence hydrogen or alkyl;
n 1 and n 2 represent independently 0-21, inclusive;
m represents independently for each occurrence 1, 2, 3, 4, 5, 6, 7, or 8;
m 1 represents independently for each occurrence 0, 1, 2, 3, 4, 5, 6, 7, or 8;
v represents independently for each occurrence 1, 2, 3, or 4;
w represents independently for each occurrence 1, 2, or 3 in accord with the rules of valence;
y represents independently for each occurrence 1, 2, 3, 4, or 5 in accord with the rules of valence;
M represents independently for each occurrence an alkali metal or a transition metal with an overall charge of +1;
A 1 represents independently for each occurrence:
A 2 represents independently for each occurrence:
A 3 represents independently for each occurrence
A 4 represents independently for each occurrence a bond, alkyl diradical, heteroalkyl diradical, alkenyl diradical, alkynyl diradical, alkylalkynyl diradical, aminoalkyl diradical, thioether, —C(O)—, —S(O)—, —S(O) 2 -, B 1 C(R) 2 B 2 , B 1 C(R)(B 2 ) 2 , B 1 C(B 2 ) 3 , B 1 N(R)(B 2 ), B 1 N(B 2 ) 2 , or has the formula:
B 1 is a bond between A 3 and A 4 ;
B 2 is a bond between A 4 and A 5 ;
R represents independently for each occurrence hydrogen or alkyl;
A 5 has the formula V:
wherein R 1-VA , R 1-VB , R 2-V ,and R 3-V represent independently for each occurrence H, halogen, amino, hydroxyl, alkyl, alkoxyl, aminoalkyl, alkenyl, alkynyl, aryl, aralkyl, heteroaryl, heteroaralkyl, thiol, thioalkyl, silyl, nitro, nitrile, acyl, acylamino, —COR, or —CO 2 R, where R is defined as above;
A 6 has the formula:
B 3 is a bond between A 6 and A 7 ;
B 4 is a bond between A 6 and A 1 ;
A 7 has the formula:
p represents independently for each occurrence 1, 2, 3, or 4;
B 5 is a bond between A 5 and A 7 ;
A 8 has the formula:
B 6 is a bond between A 8 and A 1 ;
B 7 is a bond between A 8 and A 9 ;
A 9 has the formula:
B 8 is a bond between A 5 and A 9 ;
A 10 has the formula:
B 9 is a bond between A 10 and A 11 ;
B 10 is a bond between A 10 and O;
A 11 has the formula:
B 11 is a bond between A 5 and A 11 .
46. The single-stranded oligonucleotide of claim 45 , wherein R 1-VA is alkyl.
47. The single-stranded oligonucleotide of claim 46 , wherein R 1-VA is methyl.
48. The single-stranded oligonucleotide of claim 45 , wherein R 1-VB is hydrogen.
49. The single-stranded oligonucleotide of claim 45 , wherein R 1-VA is methyl; and R 1-VB is hydrogen.
50. The single-stranded oligonucleotide of claim 45 , wherein R 2-V is hydrogen, alkyl, halogen, hydroxyl or amino.
51. The single-stranded oligonucleotide of claim 50 , wherein R 2-V is hydrogen.
52. The single-stranded oligonucleotide of claim 45 , wherein R 3-V is alkoxyl.
53. The single-stranded oligonucleotide of claim 52 , wherein R 3-V is methoxy.
54. The single-stranded oligonucleotide of claim 45 , wherein R 1-VA is methyl, R 1-VB is H, each R 2-V is H, and R 3-V is methoxy.
55. The single-stranded oligonucleotide of claim 45 , wherein A 5 occurs at least two times.
56. The single-stranded oligonucleotide of claim 55 , wherein A 5 occurs at least five times.
57. A double-stranded oligonucleotide comprising a single-stranded oligonucleotide of claim 45 and a second strand.
58. A double-stranded oligonucleotide comprising a single-stranded oligonucleotide of claim 15 and a second strand.
59. The double-stranded oligonucleotide of claim 33 , wherein A 10 represents independently for each occurrence
60. The double-stranded oligonucleotide of claim 59 , wherein A 11 represents independently for each occurrence
61. The double-stranded oligonucleotide of claim 60 , wherein A 11 is
wherein each R is H and m 1 is 6.
62. The single-stranded oligonucleotide of claim 45 , wherein A 10 represents independently for each occurrence
63. The single-stranded oligonucleotide of claim 62 , wherein A 11 represents independently for each occurrence
64. The single-stranded oligonucleotide of claim 63 , wherein A 11 is
wherein each R is H and m 1 is 6.