Methods and compounds useful in conditions related to repeat expansion

1. A method of modulating the splicing of an ataxin-3 pre-mRNA containing at least one expanded repeat, comprising contacting a cell with a compound comprising a modified single-stranded RNA oligonucleotide consisting of 13 to 30 linked nucleosides and having a nucleobase sequence complementary to a repeat region of the ataxin-3 pre-mRNA, wherein the 5′-terminal nucleoside of the modified single-stranded RNA oligonucleotide comprises a phosphate moiety and an internucleoside linking group linking the 5′-terminal nucleoside to the remainder of the modified single-stranded RNA oligonucleotide, wherein the modified single-stranded RNA oligonucleotide comprises a mismatch at the ninth nucleobase from the 5′-end of the modified single-stranded RNA oligonucleotide relative to a repeat region of the expanded repeat-containing target pre-mRNA.

2. The method of claim 1 , wherein the 5′-terminal nucleoside of the modified single-stranded RNA oligonucleotide has Formula I:

wherein:

T 1 is a phosphorus moiety;

T 2 is an internucleoside linking group linking the 5′-terminal nucleoside of Formula I to the remainder of the modified single-stranded RNA oligonucleotide;

A has a formula selected from among:

Q 1 and Q 2 are each independently selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, substituted C 2 -C 6 alkynyl, and N(R 3 )(R 4 );

Q 3 is selected from among: O, S, N(R 5 ), and C(R 6 )(R 7 );

each R 3 , R 4 R 5 , R 6 and R 7 is independently selected from among: H, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, and C 1 -C 6 alkoxy;

M 3 is selected from among: O, S, NR 14 , C(R 15 )(R 16 ), C(R 15 )(R 16 )C(R 17 )(R 18 ), C(R 15 )═C(R 17 ), OC(R 15 )(R 16 ), and OC(R 15 )(Bx 2 );

R 14 is selected from among: H, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, and substituted C 2 -C 6 alkynyl;

R 15 , R 16 , R 17 and R 18 are each independently selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, and substituted C 2 -C 6 alkynyl;

if Bx 2 is present, then Bx 2 is a nucleobase and Bx 1 is selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, and substituted C 2 -C 6 alkynyl;

if Bx 2 is not present, then Bx 1 is a nucleobase;

either each of J 4 , J 5 , J 6 and J 7 is independently selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, and substituted C 2 -C 6 alkynyl;

or J 4 forms a bridge with one of J 5 or J 7 wherein the bridge comprises from 1 to 3 linked biradical groups selected from O, S, NR 19 , C(R 20 )(R 21 ), C(R 20 )═C(R 21 ), C[═C(R 20 )(R 21 )] and C(═O) and the other two of J 5 , J 6 and J 7 are independently selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl, and substituted C 2 -C 6 alkynyl;

each R 19 , R 20 and R 21 is independently selected from among: H, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, substituted C 1 -C 6 alkoxy, C 2 -C 6 alkenyl, substituted C 2 -C 6 alkenyl, C 2 -C 6 alkynyl or substituted C 2 -C 6 alkynyl;

G is selected from among: H, OH, halogen, O—[C(R 8 )(R 9 )] n —[(C═O) m —X 1 ] j —Z, and a conjugate group;

each R 8 and R 9 is independently selected from among: H, halogen, C 1 -C 6 alkyl, and substituted C 1 -C 6 alkyl;

X 1 is O, S or N(E 1 );

Z is selected from among: 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, and N(E 2 )(E 3 );

E 1 , E 2 and E 3 are each independently selected from among: H, C 1 -C 6 alkyl, and substituted C 1 -C 6 alkyl;

n is from 1 to 6;

m is 0 or 1;

j is 0 or 1;

provided that, if j is 1, then Z is other than halogen or N(E 2 )(E 3 );

each substituted group comprises one or more optionally protected substituent groups independently selected from among: a 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 ; and

each J 1 , J 2 and J 3 is independently selected from among: H and C 1 -C 6 alkyl.

3. The method of claim 2 , wherein M 3 is O.

4. The method of claim 2 , wherein each of J 4 , J 5 , J 6 and J 7 is H.

5. The method of claim 2 , wherein A has the formula:

wherein:

Q 1 and Q 2 are each independently selected from among: H, halogen, C 1 -C 6 alkyl, substituted C 1 -C 6 alkyl, C 1 -C 6 alkoxy, and substituted C 1 -C 6 alkoxy.

6. The method of claim 2 , wherein each of Qand Q 2 is H.

7. The method of claim 2 , wherein T 1 has the formula:

wherein:

R a and R c are each independently selected from among: hydroxyl, thiol, 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.

8. The method of claim 2 , wherein G is selected from among: a halogen, OCH 3 , OCF 3 , OCH 2 CH 3 , OCH 2 CF 3 , OCH 2 —CH═CH 2 , O(CH 2 ) 2 —OCH 3 , O(CH 2 ) 2 —O(CH 2 ) 2 —N(CH 3 ) 2 , OCH 2 C(═O)—N(H)CH 3 , OCH 2 C(═O)—N(H)—(CH 2 ) 2 —N(CH 3 ) 2 , and OCH 2 —N(H)—C(═NH)NH 2 .

9. The method of claim 2 , wherein G is selected from among: F, OCH 3 , and O(CH 2 ) 2 —OCH 3 .

10. The method of claim 2 , wherein the 5′-terminal nucleoside has Formula V:

wherein:

Bx is selected from among: uracil, thymine, cytosine, 5-methyl cytosine, adenine, and guanine;

T 2 is a phosphorothioate internucleoside linking group linking the 5′-terminal nucleoside of Formula V to the remainder of the modified single-stranded RNA oligonucleotide; and

G is selected from among: a halogen, OCH 3 , OCF 3 , OCH 2 CH 3 , OCH 2 CF 3 , OCH 2 —CH═CH 2 , O(CH 2 ) 2 —OCH 3 , O(CH 2 ) 2 —O(CH 2 ) 2 —N(CH 3 ) 2 , OCH 2 C(═O)—N(H)CH 3 , OCH 2 C(═O)—N (H)—(CH 2 ) 2 —N(CH 3 ) 2 , OCH 2 —N(H)—C(═NH)NH 2 , and a conjugate group.

11. The method of claim 1 , wherein the remainder of the modified single-stranded RNA oligonucleotide comprises at least one region having sugar motif:

-[( A ) x -( B ) y -( A ) z ] q -

wherein

A is a modified nucleoside of a first type,

B is a modified nucleoside of a second type;

each x and each y is independently 1 or 2;

z is 0 or 1;

q is 1-15.

12. The method of claim 11 , wherein the modifications of the first type and the modifications of the second type are selected from among: 2′-F, 2′-OMe, and F-HNA.

13. The method of claim 11 , wherein the remainder of the modified single-stranded RNA oligonucleotide comprises 1-4 3′-terminal nucleosides, each comprising the same sugar modification, wherein the sugar modification of the 1-4 3′terminal nucleosides is different from the sugar modification of the immediately adjacent nucleoside.

14. The method of claim 1 , wherein the modified single-stranded RNA oligonucleotide has two mismatches relative to a repeat region of the expanded repeat-containing target pre-mRNA.

15. The method of claim 1 , wherein the modified single-stranded RNA oligonucleotide has three mismatches relative to a repeat region of the expanded repeat-containing target pre-mRNA.

16. The method of claim 15 , wherein the mismatches are located at the 9 th , 10 th , and 11 th nucleobases from the 5′-end of the modified single-stranded RNA oligonucleotide.

17. The method of claim 1 , wherein the cell is in an animal.