Compounds and methods for modulating interaction between proteins and target nucleic acids
Provided herein are antisense compounds and methods for recruiting one or more non-cleaving protein to a target nucleic acid in a cell. In certain instances such recruitment of a non-cleaving protein alters the function or activity of the target nucleic acid. In certain such instances, the target nucleic acid a pre-mRNA and the recruitment of the non-cleaving protein results in a change in splicing of the pre-mRNA.
1. A method of inducing exon skipping in a target pre-mRNA in a cell comprising contacting the cell with an antisense compound comprising a chemically modified oligonucleotide consisting of 18 linked nucleosides; and thereby inducing exon skipping in the pre-mRNA in the cell; wherein the antisense compound comprises:
a 5′-wing region consisting of 2 linked duplex stabilizing nucleosides;
a 3′-wing region consisting of 2 linked duplex stabilizing nucleosides; and
a central gap region located between the 5′-wing region and the 3′-wing region
and consisting of 14 contiguous nucleosides comprising 2′-F modifications;
wherein each duplex stabilizing nucleoside is a 2′-methoxyethyl (2′-MOE) nucleoside, and
wherein the antisense compound is complementary to an intron of the target pre-mRNA.
2. The method of claim 1 , wherein the antisense compound binds to the target pre-mRNA and recruits at least one non-cleaving nucleic acid binding protein to the antisense compound/target pre-mRNA duplex.
3. The method of claim 2 , wherein at least one of the at least one non-cleaving nucleic acid binding proteins recruited to the compound/target pre-mRNA duplex is Interleukin Enhancer Binding Factor 2 or Interleukin Enhancer Binding Factor 3.
4. The method of claim 1 , wherein the target pre-mRNA is associated with a disease or disorder.
5. The method of claim 4 , wherein the target pre-mRNA is Bcl-x.
6. The method of claim 4 , wherein the disease or disorder is cancer.
7. The method of claim 4 , wherein the disease or disorder is Duchenne muscular dystrophy.
8. The method of claim 1 , wherein the cell is in vitro.
9. The method of claim 1 , wherein the cell is in an animal.
10. The method of claim 1 comprising performing an assay to determine whether the exon has been skipped.
11. The method of claim 1 comprising performing an assay to determine whether a protein has been recruited to the antisense compound/target pre-mRNA duplex.
12. The method of claim 11 comprising performing an assay to determine the identity of one or more protein recruited to the antisense compound/target pre-mRNA duplex.
13. The method of claim 6 , wherein the cell is in an animal.
14. The method of claim 7 , wherein the cell is in an animal.