COMPOUNDS AND METHODS FOR MODULATING INTERACTION BETWEEN PROTEINS AND TARGET NUCLEIC ACIDS

• US 20130289092A1
• Filed: 06/15/2011
• Published: 10/31/2013
• Est. Priority Date: 06/15/2010
• Status: Active Grant

• Current Assignee: Cold Spring Harbor Laboratory, Ionis Pharmaceuticals, Inc.
• Original Assignee: Cold Spring Harbor Laboratory, ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Rigo, Frank, Bennett, C. Frank, Krainer, Adrian R., Hua, Yimin
• Granted Patent: US 9,518,259 B2
• Time in Patent Office: Days
• US Class Current: 514/44.A
• CPC Class Codes: A61P 21/00 Drugs for disorders of the muscular or neuromuscular system
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding nucleic acids
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/3231 having an additional ring, e.g. LNA, ENA
• CPC Class Codes: C12N 2310/3341 5-Methylcytosine
• CPC Class Codes: C12N 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/3525 MOE, methoxyethoxy
• CPC Class Codes: C12N 2310/3533 Halogen
• CPC Class Codes: C12N 2320/33 Alteration of splicing

Abstract

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.

Claims

1-111. -111. (canceled)

112. 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 8 to 30 linked nucleosides;

and thereby inducing exon skipping in the pre-mRNA in the cell;

wherein at least one nucleoside comprises at least one 2′

-F modification.

113. The method of claim 112, 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.

115. The method of claim 112, wherein each nucleoside of the oligonucleotide is a modified nucleoside.

118. The method of claim 112, wherein at least six nucleosides comprise a 2′

-F modification.

119. The method of claim 112, wherein at least ten nucleosides comprise a 2′

-F modification.

121. The method of claim 112 comprising at least one bicyclic nucleoside.

122. The method of claim 112 comprising at least one constrained-ethyl modified nucleoside.

123. The method of claim 112, wherein the target pre-mRNA is associated with a disease or disorder.

124. The method of claim 123, wherein the target pre-mRNA is Bcl-x.

125. The method of claim 123, wherein the disease or disorder is cancer.

126. The method of claim 123, wherein the disease or disorder is Duchenne muscular dystrophy.

127. The method of claim 112, wherein the cell is in vitro.

128. The method of claim 112, wherein the cell is in an animal.

129. The method of claim 112 comprising performing an assay to determine whether the exon has been skipped.

130. The method of claim 112 comprising performing an assay to determine whether a protein has been recruited to the antisense compound/target pre-mRNA duplex.

131. The method of claim 130 comprising performing an assay to determine the identity of one or more protein recruited to the antisense compound/target pre-mRNA duplex.

132. The method of claim 112, wherein the antisense compound is complementary to an intron of the target pre-mRNA.

156. The method of claim 125, wherein the cell is in an animal.

116. (canceled)

117. (canceled)

120. (canceled)

133-155. -155. (canceled)

156-1. The method of claim 126, wherein the cell is in an animal.