Suppression effectors that target non-coding regions and uses therefore

Abstract

The invention provides a strategy for suppressing expression of an endogenous gene, wherein said strategy comprises providing suppression effectors able to bind to the non-coding regions of a gene to be suppressed, to prevent the functional expression thereof. The suppression effectors may be nucleic acids, and the non-coding regions can include the transcribed but non-translated regions of a gene. The strategy can also introduce a replacement gene.

1 - 20 . (canceled)  
     
     
         21 . A method for designing a therapeutic useful for treating a genetic disease, said method comprising: 
 a) designing a suppression effector that binds to an untranslated region of a mature RNA encoding a mutant allele, wherein said suppression effector inhibits the expression of the mutant allele; and    b) designing a replacement nucleic acid that expresses a wild-type or non-disease causing allele and that is not inhibited by the suppression effector.    
     
     
         22 . The method as in  claim 21 , wherein the suppression effector is a nucleic acid or peptide nucleic acid (PNA).  
     
     
         23 . The method as in  claim 21 , wherein the suppression effector is a peptide.  
     
     
         24 . The method as in  claim 21 , wherein the suppression effector is an antisense nucleic acid.  
     
     
         25 . The method as in  claim 21 , wherein the suppression effector cleaves or degrades mRNA.  
     
     
         26 . The method as in  claim 21 , wherein the suppression effector is a ribozyme.  
     
     
         27 . The method as in  claim 21 , wherein the suppression effector is a nucleic acid that forms a triple helix with a portion of the untranslated region of the mutant allele.  
     
     
         28 . The method as in  claim 21 , wherein the suppression effector is specific for mammalian rhodopsin RNA.  
     
     
         29 . The method as in  claim 21 , wherein the suppression effector is specific for mammalian peripherin RNA.  
     
     
         30 . The method as in  claim 21 , wherein the suppression effector is specific for mammalian collagen RNA.  
     
     
         31 . The method as in  claim 21 , wherein the replacement nucleic acid does not hybridize with, or is only partially suppressed by, the suppression effector.  
     
     
         32 . The method as in  claim 21 , wherein the replacement nucleic acid encodes a protein selected from the group consisting of mammalian rhodopsin, collagen 1A2 and peripherin.  
     
     
         33 . The method as in  claim 21 , wherein the suppression effector comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 7, 13, 14 and 16.  
     
     
         34 . The method as in  claim 21 , wherein suppression effector is operatively linked to an expression vector.  
     
     
         35 . The method as in  claim 21 , wherein the replacement nucleic acid is operatively linked to an expression vector.  
     
     
         36 . The method as in  claim 21 , wherein the suppression effector and the replacement nucleic acid are operatively linked to the same expression vector.  
     
     
         37 . The method as in  claim 21 , wherein the untranslated region is essentially a 5′ untranslated region.  
     
     
         38 . The method as in  claim 21 , wherein the untranslated region is essentially a 3′ untranslated region.  
     
     
         39 . The method as in  claim 37  or  38 , wherein the suppression effector further binds to a portion of the coding sequence.  
     
     
         40 . The method as in  claim 21 , wherein the genetic disease is an autosomal dominant disease or a polygenic disease.  
     
     
         41 . The method as in  claim 21 , wherein the genetic disease is osteogenesis imperfecta, retinitis pigmentosa, age-related macular degeneration, glaucoma, manic depression or cancer.  
     
     
         42 . A method for designing a therapeutic composition for suppressing the expression of a mutant allele of a protein, the method comprising the steps of: 
 a) designing a ribozyme that targets an untranslated region of a mature RNA encoding a mutant allele; and    b) designing a replacement nucleic acid that expresses a wild-type or non-disease causing allele and that is not targeted by the ribozyme.    
     
     
         43 . The method as in  claim 42 , wherein the ribozyme cleavage site is an NUX site.  
     
     
         44 . The method of  claim 42 , wherein the ribozyme is specific for mammalian rhodopsin RNA.  
     
     
         45 . The method of  claim 42 , wherein the ribozyme is specific for mammalian peripherin RNA.  
     
     
         46 . The method of  claim 42 , wherein the ribozyme is specific for mammalian collagen RNA.  
     
     
         47 . The method of  claim 42 , wherein the replacement nucleic acid does not hybridize with, or is only partially suppressed by, the ribozyme.  
     
     
         48 . The method of  claim 42 , wherein the replacement nucleic acid encodes a protein selected from the group consisting of mammalian rhodopsin, collagen 1A2 and peripherin.  
     
     
         49 . The method of  claim 42 , wherein the suppression effector comprises a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 7, 13, 14 and 16.  
     
     
         50 . The method of  claim 42 , wherein the ribozyme is operatively linked to an expression vector.  
     
     
         51 . The method of  claim 42 , wherein the replacement nucleic acid is operatively linked to an expression vector.  
     
     
         52 . The method of  claim 42 , wherein the ribozyme and the replacement nucleic acid are operatively linked to the same expression vector.  
     
     
         53 . The method of  claim 42 , wherein the untranslated region is essentially a 5′ untranslated region.  
     
     
         54 . The method of  claim 42 , wherein the untranslated region is essentially a 3′ untranslated region.  
     
     
         55 . The method of  claim 53  or  54 , wherein the ribozyme further binds to a portion of the coding sequence.  
     
     
         56 . The method of  claim 42 , wherein the genetic disease is an autosomal dominant disease or a polygenic disease.  
     
     
         57 . The method of  claim 42 , wherein the genetic disease is osteogenesis imperfecta, retinitis pigmentosa, age-related macular degeneration, glaucoma, manic depression or cancer.  
     
     
         58 . The method of  claim 21 , wherein the suppression effector an endogenous gene.  
     
     
         59 . The method of  claim 42 , wherein the ribozyme suppresses an endogenous gene.