Oligonucleotides comprising alternating segments and uses thereof

Abstract

The invention relates to oligonucleotides having alternating segments of sugar-modified nucleosides and 2′-deoxynucleosides, and uses thereof. The invention further related to oligonucleotides having alternating segments of sugar-modified nucleotides and 2′-deoxynucleotides, and uses thereof. Such uses include the preparation of antisense oligonucleotides and their use for the prevention or depletion of function of a target nucleic acid of interest, such as an RNA, in a system. Accordingly, and oligonucleotide of the invention is useful for therapeutic, analytical and diagnostic methods and uses, as well as component of compositions and commercial packages corresponding to such methods and uses.

We claim: 
     
         1 . An oligonucleoside comprising alternating first and second segments, wherein said first segment comprises at least one sugar-modified nucleoside, wherein said second segment comprises at least one 2′-deoxynucleoside, wherein said oligonucleoside comprises at least 2 of each of said first and second segments thereby comprising at least 4 alternating segments. 
     
     
         2 . The oligonucleoside of  claim 1 , wherein
 (a) said oligonucleoside further comprises an internucleoside linkage comprising a phosphate, thereby being an oligonucleotide,   (b) wherein said sugar-modified nucleoside comprises an attached phosphate thereby being a sugar-modified nucleotide,   (c) wherein said 2′-deoxynucleoside comprises an attached phosphate thereby being a 2′-deoxynucleotide, or   (d) any combination of (a) to (c).   
     
     
         3 . The oligonucleotide of  claim 2 , wherein said sugar modified oligonucleotide is capable of adopting a DNA-like conformation. 
     
     
         4 . The oligonucleotide of  claim 2 , wherein said sugar-modified nucleotide is selected from the group consisting of arabinonucleotides, alpha-L-locked nucleic acids, cyclohexene nucleic acids, and ribonucleotides lacking an electronegative 2′-oxygen atom. 
     
     
         5 . The oligonucleotide of  claim 3 , wherein the ribonucleotides lacking an electronegative 2′-oxygen atom are selected from the group consisting of 2′-alkyl-D-ribose and 2′-SCH 3 -D-ribose. 
     
     
         6 . The oligonucleotide of  claim 2 , wherein said segments each independently comprise about 1 to about 6 sugar-modified nucleotides or 2′-deoxynucleotides. 
     
     
         7 . The oligonucleotide of  claim 6 , wherein said segments each independently comprise about 2 to about 5 sugar-modified nucleotides or 2′-deoxynucleotides. 
     
     
         8 . The oligonucleotide of  claim 7 , wherein said segments each independently comprise about 3 to about 4 sugar-modified nucleotides or 2′-deoxynucleotides. 
     
     
         9 . The oligonucleotide of  claim 8 , wherein said segments each independently comprise about 3 sugar-modified nucleotides or 2′-deoxynucleotides. 
     
     
         10 . The oligonucleotide of  claim 2 , wherein said oligonucleotide has a structure selected from the group consisting of:
   a) (A x -D y ) n   I
     b) (D y -A x ) n   II
     c) (A x -D y ) m -A x -D y -A x   III
     d) (D y -A x ) m -D y -A x -D y   IV,
   
       wherein each of m, x and y are each independently an integer greater than or equal to 1, n is an integer greater than or equal to 2, A is a sugar-modified nucleotide and D is a 2′-deoxyribonucleotide. 
     
     
         11 . The oligonucleotide of  claim 2 , wherein said sugar-modified nucleotide comprises a 2′ substituent selected from the group consisting of fluorine, hydroxyl, amino, cyano, azido, —CH═CH 2 , —C≡CH, —alkyl, functionalized alkyl, alkoxy and functionalized alkoxy groups. 
     
     
         12 . The oligonucleotide of  claim 11 , wherein said alkyl group is a lower alkyl group. 
     
     
         13 . The oligonucleotide of  claim 12 , wherein said lower alkyl group is selected from the group consisting of methyl, ethyl and propyl groups. 
     
     
         14 . The oligonucleotide of  claim 11 , wherein said functionalized alkyl group is selected from the group consisting of methylamino, ethylamino and propylamino groups. 
     
     
         15 . The oligonucleotide of  claim 11 , wherein said alkoxy group is selected from the group consisting of methoxy, ethoxy and propoxy groups. 
     
     
         16 . The oligonucleotide of  claim 11 , wherein said functionalized alkoxy group is —O(CH 2 ) q —R, wherein q=2, 3 or 4 and —R is selected from the group consisting of —NH 2 , —OCH 3 , and —OCH 2 CH 3  groups. 
     
     
         17 . The oligonucleotide of  claim 3 , wherein the sugar-modified nucleotide is an arabinonucleotide. 
     
     
         18 . The oligonucleotide of  claim 17 , wherein the arabinonucleotide is a 2′-fluoroarabinonucleotide (2′F-ANA). 
     
     
         19 . A method of preventing or decreasing translation, reverse transcription and/or replication of a target RNA in a system, said method comprising contacting said target RNA with the oligonucleotide of  claim 2 , wherein said oligonucleotide is antisense to a target RNA. 
     
     
         20 . A method of inducing RNase H-mediated cleavage of a target RNA in a system, said method comprising contacting said target RNA with the oligonucleotide of  claim 2 , wherein said oligonucleotide is antisense to a target RNA.