Single-stranded oligonucleotide

Abstract

The invention provides a single-stranded oligonucleotide represented by the formula [Xz — Lx]m — X — Y — [Ly — Yz]n, wherein X is represented by Xa-Xb, Xa is coupled with Y, and Xb and Y hybridize. Xa is composed of 1 to 40 nucleotides and contains at least one modified-nucleotide. Xb is composed of 4 to 40 nucleotides and contains at least one modified-nucleotide. Y is composed of 4 to 40 nucleotides and contains at least one ribonucleotide. Xz and Yz are composed of 5 to 40 nucleotides and contain at least one modified-nucleotide. Nucleotide sequences X, Xz and Yz have an antisense sequence capable of hybridizing with a target RNA. Lx and Ly are composed of 0 to 20 nucleotides.

1 . A method for controlling a function of a target RNA, which method comprises a step for contacting a single-stranded oligonucleotide with a cell,
 wherein the single-stranded oligonucleotide is represented by the following formula (I):                   Xz   −   Lx         m     −   X   −   Y   −           Ly   −   Yz         n              wherein
 Y represents a group derived from an oligonucleotide Y composed of 4 to 40 nucleotides containing at least one ribonucleotide that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, 
 X represents a group derived from an oligonucleotide X composed of 5 to 80 nucleotides represented by the formula: 
         Xb   −   Xa         
  wherein
 Xb represents a group derived from an oligonucleotide Xb composed of 4 to 40 nucleotides containing at least one sugar-modified nucleotides that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, and 
 Xa represents a group derived from an oligonucleotide Xa composed of 1 to 40 nucleotides containing at least one sugar-modified nucleotides that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, and Xa is bonded with the oligonucleotide Y and the oligonucleotide Xb at both ends respectively, 
 Xz represents a group derived from an oligonucleotide Xz composed of 5 to 40 nucleotides containing at least one sugar-modified nucleotides that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, 
 Yz represents a group derived from an oligonucleotide Yz composed of 5 to 40 nucleotides containing at least one sugar-modified nucleotides that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, 
 Lx represents a group derived from an oligonucleotide Lx composed of 0 to 20 nucleotides that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, and is bonded with the Xb, 
 Ly represents a group derived from an oligonucleotide Ly composed of 0 to 20 nucleotides that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, 
 m represents 0 or 1, 
 when m represents 0, n represents 0 or 1, 
 when m represents 1, n represents 0, 
 the oligonucleotide X has a nucleotide sequence X, the oligonucleotide Xa has a nucleotide sequence Xa, the oligonucleotide Xb has a nucleotide sequence Xb, the oligonucleotide Y has a nucleotide sequence Y, the oligonucleotide Xz has a nucleotide sequence Xz, the oligonucleotide Yz has a nucleotide sequence Yz, the oligonucleotide Lx has a nucleotide sequence Lx, and the oligonucleotide Ly has a nucleotide sequence Ly, 
 the nucleotide sequence Xb is complementary to the nucleotide sequence Y, 
 the nucleotide sequence X contains an antisense sequence that is capable of hybridizing with a target RNA, 
 when m represents 1 and n represents 0, the nucleotide sequence Xz contains an antisense sequence that is capable of hybridizing with a target RNA, 
 when m represents 0 and n represents 1, the nucleotide sequence Yz contains an antisense sequence that is capable of hybridizing with a target RNA, 
 in the case of having two or more of the antisense sequences, the target RNA hybridized by each antisense sequence portion may each be the same or different, 
 Xb and Y hybridize, 
 the target RNA hybridizes with X, and 
 a portion of the target RNA hybridizes with an antisense sequence portion of the single-stranded oligonucleotide as a result of the contacting. 
 
   
     
     
         2 . The method according to  claim 1 , wherein Xb bonds to Xa on the 3′-side and Y bonds to Xa on the 5′-side. 
     
     
         3 . The method according to  claim 1 , wherein Xb bonds to Xa on the 5′-side and Y bonds to Xa on the 3′-side. 
     
     
         4 . The method according to  claim 1 , wherein the antisense sequence is a sequence each independently containing at least four contiguous nucleotides recognized by RNase H, or a sequence containing at least one sugar-modified nucleotide, and not containing four contiguous deoxyribonucleotides. 
     
     
         5 . The method according to  claim 4 , wherein at least one of the antisense sequence is a sequence containing at least four contiguous nucleotides recognized by RNase H, and the antisense sequence portion contains a sugar-modified nucleotide bound adjacent to the 5′-side and the 3′-side of the sequence portion containing the above-mentioned at least four contiguous nucleotides recognized by RNase H. 
     
     
         6 . The method according to  claim 1 , wherein the antisense sequence portion contains a phosphorothioate bond. 
     
     
         7 . The method according to  claim 1 , wherein the antisense sequence is a sequence composed of 10 to 30 nucleotides containing at least one deoxyribonucleotide. 
     
     
         8 . The method according to  claim 1 , wherein the nucleotide sequence Y is a sequence containing at least four contiguous nucleotides cleaved by RNase H. 
     
     
         9 . The method according to  claim 1 , wherein the oligonucleotide Y contains one or a plurality of sugar-modified nucleotides on at least one of the 5′-side and the 3′-side of the oligonucleotide Y. 
     
     
         10 . The method according to  claim 1 , wherein m is 0 and n is 0. 
     
     
         11 . The method according to  claim 1 , wherein m is 0 and n is 1. 
     
     
         12 . The method according to  claim 11 , wherein the nucleotides contained in the oligonucleotide Ly are mutually coupled through a phosphodiester bond. 
     
     
         13 . The method according to  claim 11 , wherein the oligonucleotide Ly is DNA or RNA. 
     
     
         14 . The method according to  claim 1 , wherein m is 1 and n is 0. 
     
     
         15 . The method according to  claim 14 , wherein the nucleotides contained in the oligonucleotide Lx are mutually coupled through a phosphodiester bond. 
     
     
         16 . The method according to  claim 14 , wherein the oligonucleotide Lx is DNA or RNA. 
     
     
         17 . The method according to  claim 1 , wherein the single-stranded oligonucleotide further contains a group derived from a functional molecule having at least one function selected from the group consisting of a labeling function, a purifying function and a target site delivery function. 
     
     
         18 . The method according to  claim 17 , wherein the functional molecule is selected from the group consisting of sugars, lipids, peptides, proteins and derivatives thereof. 
     
     
         19 . The method according to  claim 17 , wherein the functional molecule is a lipid selected from the group consisting of cholesterol, tocopherol and tocotrienol. 
     
     
         20 . The method according to  claim 17 , wherein the functional molecule is a sugar derivative that interacts with an asialoglycoprotein receptor. 
     
     
         21 . The method according to  claim 17 , wherein the functional molecule is a peptide or protein selected from the group consisting of receptor ligands and antibodies. 
     
     
         22 . The method according to  claim 1 , wherein the sugar-modified nucleotide is at least one selected from the group consisting of hexitol nucleotides, cyclohexene nucleotides, peptide nucleic acids, glycol nucleic acids, threose nucleotides, morpholine nucleic acids, tricyclo-DNA, 2′—O—methyl nucleotides, 2′—O—methoxyethyl nucleotides, 2′—O—aminopropyl nucleotide, 2′-fluoronucleotide, 2′—F—arabinonucleotides, bridged nucleotides, and 2′—O—methylcarbamoylethyl nucleotides. 
     
     
         23 . A method for controlling expression of a target gene corresponding to a target RNA, which method comprises a step for contacting the single-stranded oligonucleotide with a cell,
 wherein the single-stranded oligonucleotide is represented by the following formula (I):                   Xz   −   Lx         m     −   X   −   Y   −           Ly   −   Yz         n              wherein
 Y represents a group derived from an oligonucleotide Y composed of 4 to 40 nucleotides containing at least one ribonucleotide that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, 
 X represents a group derived from an oligonucleotide X composed of 5 to 80 nucleotides represented by the formula: 
         Xb   −   Xa         
  wherein
 Xb represents a group derived from an oligonucleotide Xb composed of 4 to 40 nucleotides containing at least one sugar-modified nucleotides that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, and 
 Xa represents a group derived from an oligonucleotide Xa composed of 1 to 40 nucleotides containing at least one sugar-modified nucleotides that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, and Xa is bonded with the oligonucleotide Y and the oligonucleotide Xb at both ends respectively, 
 Xz represents a group derived from an oligonucleotide Xz composed of 5 to 40 nucleotides containing at least one sugar-modified nucleotides that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, 
 Yz represents a group derived from an oligonucleotide Yz composed of 5 to 40 nucleotides containing at least one sugar-modified nucleotides that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, 
 Lx represents a group derived from an oligonucleotide Lx composed of 0 to 20 nucleotides that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, and is bonded with the Xb, 
 Ly represents a group derived from an oligonucleotide Ly composed of 0 to 20 nucleotides that are independently selected from the group consisting of deoxyribonucleotides, ribonucleotides and sugar-modified nucleotides, 
 m represents 0 or 1, 
 when m represents 0, n represents 0 or 1, 
 when m represents 1, n represents 0, 
 the oligonucleotide X has a nucleotide sequence X, the oligonucleotide Xa has a nucleotide sequence Xa, the oligonucleotide Xb has a nucleotide sequence Xb, the oligonucleotide Y has a nucleotide sequence Y, the oligonucleotide Xz has a nucleotide sequence Xz, the oligonucleotide Yz has a nucleotide sequence Yz, the oligonucleotide Lx has a nucleotide sequence Lx, and the oligonucleotide Ly has a nucleotide sequence Ly, 
 the nucleotide sequence Xb is complementary to the nucleotide sequence Y, 
 the nucleotide sequence X contains an antisense sequence that is capable of hybridizing with a target RNA, 
 when m represents 1 and n represents 0, the nucleotide sequence Xz contains an antisense sequence that is capable of hybridizing with a target RNA, 
 when m represents 0 and n represents 1, the nucleotide sequence Yz contains an antisense sequence that is capable of hybridizing with a target RNA, 
 in the case of having two or more of the antisense sequences, the target RNA hybridized by each antisense sequence portion may each be the same or different, 
 Xb and Y hybridize, 
 the target RNA hybridizes with X, and 
 a portion of the target RNA hybridizes with an antisense sequence portion of the single-stranded oligonucleotide as a result of the contacting.