Bicyclonucleoside and oligonucleotide analogues

Abstract

An oligo- or polynucleotide analogue having one or more structures of the general formula where B is a pyrimidine or purine nucleic acid base, or an analogue thereof, is disclosed. The use of this analogue provides an oligonucleotide analogue antisense molecule, which is minimally hydrolyzable with an enzyme in vivo, has a high sense strand binding ability, and is easily synthesized.

What is claimed is: 
     
       1. A nucleoside analogue of the following formula (I) 
       
         
           
           
               
               
           
         
         or an amidite derivative thereof; 
       
       where B is a pyrimidine or purine nucleic acid base, and X and Y are identical or different, and each represents a hydrogen atom, an alkyl group, an alkenyl group, an alkynyl group, a cycloalkyl group, an aralkyl group, an aryl group, an acyl group, or a silyl group, or an amidite derivative thereof. 
     
     
       2. A nucleoside analogue as claimed in  claim 1 , wherein X and Y each represents a hydrogen atom. 
     
     
       3. A mononucleoside amidite derivative as claimed in  claim 1 , wherein X is 4,4-dimethoxytrityl (DMTr), and Y is a 2-cyanoethoxy(diisopropylamino)phosphano group. 
     
     
       4. An oligonucleotide or polynucleotide analogue having one or more structures or the formula (Ia) 
       
         
           
           
               
               
           
         
       
       where B is a pyrimidine or purine nucleic acid base. 
     
     
       5. An oligonucleotide or polynucleotide analogue of the formula (II) 
       
         
           
           
               
               
           
         
         where B 1  and B are identical or different, and each Represents a pyrimidine or purine nucleic acid base, R is a hydrogen atom, a hydroxyl group, a halogen atom, or an alkoxy group, 
         W 1  and W 2  are identical or different, and each represents a hydrogen atom, an alkyl group, an alkenyl group, an alkynyl group, a cycloalkyl group, an aralkyl group, an aryl group, an acyl group, a silyl group, a phosphoric acid residue, a naturally occurring nucleoside or a synthetic nucleoside bound via a phosphodiester bond, or an oligonucleotide or polynucleotide containing the nucleoside, n 1  or n 2  are identical or different, and each denotes an integer of 0 to 50, provided that n 1  and n 2  are not both zero, and that not all of the n 2  are zero at the same time, n 3  denotes an integer of 1 to 50, provided that when n 1  and/or n 2  are or is 2 or more, B 1  and B need not be identical, and R need not be identical. 
       
     
     
       6. The nucleoside analogue according to  claim 1  wherein the amidite derivative is a phosphoramidite. 
     
     
       7. The nucleoside analogue according to  claim 4  wherein the amidite derivative is a phosphoramidite. 
     
     
       8. The nucleoside analogue according to  claim 5  wherein the amidite derivative is a phosphoramidite. 
     
     
       9. The nucleoside analogue according to claim 1, which is purified. 
     
     
       10. The nucleoside analogue according to claim 1, wherein the nucleic acid base is cytosine, thymine, adenine, guanine, or a derivative thereof. 
     
     
       11. The oligonucleotide or polynucleotide analogue of claim 4, wherein the one or more structures of formula (Ia) are present at two or more locations and separated from each other by one or more naturally occurring nucleotides. 
     
     
       12. The oligonucleotide or polynucleotide analogue of claim 4, which has a length of 2 to 50 nucleotide and nucleotide analogue units. 
     
     
       13. The oligonucleotide or polynucleotide analogue of claim 4, which has a length of 10 to 30 nucleotide and nucleotide analogue units. 
     
     
       14. The oligonucleotide or polynucleotide analogue of claim 4, wherein the melting temperature of said oligonucleotide or polynucleotide analogue bound to a complementary DNA strand is at least about 2° C. greater than the melting temperature of a corresponding oligonucleotide or polynucleotide containing naturally occurring nucleotides in a 100 mM NaCl, 10 mM phosphate buffer (pH 7.2) solution. 
     
     
       15. The oligonucleotide or polynucleotide analogue of claim 4, wherein the melting temperature of said oligonucleotide or polynucleotide analogue bound to a complementary RNA strand is at least about 4° C. greater than the melting temperature of a corresponding oligonucleotide or polynucleotide containing naturally occurring nucleotides in a 100 mM NaCl, 10 mM phosphate buffer (pH 7.2) solution. 
     
     
       16. The oligonucleotide or polynucleotide analogue of claim 4, wherein the nucleic acid base is cytosine, thymine, adenine, guanine, or a derivative thereof. 
     
     
       17. A pharmaceutical composition comprising the oligonucleotide or polynucleotide analogue of any of claims 4 or 5. 
     
     
       18. The pharmaceutical composition of claim 17, further comprising one or more buffers, stabilizers, pharmaceutical carriers, or combinations thereof. 
     
     
       19. The pharmaceutical composition of claim 17, in the form of a parenteral, liposomal, or topical preparation. 
     
     
       20. The pharmaceutical composition of claim 17, wherein the oligonucleotide or polynucleotide analogue has a length of 2 to 50 nucleotide and nucleotide analogue units. 
     
     
       21. The pharmaceutical composition of claim 17, wherein the oligonucleotide or polynucleotide analogue has a length of 10 to 30 nucleotide and nucleotide analogue units. 
     
     
       22. The pharmaceutical composition of claim 17, wherein the oligonucleotide or polynucleotide analogue inhibits transcription of messenger RNA. 
     
     
       23. The pharmaceutical composition of claim 17, wherein the oligonucleotide or polynucleotide analogue inhibits the biosynthesis of a potentially pathogenic protein. 
     
     
       24. The pharmaceutical composition of claim 17, wherein the oligonucleotide or polynucleotide analogue suppresses the proliferation of an infectious virus. 
     
     
       25. A product comprising DNA or RNA annealed to the oligonucleotide or polynucleotide analogue of claim 4 or claim 5. 
     
     
       26. The product of claim 25, wherein said product is formed in vivo. 
     
     
       27. The product of claim 25, which comprises DNA. 
     
     
       28. The product of claim 25, which comprises RNA. 
     
     
       29. A method of increasing the melting temperature of an annealing product between a natural DNA or RNA-based sense strand and an antisense strand, comprising (a) incorporating into the antisense strand one of more structures of the formula (Ia) of claim 4; and (b) contacting said oligonucleotide or polynucleotide analogue with said complementary DNA or RNA. 
     
     
       30. The method of claim 29, wherein the melting temperature of the oligonucleotide or polynucleotide analogue for the complementary DNA is increased at least about 2° C. compared to the melting temperature of a corresponding oligonucleotide or polynucleotide containing naturally occurring nucleotides in a 100 mM NaCl, 10 mM phosphate buffer (pH 7.2) solution. 
     
     
       31. The method of claim 29, wherein the melting temperature of the oligonucleotide or polynucleotide analogue for the complementary RNA is increased at least about 4° C. compared to the melting temperature of a corresponding oligonucleotide or polynucleotide containing naturally occurring nucleotides in a 100 mM NaCl, 10 mM phosphate buffer (pH 7.2) solution. 
     
     
       32. The nucleoside analog according to claim 1, wherein and X and Y are identical or different, and each represents a hydrogen atom, an alkyl group, an alkenyl group, an alkynyl group, a cycloalkyl group, an aryl group, an acyl group, or a silyl group.