Gapped oligomeric compounds having linked bicyclic sugar moieties at the termini

Abstract

The present invention relates to bicyclic nucleosides and oligomeric compounds comprising at least one such nucleoside. These oligomeric compounds typically have enhanced binding affinity and nuclease resistance properties compared to unmodified oligomeric compounds. The oligomeric compounds are useful, for example, for investigative and therapeutic purposes.

1 . An oligomeric compound comprising the structure:  
         T 1 -(Nu 1 -L 1 ) n1 -(Nu 2 -L 2 ) n2 -(Nu 3 -L 3 ) n3 -T 2    
       wherein: 
 each Nu 1  and Nu 3  is, independently, a high affinity modified nucleoside, wherein at least one of Nu 1  and Nu 3  is a bicyclic sugar modified nucleoside comprising a 4′-CH 2 —O-2′ bridge or a 4′-(CH 2 ) 2 —O-2′ bridge;  
 each Nu 2  is a 2′-deoxy nucleoside;  
 each L 1 , L 2  and L 3  is, independently, an internucleoside linking group;  
 each T 1  and T 2  is, independently, H, a hydroxy protecting group, an optionally linked conjugate group, or a covalent attachment to a solid support medium;  
 n1 is from 1 to about 6;  
 n2 is from 11 to about 18; and  
 n3 is from 2 to about 6.  
 
     
     
         2 . The oligomeric compound of  claim 1  wherein each of the high affinity modified nucleosides is, independently, a bicyclic sugar modified nucleoside, a 2′-O—(CH 2 ) 2 —O—CH 3  modified nucleoside, a 2′-F modified nucleoside, or a 2′-O—CH 2 —C(═O)—NR 1 R 2  modified nucleoside, where each R 1  and R 2  is, independently, H, a nitrogen protecting group, substituted or unsubstituted C 1 -C 10  alkyl, substituted or unsubstituted C 2 -C 10  alkenyl, substituted or unsubstituted C 2 -C 10  alkynyl, wherein the substitution is OR 3 , SR 3 , NH 3   + , NR 3 R 4 , guanidino or acyl, wherein the acyl is acid amide or an ester, or R 1  and R 2 , together, are a nitrogen protecting group, or are joined in a ring structure that optionally includes an additional heteroatom selected from N and O.  
     
     
         3 . The oligomeric compound of  claim 2  wherein each of the bicyclic sugar modified nucleosides independently has a 4′-CH 2 —O-2′ bridge or a 4′-(CH 2 ) 2 —O-2′ bridge.  
     
     
         4 . The oligomeric compound of  claim 2  wherein each R 1  and R 2  each is, independently, H, a nitrogen protecting group, or C 1 -C 10  alkyl.  
     
     
         5 . The oligomeric compound of  claim 1  wherein T 1  is H or a hydroxyl protecting group.  
     
     
         6 . The oligomeric compound of  claim 1  wherein T 2  is H or a hydroxyl protecting group.  
     
     
         7 . The oligomeric compound of  claim 1  wherein each of the hydroxyl protecting groups is, independently, 4,4′-dimethoxytrityl, monomethoxytrityl, 9-phenylxanthen-9-yl, 9-(p-methoxyphenyl)xanthen-9-yl, t-butyl, t-butoxymethyl, methoxymethyl, tetrahydropyranyl, 1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 2-trimethylsilylethyl, p-chlorophenyl, 2,4-dinitrophenyl, benzyl, 2,6-dichlorobenzyl, diphenylmethyl, p,p-dinitrobenzhydryl, p-nitrobenzyl, triphenylmethyl, trimethylsilyl, triethylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triphenylsilyl, benzoylformate, acetyl, chloroacetyl, trichloroacetyl, trifluoroacetyl, pivaloyl, benzoyl, p-phenylbenzoyl, mesyl, tosyl, 4,4′,4″-tris-(benzyloxy)trityl, 4,4′,4″-tris-(4,5-dichlorophthalimido)trityl, 4,4′,4″-tris(levulinyloxy)trityl, 3-(imidazolylmethyl)-4,4′-dimethoxytrityl, 4-decyloxytrityl, 4-hexadecyloxytrityl, 9-(4-octadecyloxyphenyl)xanthene-9-yl, 1,1-bis-(4-methoxyphenyl)-1′-pyrenyl methyl, p-phenylazophenyloxycarbonyl, 9-fluorenylmethoxycarbonyl, 2,4-dinitrophenylethoxycarb onyl, 4-(methylthiomethoxy)butyryl, 2-(methylthiomethoxymethyl)-benzoyl, 2-(isopropyl-thiomethoxymethyl)benzoyl, 2-(2,4-dinitrobenzenesulphenyloxymethyl)benzoyl, or levulinyl group.  
     
     
         8 . The oligomeric compound of  claim 1  wherein one of T 1  and T 2  is a covalent attachment to a support medium.  
     
     
         9 . The oligomeric compound of  claim 8  wherein the support medium is a controlled pore glass, oxalyl-controlled pore glass, silica-containing particles, polymers of polystyrene, copolymers of polystyrene, copolymers of styrene and divinylbenzene, copolymers of dimethylacrylamide and N,N′-bisacryloylethylenediamine, soluble support medium, or PEPS.  
     
     
         10 . The oligomeric compound of  claim 1  wherein each L 1 , L 2  and L 3  is, independently, phosphodiester, phosphorothioate, chiral phosphorothioate, phosphorodithioate, phosphotriester, aminoalkylphosphotriester, methyl phosphonate, alkyl phosphonate, 5′-alkylene phosphonate, chiral phosphonate, phosphinate, phosphoramidate, 3′-amino phosphoramidate, aminoalkylphosphoramidate, thionophosphoramidate, thionoalkylphosphonate, thionoalkylphosphotriester, selenophosphate, or boranophosphate.  
     
     
         11 . The oligomeric compound of  claim 10  wherein each L 1 , L 2  and L 3  is, independently, a phosphodiester or a phosphorothioate internucleoside linking group.  
     
     
         12 . The oligomeric compound of  claim 10  wherein each L 1 , L 2  and L 3  is a phosphodiester internucleoside linking group.  
     
     
         13 . The oligomeric compound of  claim 1  wherein each L 1 , L 2  and L 3  is, independently, siloxane, sulfide, sulfoxide, sulfone, formacetyl, thioformacetyl, methylene formacetyl, thioformacetyl, sulfamate, methyleneimino, methylenehydrazino, sulfonate, sulfonamide, or amide.  
     
     
         14 . The oligomeric compound of  claim 13  wherein each of the internucleoside linking groups is, independently, —CH 2 —NH-O—CH 2 —, —CH 2 —N(CH 3 )—O—CH 2 — or —CH 2 —O—N(CH 3 )—CH 2 —, —CH 2 —N(CH 3 )—N(CH 3 )—CH 2 —, or —O—N(CH 3 )—CH 2 —CH 2 —.  
     
     
         15 . The oligomeric compound of  claim 1  wherein each nucleoside comprises a heterocyclic base moiety that is, independently, adenine, guanine, thymine, cytosine, uracil, 5-methylcytosine, 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine, 2-thiocytosine, 5-halouracil, 5-halocytosine, 5-propynyl uracil, 5-propynyl cytosine, 6-azo uracil, 6-azo cytosine, 6-azo thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-substituted adenines and guanines, 5-substituted uracils and cytosines, 7-methylguanine, 7-methyladenine, 8-azaguanine, 8-azaadenine, 7-deazaguanine, 7-deazaadenine, 3-deazaguanine, or 3-deazaadenine.  
     
     
         16 . The oligomeric compound of  claim 1  wherein n1 is from 1 to about 5.  
     
     
         17 . The oligomeric compound of  claim 1  wherein n1 is from 1 to about 3.  
     
     
         18 . The oligomeric compound of  claim 1  wherein n1 is from 2 to about 3.  
     
     
         19 . The oligomeric compound of  claim 1  wherein n3 is from 2 to about 5.  
     
     
         20 . The oligomeric compound of  claim 1  wherein n3 is from 2 to about 3.  
     
     
         21 . The oligomeric compound of  claim 1  wherein n2 is from 12 to about 18.  
     
     
         22 . The oligomeric compound of  claim 1  wherein n2 is from 12 to about 16.  
     
     
         23 . The oligomeric compound of  claim 1  wherein n2 is from 14 to about 16.  
     
     
         24 . The oligomeric compound of  claim 1  wherein the total of n1, n2 and n3 is from 14 to about 30.  
     
     
         25 . The oligomeric compound of  claim 1  wherein the total of n1, n2 and n3 is from 14 to 24.  
     
     
         26 . The oligomeric compound of  claim 1  wherein the total of n1, n2 and n3 is from 14 to 21.  
     
     
         27 . The oligomeric compound of  claim 1  wherein the total of n1, n2 and n3 is from 16 to 21.  
     
     
         28 . The oligomeric compound of  claim 1  wherein n1 is from 1 to about 3, n2 is 12 or 13 and n3 is 2 or 3.  
     
     
         29 . The oligomeric compound of  claim 1  wherein n1 is 3, n2 is 12 and n3 is 3.  
     
     
         30 . The oligomeric compound of  claim 1  wherein n1 is from 1 to about 3, n2 is 14 or 15 and n3 is 2 or 3.  
     
     
         31 . The oligomeric compound of  claim 1  wherein n1 is 2, n2 is 14 and n3 is 2.  
     
     
         32 . The oligomeric compound of  claim 1  wherein n1 is from 1 to about 3, n2 is 16 or 17 and n3 is 2 or 3.  
     
     
         33 . The oligomeric compound of  claim 1  wherein n1 is 2, n2 is 16 and n3 is 2.  
     
     
         34 . The oligomeric compound of  claim 1  wherein at least one Nu 1  nucleoside and at least one Nu 3  nucleside is an LNA or ENA.  
     
     
         35 . The oligomeric compound of  claim 1  wherein at least one of the 5′-most or 3′-most terminal affinity modified nucleosides is an LNA or ENA.  
     
     
         36 . A method of inhibiting gene expression comprising contacting one or more cells, a tissue, or an animal with an oligomeric compound of  claim 1 .  
     
     
         37 . An oligomeric compound comprsing the structure:  
       
         
           
           
               
               
           
         
       
       wherein: 
 each Bx is a heterocyclic base moiety;  
 each X is, independently, O or S;  
 T 1  and T 2  are each, independently, H, a hydroxy protecting group, an optionally linked conjugate group, or a covalent attachment to a solid support medium;  
 each m is, independently, 1 or 2;  
 na is from 1 to about 6;  
 nb is from 11 to about 18; and  
 nc is from 2 to about 6.  
 
     
     
         38 . The oligomeric compound of  claim 37  wherein each m is 1.  
     
     
         39 . The oligomeric compound of  claim 37  wherein each m is 2.  
     
     
         40 . The oligomeric compound of  claim 37  wherein at least one of T 1  and T 2  is H or a hydroxyl protecting group.  
     
     
         41 . The oligomeric compound of  claim 40  wherein each of the hydroxyl protecting groups is, independently, 4,4′-dimethoxytrityl, monomethoxytrityl, 9-phenylxanthen-9-yl, 9-(p-methoxyphenyl)xanthen-9-yl, t-butyl, t-butoxymethyl, methoxymethyl, tetrahydropyranyl, 1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 2-trimethylsilylethyl, p-chlorophenyl, 2,4-dinitrophenyl, benzyl, 2,6-dichlorobenzyl, diphenylmethyl, p,p-dinitrobenzhydryl, p-nitrobenzyl, triphenylmethyl, trimethylsilyl, triethylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triphenylsilyl, benzoylformate, acetyl, chloroacetyl, trichloroacetyl, trifluoroacetyl, pivaloyl, benzoyl, p-phenylbenzoyl, mesyl, tosyl, 4,4′,4″-tris-(benzyloxy)trityl, 4,4′,4″-tris-(4,5-dichlorophthalimido)trityl, 4,4′,4″-tris(levulinyloxy)trityl, 3-(imidazolylmethyl)-4,4′-dimethoxytrityl, 4-decyloxytrityl, 4-hexadecyloxytrityl, 9-(4-octadecyloxyphenyl)xanthene-9-yl, 1,1-bis-(4-methoxyphenyl)-1′-pyrenyl methyl, p-phenylazophenyloxycarbonyl, 9-fluorenylmethoxycarbonyl, 2,4-dinitrophenylethoxycarb onyl, 4-(methylthiomethoxy)butyryl, 2-(methylthiomethoxymethyl)-benzoyl, 2-(isopropyl-thiomethoxymethyl)benzoyl, 2-(2,4-dinitrobenzenesulphenyloxymethyl)benzoyl, or levulinyl group.  
     
     
         42 . The oligomeric compound of  claim 37  wherein one of T 1  and T 2  is a covalent attachment to a support medium.  
     
     
         43 . The oligomeric compound of  claim 42  wherein the support medium is a controlled pore glass, oxalyl-controlled pore glass, silica-containing particles, polymers of polystyrene, copolymers of polystyrene, copolymers of styrene and divinylbenzene, copolymers of dimethylacrylamide and N,N′-bisacryloylethylenediamine, soluble support medium, or PEPS.  
     
     
         44 . The oligomeric compound of  claim 37  wherein each L 1 , L 2  and L 3  is, independently, a phosphodiester or a phosphorothioate internucleoside linking group.  
     
     
         45 . The oligomeric compound of  claim 44  wherein each L 1 , L 2  and L 3  is a phosphodiester internucleoside linking group.  
     
     
         46 . The oligomeric compound of  claim 37  wherein each Bx is, independently, adenine, guanine, thymine, cytosine, uracil, 5-methylcytosine, 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine, 2-thiocytosine, 5-halouracil, 5-halocytosine, 5-propynyl uracil, 5-propynyl cytosine, 6-azo uracil, 6-azo cytosine, 6-azo thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-substituted adenines and guanines, 5-substituted uracils and cytosines, 7-methylguanine, 7-methyladenine, 8-azaguanine, 8-azaadenine, 7-deazaguanine, 7-deazaadenine, 3-deazaguanine, or 3-deazaadenine.  
     
     
         47 . The oligomeric compound of  claim 37  wherein na is from 1 to about 5.  
     
     
         48 . The oligomeric compound of  claim 37  wherein na is from 1 to about 3.  
     
     
         49 . The oligomeric compound of  claim 37  wherein na is from 2 to about 3.  
     
     
         50 . The oligomeric compound of  claim 37  wherein nc is from 2 to about 5.  
     
     
         51 . The oligomeric compound of  claim 37  wherein nc is from 2 to about 3.  
     
     
         52 . The oligomeric compound of  claim 37  wherein nb is from 12 to about 18.  
     
     
         53 . The oligomeric compound of  claim 37  wherein nb is from 12 to about 16.  
     
     
         54 . The oligomeric compound of  claim 37  wherein nb is from 14 to about 16.  
     
     
         55 . The oligomeric compound of  claim 37  wherein the total of na, nb and nc is from 14 to about 30.  
     
     
         56 . The oligomeric compound of  claim 37  wherein the total of na, nb and nc is from 14 to 24.  
     
     
         57 . The oligomeric compound of  claim 37  wherein the total of na, nb and nc is from 14 to 21.  
     
     
         58 . The oligomeric compound of  claim 37  wherein the total of na, nb and nc is from 16 to 21.  
     
     
         59 . The oligomeric compound of  claim 37  wherein na is from 1 to about 3, nb is 12 or 13 and nc is 2 or 3.  
     
     
         60 . The oligomeric compound of  claim 37  wherein na is 3, nb is 12 and nc is 3.  
     
     
         61 . The oligomeric compound of  claim 37  wherein na is from 1 to about 3, nb is 14 or 15 and nc is 2 or 3.  
     
     
         62 . The oligomeric compound of  claim 37  wherein na is 2, nb is 14 and nc is 2.  
     
     
         63 . The oligomeric compound of  claim 37  wherein na is from 1 to about 3, nb is 16 or 17 and nc is 2 or 3.  
     
     
         64 . The oligomeric compound of  claim 37  wherein na is 2, nb is 16 and nc is 2.  
     
     
         65 . A method of inhibiting gene expression comprising contacting one or more cells, a tissue, or an animal with an oligomeric compound of  claim 37.