Phosphoramidites for synthetic RNA in the reverse direction, efficient RNA synthesis and convenient introduction of 3'-end ligands, chromophores and modifications of synthetic RNA

A compound of Formula Ia or Ib:

• or a salt thereof, wherein:
• J is H or
• R1 is a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C3-C20)cycloalkyl group, or a substituted or unsubstituted (C3-C20)cycloalkyl(C1-C12)alkyl group, wherein the alkyl or cycloalkyl groups optionally include intervening heteroatoms independently selected from NH, NR7, O and S;
• R2 is a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C3-C20)cycloalkyl group, or a substituted or unsubstituted (C3-C20)cycloalkyl(C1-C12)alkyl group, wherein the alkyl or cycloalkyl groups optionally include intervening heteroatoms independently selected from NH, NR7, O and S;
• or R1 and R2 taken together with the nitrogen atom to which they are bound form a 4-7 membered non-aromatic heterocyclyl, wherein the heterocyclyl formed may optionally include intervening heteroatoms independently selected from NH, NR7, O and S;
• R3 is a phosphate protecting group;
• R4 is a -halo, —R5, —NR7R8, —OR9, —SR10, or 2′-blocking group;
• or when Structural Formula Ia or Ib is:
• wherein R4 is further selected from O—Si(R11)3 or O—CH2—Si(R11)3;
• or when Structural Formula Ia or Ib is:
• R4 is further selected from —OC(═O)R12;
• each R5 is independently a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C2-C12)alkenyl group, a substituted or unsubstituted (C2-C12)alkynyl group, or a substituted or unsubstituted phenyl, wherein the alkyl, alkenyl, alkynyl and the phenyl groups optionally includes intervening heteroatoms independently selected from NH, NR5, O and S;
• and may optionally terminate with —NR7R8, (C1-C4)alkylamino, di(C1-C4)alkylamino, —OR9, (C1-C6)alkoxy, benzyl or substituted benzyl, —SR10;
• or —S—(C1-C6)alkyl group;
• R6 is —H or —O—Z;
• each R7 is independently a fluorenylmethyloxycarbonyl;
• —C(═O)—(CH2)1-16NR8C(═O)CF3;
• —C(═O)—(CH2)1-16NR8C(═O)-phthalimide;
• —C(═O)—(CH2)1-16-phthalimide;
• NR8C(═O)-phthalimide;
• a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C2-C12)alkenyl group, or a substituted or unsubstituted (C2-C12)alkynyl group;
• each R8 is H or a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C2-C12)alkenyl group, or a substituted or unsubstituted (C2-C12)alkynyl group;
• each R9 is independently —C(═O)—(CH2)1-16CH3;
• a substituted or unsubstituted (C2-C12)alkenyl group, or a substituted or unsubstituted (C2-C12)alkynyl group;
• each R10 is independently —S(C1-C6)alkyl, —C(═O)—(CH2)1-16CH3;
• a substituted or unsubstituted (C2-C12)alkenyl group, or a substituted or unsubstituted (C2-C12)alkynyl group;
• each R11 is independently a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C2-C12)alkenyl group, or a substituted or unsubstituted (C2-C12)alkynyl group;
• provided that if R4 is —O—Si(R11)3, and two R11 groups are both methyl, the other is not t-butyl or if R4 is —O—CH2—Si(R11)3, then the three R11 groups cannot all be isopropyl;
• each R12 is independently a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C2-C12)alkenyl group, or a substituted or unsubstituted (C2-C12)alkynyl group, or a substituted or unsubstituted aryl group;
• Z is an unsubstituted or substituted aryl group, an unsubstituted or substituted triarylmethyl group, an unsubstituted or substituted trityl group, an unsubstituted or substituted tetrahydropyranyl group, or an unsubstituted or substituted 9-phenylxanthyl;
• Bn is hydrogen or an optionally substituted nucleobase optionally functionalized at each exocyclic amine with an amine protecting group,
• provided that the compound is not represented by one of the following structural formulas:
• wherein X is tert-butyldimethylsilyl or triisopropylsiloloxymethyl.

A method of preparing an oligonucleotide by bond formations in the 5′- to 3′-direction for the synthesis of RNA oligomers and enantiomers thereof, said method comprises the following steps

• a) cleavage of Z from a compound represented by the following structural formula:
• thereby forming a compound represented by structural formula (XX):
• b) reacting the compound represented by structural formula XX with a compound of structural formula XXI:
• thereby forming 2-mer compound represented by the following structural formula:
• c) reacting the 2-mer compound with a capping agent;
• d) oxidizing or sulfurizing the trivalent phosphorous group of the 2-mer compound to form a compound of structural formula XXII:
• e) cleavage of Z from the compound represented by structural formula XXII, thereby forming a compound of structural formula XXIII:
• f) reacting the compound represented by structural formula XXIII with a compound represented by the following structural formula:
• thereby forming a 3-mer represented by the following structural formula XXIV:
• g) cleavage of Z from the compound represented by structural formula XXIV;
• h) repeating steps a) through g) n times, thereby forming a oligonucleotide represented by the following structural formula:
• or a salt thereof, wherein:
• Q is a support comprised of:
• a) a linking group and a spacer that can be cleaved to form a hydroxy group;
• or b) an aliphatic chain, aromatic group, substituted or unsubstituted aromatic, a substituted or unsubstituted phenoxy, or levulinyl;
• each R1 is independently a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C3-C20)cycloalkyl group, or a substituted or unsubstituted (C3-C20)cycloalkyl(C1-C12)alkyl group, wherein the alkyl or cycloalkyl groups optionally include intervening heteroatoms independently selected from NH, NR7, O and S;
• each R2 is independently a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C3-C20)cycloalkyl group, or a substituted or unsubstituted (C3-C20)cycloalkyl(C1-C12)alkyl group, wherein the alkyl or cycloalkyl groups optionally include intervening heteroatoms independently selected from NH, NR7, O and S;
• or each occurrence of R1 and R2 taken together with the nitrogen atom to which they are bound independently forms a 4-7 membered non-aromatic heterocyclyl, wherein the heterocyclyl formed may optionally include intervening heteroatoms independently selected from NH, NR7, O and S;
• each R3 is independently a phosphate protecting group;
• each R4 is independently a -halo, —R5, —NR7R8, —OR9, —SR10, or 2′-blocking group;
• or when a 1-mer is in the β-D-ribose, β-L-ribose, α-D-ribose or α-L-ribose configuration, wherein R4 is further selected from O—Si(R11)3 or O—CH2—Si(R11)3;
• or when a 1-mer is in the β-D-arabinose, β-L-arabinose, α-D-arabinose or α-L-arabinose configuration,
• R4 is further selected from —OC(═O)R12;
• each R5 is independently a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C2-C12)alkenyl group, a substituted or unsubstituted (C2-C12)alkynyl group, or a substituted or unsubstituted phenyl, wherein the alkyl, alkenyl, alkynyl and the phenyl groups optionally includes intervening heteroatoms independently selected from NH, NRS, O and S;
• and may optionally terminate with —NR7R8, (C1-C4)alkylamino, di(C1-C4)alkylamino, —OR9, (C1-C6)alkoxy, benzyl or substituted benzyl, —SR10;
• or —S—(C1-C6)alkyl group;
• each R7 is independently a fluorenylmethyloxycarbonyl;
• —C(═O)—(CH2)1-16NR8C(═O)CF3;
• —C(═O)—(CH2)1-16NR8C(═O)-phthalimide;
• —C(═O)—(CH2)1-16-phthalimide;
• NR8C(═O)-phthalimide;
• a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C2-C12)alkenyl group, or a substituted or unsubstituted (C2-C12)alkynyl group;
• each R8 is independently H or a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C2-C12)alkenyl group, or a substituted or unsubstituted (C2-C12)alkynyl group;
• each R9 is independently —C(═O)—(CH2)1-16CH3;
• a substituted or unsubstituted (C2-C12)alkenyl group, or a substituted or unsubstituted (C2-C12)alkynyl group;
• each R10 is independently —S(C1-C6)alkyl, —C(═O)—(CH2)1-16CH3;
• a substituted or unsubstituted (C2-C12)alkenyl group, or a substituted or unsubstituted (C2-C12)alkynyl group;
• each R11 is independently a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C2-C12)alkenyl group, or a substituted or unsubstituted (C2-C12)alkynyl group;
• each R12 is independently a substituted or unsubstituted (C1-C12)alkyl group, a substituted or unsubstituted (C2-C12)alkenyl group, or a substituted or unsubstituted (C2-C12)alkynyl group, or a substituted or unsubstituted aryl group;
• each Z is independently an unsubstituted or substituted aryl group, an unsubstituted or substituted triarylmethyl group, an unsubstituted or substituted trityl group, an unsubstituted or substituted tetrahydropyranyl group, or an unsubstituted or substituted 9-phenylxanthyl;
• each Bn is independently hydrogen or an optionally substituted nucleobase optionally functionalized at each exocyclic amine with an amine protecting group, wherein the nucleobase is independently selected from:
• N6,N6-dimethyl adenine, N1 methyladenine, 7-deazaadenine, 7-deaza-8-azaadenine, 3-deazaadenine, ethenoadenine, isoguanine, N1-methylguanine, 7-iodo-7-deazaguanine, 7-deaza-7-iodoadenine, 7-deaza-7-iodo-6-oxopurine, 5-iodo-5-methyl-7-deazaguanine, 7-deazaguanine substituted with —C≡C(CH2)1-8-pthlamide, 7-deaza-8-azaguanine, 8-methylguanine, 8-bromoguanine, 8-aminoguanine, hypoxanthine, 6-methoxypurine, 7-deaza-6-oxopurine, 6-oxopurine, 2-aminopurine, 2,6-diaminopurine, 8-bromopurine, 8-aminopurine, 8-alkylaminopurine, 8-alkylaminopurine, thymine, N-3 methyl thymine, 5-acetoxymethylcytosine, 5-azacytosine, isocytosine, N-4(C1-C6)alkylcytosine, N-3(C1-C6)alkylcytidine, 5-propynylcytosine, 5-iodo-cytosine, 5-(C1-C6)alkylcytosine, 5-aryl(C1-C6)alkylcytosine, 5-trifluoromethylcytosine, 5-methylcytosine, ethenocytosine, cytosine and uracil substituted with —CH═CH—C(═O)NH(C1-C6)alkyl, cytosine and uracil substituted with —C≡C—CH2-phthalimide, NH(C1-C6)alkyl, 4-thiouracil, 2-thiouracil, N3-thiobenzoylethyluracil, 5-propynyluracil, 5-acetoxymethyluracil, 5-fluorouracil, 5-chlorouracil, 5-bromouracil, 5-iodouracil, N-3-(C1-C6)alkyluracil, 5-(3-aminoallyl)-uracil, 5-(C1-C6)alkyluracil, 5-aryl(C1-C6)alkyluracil, 5-trifluoromethyluracil, 4-triazolyl-5-methyluracil, 2-pyridone, 2-oxo-5-methylpyrimidine, 2-oxo-4-methylthio-5-methylpyrimidine, 2-thiocarbonyl-4-oxo-5-methylpyrimidine, and 4-oxo-5-methylpyrimidine;
• wherein any substitutable nitrogen atom within the nucleobase or on the exocyclic amine is optionally and independently substituted with fluorenylmethyloxycarbonyl;
• —C(═O)OPh;
• —C(═O)(C1-C16)alkyl;
• —C(═O)CH2CH2CH═CH2I;
• —C(═O)(C1-C16)alkylene-C(═O)OH;
• —C(═O)(C1-C16)alkylene-C(═O)O(C1-C6)alkyl;
• ═CR8N(C1-C6)alkyl)2;
• —C(═O)—NR8—(CH2)1-16NR8C(═O)CF3;
• —C(═O)—(CH2)1-16NR8C(═O)CF3;
• —C(═O)—NR8(CH2)1-16NR8C(═O)-phthalimide;
• —C(═O)—(CH2)1-16-phthalimide;
• and
• wherein any substitutable oxygen atom within the nucleobase is optionally and independently substituted with —C(═O)N(C1-C6alkyl)2-C(═O)N(phenyl)2;
• and
• n is 1 to 150.