Oligomer phosphoramidite compositions and processes for synthesizing the same

A method of linking a nucleotide to a further nucleotide, nucleoside, oligonucleoside or oligonucleotide having a 5′-hydroxyl group thereon comprising treating said further nucleotide, nucleoside, oligonucleoside or oligonucleotide having a 5′-hydroxyl group with a phosphoramidite composition to form an extended compound, said phosphoramidite composition comprising a phosphoramidite compound of the formula:

• 24
• wherein:
• T3 is a protected hydroxyl group, a nucleoside, a nucleotide, an oligonucleoside or an oligonucleotide;
• Bx is a protected or unprotected heterocyclic base moiety;
• each R1 is, independently, H, a protected hydroxyl group, a sugar substituent group or a protected sugar substituent group;
• R0 is a phosphorus protecting group;
• and
• -each L1 and L2 is, independently, C1-6 alkyl;
• or L1 and L2 are joined together to form a 4- to 7-membered heterocyclic ring system including the nitrogen atom to which L1 and L2 are attached, wherein said ring system optionally includes at least one additional heteroatom selected from O, N and S;
• said phosphoramidite composition further comprising at least about 1% by weight of at least one 3′-hydroxy nucleoside, a PIII species different from said phosphoramidite compound where covalent attachment of groups to the PIII phosphorus of said PIII species is through oxygen or sulfur, or a PV species where covalent attachment of groups to the PV species is by oxygen, sulfur or nitrogen.

A method of preparing an oligomer having at least one moiety of formula:

• 25
• wherein:
• each X1 and X2 is, independently, O or S;
• Bx is a protected or unprotected heterocyclic base moiety;
• and
• R1 is H, a protected hydroxyl group, a sugar substituent group, or a protected sugar substituent group;
• comprising the steps of:
• (a) providing a compound having one of the formulas:
• 26
• wherein:
• T1 is a hydroxyl protecting group;
• and
• T2 is a covalent attachment to a solid support or a solid support bound nucleoside, nucleotide, oligonucleoside or oligonucleotide;
• (b) removing the T1 group to form said compound having a 5′-hydroxyl group;
• and
• (c) treating said compound having a 5′-hydroxyl group with a phosphoramidite composition to form an extended compound, said phosphoramidite composition comprising a phosphoramidite compound of the formula:
• 27
• wherein:
• T3 is a protected hydroxyl group, a nucleoside, a nucleotide, an oligonucleoside or an oligonucleotide;
• R0 is a phosphorus protecting group;
• and
• each L1 and L2 is, independently, C1-6 alkyl;
• or L1 and L2 are joined together to form a 4- to 7-membered heterocyclic ring system including the nitrogen atom to which said L1 and L2 are attached, said ring system optionally including at least one additional heteroatom selected from O, N and S;
• said phosphoramidite composition further comprising at least about 1% by weight of at least one 2′-hydroxy nucleoside, a PIII species different from said phosphoramidite compound where covalent attachment of groups to the PIII phosphorus of said PIII species is through oxygen or sulfur, or a PV species where covalent attachment of groups to the PV species is through oxygen, sulfur or nitrogen.

A composition comprising at least one phosphoramidite compound of the formula:

• 29
• wherein:
• T3 is a protected hydroxyl group, a nucleoside, a nucleotide, an oligonucleoside or an oligonucleotide;
• Bx is a protected or unprotected heterocyclic base moiety;
• each R1 is, independently, H, a protected hydroxyl group, a sugar substituent group or a protected sugar substituent group;
• R0 is a phosphorus protecting group;
• and
• each L1 and L2 is, independently, C1-6 alkyl;
• or L1 and L2 are joined together to form a 4- to 7-membered heterocyclic ring system including the nitrogen atom to which L1 and L2 are attached, wherein said ring system optionally includes at least one additional heteroatom selected from O, N and S;
• and
• said composition further comprising at least about 1% by weight of at least one 3′-hydroxy nucleoside, 2′-hydroxy nucleoside, PIII species different from said phosphoramidite compound where covalent attachment of groups to the PIII phosphorus of said PIII species is through oxygen or sulfur, or a PV species where covalent attachment of groups to the PV species is through oxygen, sulfur or nitrogen.

A composition comprising at least one phosphoramidite compound of the formula:

• 31
• wherein:
• T3 is a protected hydroxyl group, a nucleoside, a nucleotide, an oligonucleoside or an oligonucleotide;
• Bx is a protected or unprotected heterocyclic base moiety;
• each R1 is, independently, H, a protected hydroxyl group, a sugar substituent group or a protected sugar substituent group;
• R0 is a phosphorus protecting group;
• and
• each L1 and L2 is, independently, C1-6 alkyl;
• or L1 and L2 are joined together to form a 4- to 7-membered heterocyclic ring system with the nitrogen atom to which L1 and L2 are attached, wherein said ring system optionally includes at least one additional heteroatom selected from O, N and S;
• said composition further comprising at least about 1% by weight of at least one 3′-hydroxy nucleoside, 2′-hydroxy nucleoside, PIII species different from said phosphoramidite compound where covalent attachment of groups to the PIII phosphorus of said PIII species is through oxygen or sulfur, or a PV species where covalent attachment of groups to the PV species is through oxygen, sulfur or nitrogen.

A composition comprising at least one phosphoramidite compound of the formula:

• 33
• wherein:
• T3 is a protected hydroxyl group, a nucleoside, a nucleotide, an oligonucleoside or an oligonucleotide;
• Bx is a protected or unprotected heterocyclic base moiety;
• each R1 is, independently, H, a protected hydroxyl group, a sugar substituent group or a protected sugar substituent group;
• R0 is a phosphorus protecting group;
• and
• each L1 and L2 is, independently, C1-6 alkyl;
• or L1 and L2 are joined together to form a 4- to 7-membered heterocyclic ring system including the nitrogen atom to which said L1 and L2 are attached, wherein said ring system optionally includes at least one additional heteroatom selected from O, N and S;
• and
• said composition further comprising at least about 1% by weight of at least one PIII species different from said phosphoramidite compound where covalent attachment of groups to the PIII phosphorus of said PIII species is through oxygen or sulfur, or a PV species where covalent attachment of groups to the PV species is through oxygen, sulfur or nitrogen.