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US 2019/0169223 A1Published application
Oligonucleotide production method
AssigneeNissan Chemical Corporation
InventorYudai SUGAWARA
Life of this patent
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Abstract
The invention provides a novel method for producing an oligonucleotide using a nucleoside or oligonucleotide that is easy to isolate and has high storage stability. The oligonucleotide production method includes a step of subjecting a nucleoside or oligonucleotide having a pseudo solid phase-protecting group in at least one location selected from the group consisting of 2′-position, 3′-position, 5′-position and a nucleobase moiety and having a 5′-hydroxyl group or a 3′-hydroxyl group, to H-phosphonation to convert the 5′-hydroxyl group or the 3′-hydroxyl group into an H-phosphonated form.
Claims37
A production method of an oligonucleotide comprising a step of subjecting a 5′-hydroxyl group or 3′-hydroxyl group of a nucleoside or oligonucleotide having a pseudo solid phase-protecting group in at least one location selected from the group consisting of 2′-position, 3′-position, 5′-position and a nucleobase moiety and having a 5′-hydroxyl group or a 3′-hydroxyl group, to H-phosphonation to convert the 5′-hydroxyl group or the 3′-hydroxyl group into an H-phosphonated form.
A compound represented by the following formula (XI), or a salt thereof:
- wherein
- n is an integer of 1 or greater,
- BaseZ independently at each occurrence is a nucleobase, a nucleobase protected with a basic protecting group, or a nucleobase protected with a pseudo solid phase-protecting group,
- XZ independently at each occurrence is a hydrogen atom, a halogen atom, a hydroxyl group, a hydroxyl group protected with a basic protecting group, an organic group bridged to the 4-carbon atom, or a hydroxyl group protected with a pseudo solid phase-protecting group,
- Y independently at each occurrence is a hydrogen atom, a hydroxyl group, a hydroxyl group protected with a basic protecting group, a thiol group, a thiol group protected with a basic protecting group, a borohydride group, a mono-C1-6 alkylamino group or a di-C1-6 alkylamino group,
- Z is a hydrogen atom, a basic protecting group, a temporary protecting group or a pseudo solid phase-protecting group, and
- the compound or salt thereof satisfies at least one of that at least one BaseZ is a nucleobase protected with a pseudo solid phase-protecting group, that at least one XZ is a hydroxyl group protected with a pseudo solid phase-protecting group, and that Z is a pseudo solid phase-protecting group.
4 more elements
A compound represented by the following formula (XII), or a salt thereof:
- wherein
- n is an integer of 1 or greater,
- BaseZ independently at each occurrence is a nucleobase, a nucleobase protected with a basic protecting group, or a nucleobase protected with a pseudo solid phase-protecting group,
- XZ independently at each occurrence is a hydrogen atom, a halogen atom, a hydroxyl group, a hydroxyl group protected with a basic protecting group, an organic group bridged to the 4-carbon atom, or a hydroxyl group protected with a pseudo solid phase-protecting group,
- Y independently at each occurrence is a hydrogen atom, a hydroxyl group, a hydroxyl group protected with a basic protecting group, a thiol group, a thiol group protected with a basic protecting group, a borohydride group, a mono-C1-6 alkylamino group or a di-C1-6 alkylamino group,
- Z is a hydrogen atom, a basic protecting group, a temporary protecting group or a pseudo solid phase-protecting group, and
- the compound or salt thereof satisfies at least one of that at least one BaseZ is a nucleobase protected with a pseudo solid phase-protecting group, that at least one XZ is a hydroxyl group protected with a pseudo solid phase-protecting group, and that Z is a pseudo solid phase-protecting group.
4 more elements
A compound represented by the following formula (XIII), or a salt thereof:
- wherein
- n is an integer of 1 or greater,
- BaseZ independently at each occurrence is a nucleobase, a nucleobase protected with a basic protecting group, or a nucleobase protected with a pseudo solid phase-protecting group,
- XZ independently at each occurrence is a hydrogen atom, a halogen atom, a hydroxyl group, a hydroxyl group protected with a basic protecting group, an organic group bridged to the 4-carbon atom, or a hydroxyl group protected with a pseudo solid phase-protecting group,
- W is a hydrogen atom or a temporary protecting group,
- Y independently at each occurrence is a hydrogen atom, a hydroxyl group, a hydroxyl group protected with a basic protecting group, a thiol group, a thiol group protected with a basic protecting group, a borohydride group, a mono-C1-6 alkylamino group or a di-C1-6 alkylamino group,
- Z is a hydrogen atom, a basic protecting group, a temporary protecting group or a pseudo solid phase-protecting group,
- the compound or salt thereof satisfies at least one of that at least one BaseZ is a nucleobase protected with a pseudo solid phase-protecting group, that at least one XZ is a hydroxyl group protected with a pseudo solid phase-protecting group, and that Z is a pseudo solid phase-protecting group, and
- at least one of the pseudo solid phase-protecting groups is represented by the formula (I):
- wherein
- * indicates a bond to a group protected by the pseudo solid phase-protecting group,
- R1 is a C1-40 alkyl group, a C2-40 alkenyl group or a C2-40 alkynyl group, s is an integer of 1 to 5,
- L1 is a single bond, a C1-6 alkylene group, a C2-6 alkenylene group or a C2-6 alkynylene group,
- L2 is a single bond, —COO—, —CON(R2)— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —OCO—, —N(R2)CO— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —C(O)— or —O—,
- L3 is a single bond, a C1-6 alkylene group, a C2-6 alkenylene group or a C2-6 alkynylene group,
- L4 is a single bond, —COO—, —CON(R2)— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —OCO—, —N(R2)CO— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —C(O)— or —O—,
- L5 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group,
- L6 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group, and
- m is 0 or 1 with the proviso that when m is 0, L4 is not a single bond.
16 more elements
A compound represented by the following formula (XIV), or a salt thereof:
- wherein
- n is an integer of 1 or greater,
- BaseZ independently at each occurrence is a nucleobase, a nucleobase protected with a basic protecting group, or a nucleobase protected with a pseudo solid phase-protecting group,
- XZ independently at each occurrence is a hydrogen atom, a halogen atom, a hydroxyl group, a hydroxyl group protected with a basic protecting group, an organic group bridged to the 4-carbon atom, or a hydroxyl group protected with a pseudo solid phase-protecting group,
- W is a hydrogen atom or a temporary protecting group,
- Y independently at each occurrence is a hydrogen atom, a hydroxyl group, a hydroxyl group protected with a basic protecting group, a thiol group, a thiol group protected with a basic protecting group, a borohydride group, a mono-C1-6 alkylamino group or a di-C1-6 alkylamino group,
- Z is a hydrogen atom, a basic protecting group, a temporary protecting group or a pseudo solid phase-protecting group,
- the compound or salt thereof satisfies at least one of that at least one BaseZ is a nucleobase protected with a pseudo solid phase-protecting group, that at least one XZ is a hydroxyl group protected with a pseudo solid phase-protecting group, and that Z is a pseudo solid phase-protecting group, and
- at least one of the pseudo solid phase-protecting groups is represented by the formula (I):
- wherein
- * indicates a bond to a group protected by the pseudo solid phase-protecting group,
- R1 is a C1-40 alkyl group, a C2-40 alkenyl group or a C2-40 alkynyl group, s is an integer of 1 to 5,
- L1 is a single bond, a C1-6 alkylene group, a C2-6 alkenylene group or a C2-6 alkynylene group,
- L2 is a single bond, —COO—, —CON(R2)— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —OCO—, —N(R2)CO— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —C(O)— or —O—,
- L3 is a single bond, a C1-6 alkylene group, a C2-6 alkenylene group or a C2-6 alkynylene group,
- L4 is a single bond, —COO—, —CON(R2)— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —OCO—, —N(R2)CO— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —C(O)— or —O—,
- L5 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group,
- L6 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group, and
- m is 0 or 1 with the proviso that when m is 0, L4 is not a single bond.
16 more elements
A pseudo solid phase-protecting group represented by the following formula (I):
- wherein
- * indicates a bond to at least one selected from the group consisting of 2′-, 3′- and 5′-hydroxyl groups and a nucleobase moiety of a nucleoside or oligonucleotide,
- R1 is a C1-40 alkyl group, a C2-40 alkenyl group or a C2-40 alkynyl group, s is an integer of 1 to 5,
- L1 is a single bond, a C1-6 alkylene group, a C2-6 alkenylene group or a C2-6 alkynylene group,
- L2 is a single bond, —COO—, —CON(R2)— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —OCO—, —N(R2)CO— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —C(O)— or —O—,
- L3 is a single bond, a C1-6 alkylene group, a C2-6 alkenylene group or a C2-6 alkynylene group,
- L4 is a single bond, —COO—, —CON(R2)— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —OCO—, —N(R2)CO— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —C(O)— or —O—,
- L5 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group,
- L6 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group, and
- m is 0 or 1 with the proviso that when m is 0, L4 is not a single bond.
7 more elements
A method for producing a nucleoside or oligonucleotide, comprising reacting a nucleoside or oligonucleotide having:
- a hydroxyl group or a protected hydroxyl group independently at 3′-position and 5′-position, and
- a hydroxyl group in at least one location selected from the group consisting of 2′-position, 3′-position, 5′-position and a nucleobase moiety, or a hydroxyl or amino group in at least one location of 2′-position and a nucleobase moiety, with
- a carboxyl compound represented by the following formula (X-1):
- wherein
- R1 is a C1-40 alkyl group, a C2-40 alkenyl group or a C2-40 alkynyl group, s is an integer of 1 to 5,
- L1 is a single bond, a C1-6 alkylene group, a C2-6 alkenylene group or a C2-6 alkynylene group,
- L2 is a single bond, —COO—, —CON(R2)— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —OCO—, —N(R2)CO— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —C(O)— or —O—,
- L3 is a single bond, a C1-6 alkylene group, a C2-6 alkenylene group or a C2-6 alkynylene group,
- L4 is —COO—, —CON(R2)— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —OCO—, —N(R2)CO— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —C(O)— or —O—, or with
- an acid halide represented by the following formula (X-2):
- wherein X is a halogen atom, and R1, L1, L2, L3 and L4 are the same as defined in the formula (X-1), or with
- an alkyl halide compound represented by the following formula (X-3):
- wherein X is a halogen atom, R1, L1, L2 and L3 are the same as defined in the formula (X-1),
- L4 is a single bond, —COO—, —CON(R2)— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —OCO—, —N(R2)CO— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —C(O)— or —O—,
- L5 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group, and
- L6 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group;
- thereby producing a nucleoside or oligonucleotide having, in at least one location selected from the group consisting of 2′-position, 3′-position, 5′-position and a nucleobase moiety, a pseudo solid phase-protecting group represented by the following formula (I):
- wherein * indicates a bond to at least one selected from the group consisting of the 2′-position, the 3′-position, the 5′-position and the nucleobase moiety,
- R1 is a C1-40 alkyl group, a C2-40 alkenyl group or a C2-40 alkynyl group, s is an integer of 1 to 5,
- L1 is a single bond, a C1-6 alkylene group, a C2-6 alkenylene group or a C2-6 alkynylene group,
- L2 is a single bond, —COO—, —CON(R2)— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —OCO—, —N(R2)CO— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —C(O)— or —O—,
- L3 is a single bond, a C1-6 alkylene group, a C2-6 alkenylene group or a C2-6 alkynylene group,
- L4 is a single bond, —COO—, —CON(R2)— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —OCO—, —N(R2)CO— (wherein R2 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group), —C(O)— or —O—,
- L5 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group,
- L6 is a hydrogen atom, a C1-6 alkyl group, a C1-6 haloalkyl group, a C2-6 alkenyl group or a C2-6 haloalkenyl group, and
- m is 0 or 1 with the proviso that when m is 0, L4 is not a single bond.
23 more elements
Dependencies are inferred from the claim text.