US2018291056A1PendingUtilityA1
Oligonucleotide manufacturing method
Est. expiryDec 22, 2035(~9.4 yrs left)· nominal 20-yr term from priority
C07H 21/04Y02P20/55
52
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Claims
Abstract
The present invention aims to provide a more stable and efficient method for producing oligonucleotide, particularly, oligonucleotide having various functional groups linked to the 3′-terminal and the like. Efficient production of oligonucleotide becomes possible by a production method of an oligonucleotide represented by the formula (Ia-2) (each symbol is as defined in the DESCRIPTION) and having a functional group at the 3′-terminal, the method including a step of subjecting an oligonucleic acid with 3′-terminal protected by a silyl-protecting group to 3′-terminal-selective deprotection under desilylation conditions that do not affect protecting groups other than the silyl group, subjecting same to phosphitylation conditions with a phosphoramidite reagent that do not affect protecting groups on the oligonucleic acid to give a 3′-terminal-phosphoramidited oligonucleotide represented by the formula (Ia-1) (each symbol is as defined in the DESCRIPTION), and linking a functional group to the 3′-terminal of the 3′-terminal phosphoramidited oligonucleotide directly or via a linker, and the like.
Claims
exact text as granted — not AI-modified1 . A method for producing n-mer, wherein n is an integer of two or more, oligonucleotide wherein a 5′-position hydroxyl group or 5′-position phosphoric acid group is protected and a 3′-position hydroxyl group or 3′-position amino group is not protected, said method comprising:
reacting an n-mer oligonucleotide wherein a 5′-position hydroxyl group or 5′-position phosphoric acid group is protected and a 3′-position hydroxyl group or 3′-position amino group is protected by a silyl-protecting group with a fluoride ion source in a solvent in the presence of 1 or not less than 2 kinds of organic bases, wherein the fluoride ion source is a salt of at least one kind of the 1 or not less than 2 kinds of organic bases and hydrogen fluoride.
2 . The method according to claim 1 , wherein said n-mer oligonucleotide wherein a 5′-position hydroxyl group or 5′-position phosphoric acid group is protected and a 3′-position hydroxyl group or 3′-position amino group is protected by a silyl-protecting group is a compound of formula (I):
wherein:
each A 1 in the number of s and A 1 outside s is independently an oxygen atom or —NH—,
each Base in the number of s and Base outside s is independently an optionally protected nucleic acid base,
P 1 is a hydroxyl-protecting group or a phosphoric acid group as —O—P 1 in which one of the hydroxyl groups is replaced by —OL n1 -OH wherein L n1 is an organic group and hydroxyl group is protected,
each P 2 in the number of s is independently a phosphoric acid-protecting group,
each R 40 in the number of s is independently an oxygen atom or a sulfur atom,
each Y in the number of s and Y outside s is independently a hydrogen atom, an optionally protected hydroxyl group, a halogen atom, or an organic group that crosslinks to the 4-position carbon atom,
P 3 is a silyl-protecting group, and
s is an integer of one or more.
3 . The method according to claim 1 , wherein said organic base is present in an amount of not less than 1 molar equivalent relative to the fluoride ion source.
4 . The method according to claim 1 , wherein said organic base is a mixture of a strong base and a weak base, a mixture of not less than 2 kinds of weak bases or a single weak base.
5 . The method according to claim 4 , wherein said strong base has pKa≥8 and said weak base has a pKa of 4≤pKa<8.
6 . The method according to claim 1 , wherein a strong base as the organic base is present in an amount of not more than ⅓ molar equivalents.
7 . The method according to claim 1 , wherein said organic base is one or more members selected from the group consisting of methylamine, dimethylamine, trimethylamine, ethylamine, diethylamine, triethylamine, propylamine, isopropylamine, diisopropylamine, diisopropylethylamine, butylamine, isobutylamine, tert-butylamine, 1,4-diazabicyclo[2.2.2]octane, and morpholine.
8 . The method according to claim 1 , wherein said organic base is one or more members selected from the group consisting of pyridine, 2,6-dimethylpyridine, 2,4,6-trimethylpyridine, piperazine, piperidine, imidazole, N-methylimidazole, N-methylmorpholine, N-ethylmorpholine, aniline, toluidine, dimethylaniline, ethylaniline, diethylaniline, ethylmethylaniline, and anisidine.
9 . The method according to claim 1 , wherein said organic base is a mixture of triethylamine and pyridine.
10 . The method according to claim 1 , wherein said fluoride ion source is one or more members selected from the group consisting of triethylamine pentahydrofluoride, triethylamine trihydrofluoride, and pyridine hydrofluoride.
11 . The method according to claim 1 , wherein said silyl-protecting group is a silyl-protecting group in which 3 substituents on silicon are selected from the group consisting of an alkyl group, an aryl group, an aralkyl group, an alkoxy group, an aryloxy group, an aralkyloxy group, an alkylthio group and an arylthio group, and at least one of them is selected from an aryl group, an alkoxy group, an aryloxy group, and an aralkyloxy group.
12 . The method according to claim 1 , wherein at least one of Base in the number of s+1 is protected by a protecting group represented by the formula: -L-Y L —Z, wherein:
L is a group (linker) represented by the formula (a1):
wherein ** is the bonding position to nucleic acid;
* is the bonding position to Y L ;
L 1 is an optionally substituted divalent C 1-22 hydrocarbon group, an oxygen atom or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group); and
L 2 is a single bond or a group represented by the formula: *C (R 3a )(R 3b )—O—R 1 **, formula: *C(═O) N(R 2 )—R 1 —N(R 3a )** or formula: *C(═O)N(R 2 )—R 1 —C(R 3a )(R 3b )** wherein * is the bonding position to L 1 , ** is the bonding position to CR c R d , R 1 is an optionally substituted C 1-22 alkylene group, R 2 and R 3a are each independently a hydrogen atom or an optionally substituted C 1-22 alkyl group, or R 2 and R 3a are optionally joined to form an optionally substituted C 1-22 alkylene bond, R 3b is a hydrogen atom or an optionally substituted C 1-22 alkyl group;
R c and R d are each independently a hydrogen atom, an optionally substituted C 1-22 alkyl group or R c and R d are optionally joined to form a single carbonyl group;
Y L is a single bond, an oxygen atom, or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group), a sulfur atom; and
Z is a group represented by the formula (a2):
wherein * is the bonding position to Y L ;
R 4 is a hydrogen atom, or when R b is a group represented by the following formula (a3), R 4 is optionally a single bond or —O— in combination with R 6 to form a fluorenyl group or a xanthenyl group together with ring B;
each R 5 in the number of k is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
k is an integer of 1 to 4;
ring A optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a is a hydrogen atom or a phenyl group optionally substituted by a halogen atom; and
R b is a hydrogen atom, or a group represented by the formula (a3):
wherein * is the bonding position;
j is an integer of 0 to 4;
each R 7 in the number of j is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
R 6 is a hydrogen atom, or is optionally a single bond or —O— in combination with R 4 to form a fluorenyl group or a xanthenyl group together with ring A; and
ring B optionally has, in addition to OR 7 in the number of j, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a and R b are optionally joined to form a single carbonyl group;
a group represented by the formula (a2′):
wherein * is the bonding position to Y L ; and
other symbols are each as defined for the formula (a2), or a group represented by the formula (a2″):
wherein * is the bonding position to Y L ;
ring A′ optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
each symbol is as defined for the formula (a2), or
a protecting group represented by the formula: —Z′
wherein ** is the bonding position to nucleic acid; and
each symbol is as defined for the formula (a2″).
13 . The method according to claim 12 , wherein L is a succinyl group.
14 . The method according to claim 12 , wherein R 5 and/or R 7 are/is an alkyl group having 10 to 40 carbon atoms.
15 . The method according to claim 12 , wherein R 5 is an octadecyl group.
16 . The method according to claim 1 , wherein Base at the 3′-terminal nucleoside is protected by a protecting group represented by the formula: -L-Y L —Z, wherein:
L is a group (linker) represented by the formula (a1):
wherein ** is the bonding position to nucleic acid;
* is the bonding position to Y L ;
L 1 is an optionally substituted divalent C 1-22 hydrocarbon group, an oxygen atom or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group); and
L 2 is a single bond or a group represented by the formula: *C (R 3a )(R 3b )—O—R 1 **, formula: *C(═O)N(R 2 )—R 1 —N(R 3a )** or formula: *C(═O)N(R 2 )—R 1 —C(R 3a )(R 3b )** wherein * is the bonding position to L 1 , ** is the bonding position to CR c R d , R 1 is an optionally substituted C 1-22 alkylene group, R 2 and R 3a are each independently a hydrogen atom or an optionally substituted C 1-22 alkyl group, or R 2 and R 3a are optionally joined to form an optionally substituted C 1-22 alkylene bond, R 3b is a hydrogen atom or an optionally substituted C 1-22 alkyl group;
R c and R d are each independently a hydrogen atom, an optionally substituted C 1-22 alkyl group or R c and R d are optionally joined to form a single carbonyl group;
Y L is a single bond, an oxygen atom, or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group), a sulfur atom; and
Z is a group represented by the formula (a2):
wherein * is the bonding position to Y L ;
R 4 is a hydrogen atom, or when R b is a group represented by the following formula (a3), R 4 is optionally a single bond or —O— in combination with R 6 to form a fluorenyl group or a xanthenyl group together with ring B;
each R 5 in the number of k is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
k is an integer of 1 to 4;
ring A optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a is a hydrogen atom or a phenyl group optionally substituted by a halogen atom; and
R b is a hydrogen atom, or a group represented by the formula (a3):
wherein * is the bonding position;
j is an integer of 0 to 4;
each R 7 in the number of j is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
R 6 is a hydrogen atom, or is optionally a single bond or —O— in combination with R 4 to form a fluorenyl group or a xanthenyl group together with ring A; and
ring B optionally has, in addition to OR 7 in the number of j, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a and R b are optionally joined to form a single carbonyl m group;
a group represented by the formula (a2′):
wherein * is the bonding position to Y L ; and
other symbols are each as defined for the formula (a2), or a group represented by the formula (a2″):
wherein * is the bonding position to Y L ;
ring A′ optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
each symbol is as defined for the formula (a2), or
a protecting group represented by the formula: —Z′
wherein ** is the bonding position to nucleic acid; and
each symbol is as defined for the formula (a2″).
17 . A method for producing a phosphoramidited oligonucleotide, comprising:
(1) reacting a phosphitylating agent precursor represented by formula (1):
wherein
X is an oxygen atom or a sulfur atom;
R 10 is an aromatic ring, a hydroxy-protecting group or a thiol-protecting group;
each R 20 and R 30 is independently an alkyl group, and the alkyl group may form, together with the adjacent nitrogen atom, a ring,
with an activator in a solvent to obtain a phosphitylating agent represented by formula (2):
wherein
Za is a group derived from the activator, and other symbols are each as defined above:
(2) reacting an n-mer oligonucleotide, wherein n is an integer of two or more, in which one of a 5′-position hydroxyl group and a 5′-position phosphoric acid group, or one of a 3′-position hydroxyl group and a 3′-position amino group is protected, and the other is not protected, with said phosphitylating agent in a solvent in the presence of a base to phosphitylate a terminal hydroxyl group of said oligonucleotide.
18 . The method according to claim 17 , wherein said n-mer oligonucleotide has the following structure (Ia):
wherein
each A 1 in the number of q and A 1 outside q is independently an oxygen atom or —NH—,
each Base A in the number of q and Base A outside q is independently an optionally protected nucleic acid base,
P 1a is a hydroxyl-protecting group or a phosphoric acid group as —O—P 1a in which one of hydroxyl groups is replaced by —OL n1 -OH wherein L n1 is an organic group and hydroxyl group is protected,
each P 2a in the number of q is independently a phosphoric acid-protecting group,
each R 40a in the number of q is independently an oxygen atom or a sulfur atom,
each Y a in the number of q and Y a outside q is independently a hydrogen atom, an optionally protected hydroxyl group, a halogen atom or an organic group that crosslinks to the 4-position carbon atom, and
q is any integer of one or more.
19 . The method according to claim 17 , wherein said n-mer oligonucleotide has the following structure (Ia′):
wherein
each A 1 in the number of q and A 1 outside q is independently an oxygen atom or —NH—,
each Base A in the number of q and Base A outside q is independently an optionally protected nucleic acid base,
P 1a′ is a hydroxyl- or amino-protecting group, or a phosphoric acid group as -A 1 -P 1a′ in which one of hydroxyl groups is replaced by —OL n1 -OH wherein L n1 is an organic group and hydroxyl group is protected,
each P 2a in the number of q is independently a phosphoric acid-protecting group,
each R 40a in the number of q is independently an oxygen atom or a sulfur atom,
each Y a in the number of q and Y a outside q is independently a hydrogen atom, an optionally protected hydroxyl group, a halogen atom or an organic group that crosslinks to the 4-position carbon atom, and
q is any integer of one or more.
20 . The method according to claim 17 , wherein at least one of Base A in the number of q+1 is protected by a protecting group represented by the formula: -L-Y L —Z, wherein:
L is a group (linker) represented by the formula (a1):
wherein ** is the bonding position to nucleic acid;
* is the bonding position to Y L ;
L 1 is an optionally substituted divalent C 1-22 hydrocarbon group, an oxygen atom or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group); and
L 2 is a single bond or a group represented by the formula: *C(R 3a )(R 3b )—O—R 1 **, formula: *C(═O) N(R 2 )—R 1 —N(R 3a )** or formula: *C(═O)N(R 2 )—R 1 —C(R 3a )(R 3b )** wherein * is the bonding position to L 1 , ** is the bonding position to CR c R d , R 1 is an optionally substituted C 1-22 alkylene group, R 2 and R 3a are each independently a hydrogen atom or an optionally substituted C 1-22 alkyl group, or R 2 and R 3a are optionally joined to form an optionally substituted C 1-22 alkylene bond, R 3b is a hydrogen atom or an optionally substituted C 1-22 alkyl group;
R c and R d are each independently a hydrogen atom, an optionally substituted C 1-22 alkyl group or R c and R d are optionally joined to form a single carbonyl group;
Y L is a single bond, an oxygen atom, or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group), a sulfur atom; and
Z is a group represented by the formula (a2):
wherein * is the bonding position to Y L ;
R 4 is a hydrogen atom, or when R b is a group represented by the following formula (a3), R 4 is optionally, a single bond or —O— in combination with R 6 to form a fluorenyl group or a xanthenyl group together with ring B;
each R 5 in the number of k is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
k is an integer of 1 to 4;
ring A optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a is a hydrogen atom or a phenyl group optionally substituted by a halogen atom; and
R b is a hydrogen atom, or a group represented by the formula (a3):
wherein * is the bonding position;
j is an integer of 0 to 4;
each R 7 in the number of j is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
R 6 is a hydrogen atom, or is optionally a single bond or —O— in combination with R 4 to form a fluorenyl group or a xanthenyl group together with ring A; and
ring B optionally has, in addition to OR 7 in the number of j, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a and R b are optionally joined to form a single carbonyl group;
a group represented by the formula (a2′):
wherein * is the bonding position to Y L ; and
other symbols are each as defined for the formula (a2), or a group represented by the formula (a2″):
wherein * is the bonding position to Y L ;
ring A′ optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
each symbol is as defined for the formula (a2), or
a protecting group represented by the formula: —Z′
wherein ** is the bonding position to nucleic acid; and
each symbol is as defined for the formula (a2″).
21 . The method according to claim 17 , wherein said activator is a weak acidic activator with a pKa of not less than 5.
22 . The method according to claim 17 , wherein said activator is an azole compound.
23 . The method according to claim 17 , wherein said activator is dicyanoimidazole or dichloroimidazole.
24 . The method according to claim 17 , wherein said activator is reacted in an amount of 1.5 to 20 molar equivalents relative to said phosphitylating agent precursor.
25 . The method according to claim 17 , wherein said solvent used in said reacting (1) dissolves said phosphitylating agent precursor, renders said activator poorly soluble and is free of an acidic or basic functional groups.
26 . The method according to claim 17 , wherein said solvent used in said reacting (1) is one or more members selected from the group consisting of toluene, benzene, o-xylene, m-xylene, p-xylene, ethylbenzene, pentane, hexane, heptane, octane, cyclopentane, cyclohexane, diethyl ether, diisopropyl ether, tert-butyl methyl ether, cyclopentylmethylether, and carbon tetrachloride.
27 . The method according to claim 17 , wherein said solvent used in said reacting (1) is toluene.
28 . The method according to claim 17 , wherein said base used in said reacting (2) is base with pKa of 5 to 8.
29 . The method according to claim 17 , wherein said base used in said reacting (2) is one or more members selected from the group consisting of collidine, N-methylmorpholine, and diethylaniline.
30 . The method according to claim 17 , further comprising:
separating an insoluble material between said reacting (1) and said reacting (2).
31 . A method for producing oligonucleotide having a functional group at the 3′-terminal and represented by formula (Ia-2):
wherein
each A 1 in the number of q and A 1 outside q is independently an oxygen atom or —NH—,
each Base A in the number of q and Base A outside q is independently an optionally protected nucleic acid base,
P 1a is a hydroxyl-protecting group or a phosphoric acid group as —O—P 1a in which one of hydroxyl groups is replaced by —OL n1 -OH wherein L n1 is an organic group and hydroxyl group is protected,
each P 2a in the number of q is independently a phosphoric acid-protecting group,
each R 40a in the number of q is independently an oxygen atom or a sulfur atom,
each Y a in the number of q and V outside q is independently a hydrogen atom, an optionally protected hydroxyl group, a halogen atom or an organic group that crosslinks to the 4-position carbon atom,
q is any integer of one or more,
Lx is a single bond or linker, and
G is a functional group,
said method comprising:
(a) preparing a 3′-terminal phosphoramidited oligonucleotide represented by formula (Ia-1):
wherein
X is an oxygen atom or a sulfur atom,
R 10 is an aromatic ring, a hydroxy-protecting group or a thiol-protecting group,
each R 30 is independently an alkyl group, and each of other symbols is as defined above,
by a method according to claim 18 ; and
(b) linking a functional group to a 3′-terminal of said 3′-terminal phosphoramidited oligonucleotide directly or via a linker.
32 . A method for producing an oligonucleotide having a functional group at the 5′-terminal and the represented by formula (Ia′-2):
wherein:
each A 1 in the number of q and A 1 outside q is independently an oxygen atom or —NH—,
each Base A in the number of q and Base A outside q is independently an optionally protected nucleic acid base,
each P 2a in the number of q is independently a phosphoric acid-protecting group,
each R 40a in the number of q is independently an oxygen atom or a sulfur atom,
each Y a in the number of q and Y a outside q is independently a hydrogen atom, an optionally protected hydroxyl group, a halogen atom or an organic group that crosslinks to the 4-position carbon atom,
q is any integer of one or more,
Lx is a single bond or linker,
G is a functional group, and
P 1a′ hydroxyl- or amino-protecting group or a phosphoric acid group as -A 1 -P 1a′ in which one of hydroxyl groups is replaced by —OL n1 -OH wherein L n1 is an organic group and hydroxyl group is protected,
said method comprising:
(a) preparing a 5′-terminal phosphoramidited oligonucleotide represented by formula (Ia′-1):
wherein
X is an oxygen atom or a sulfur atom,
R 10 is an aromatic ring, a hydroxy-protecting group or a thiol-protecting group,
each R 30 is independently an alkyl group, and each of other symbols is as defined above, by a method according to claim 19 ; and
(b) linking a functional group to a 5′-terminal of the 5′-terminal phosphoramidited oligonucleotide directly or via a linker.
33 . The method according to claim 31 , wherein at least one of Base A in the number of q+1 is protected by a protecting group represented by the formula: -L-Y L —Z, wherein:
L is a group (linker) represented by the formula (a1):
wherein ** is the bonding position to nucleic acid;
* is the bonding position to Y L ;
L 1 is an optionally substituted divalent C 1-22 hydrocarbon group, an oxygen atom or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group); and
L 2 is a single bond or a group represented by the formula: *C(R 3a )(R 3b )—O—R 1 **, formula: *C(═O)N(R 2 )—R 1 —N(R 3a )** or formula: *C(═O)N(R 2 )—R 1 —C(R 3a )(R 3b )** wherein * is the bonding position to L 1 , ** is the bonding position to CR c R d , R 1 is an optionally substituted C 1-22 alkylene group, R 2 and R 3a are each independently a hydrogen atom or an optionally substituted C 1-22 alkyl group, or R 2 and R 3a are optionally joined to form an optionally substituted C 1-22 alkylene bond, R 3b is a hydrogen atom or an optionally substituted C 1-22 alkyl group;
R c and R d are each independently a hydrogen atom, an optionally substituted C 1-22 alkyl group or R c and R d are optionally joined to form a single carbonyl group;
Y L is a single bond, an oxygen atom, or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group), a sulfur atom; and
Z is a group represented by the formula (a2):
wherein * is the bonding position to Y L ;
R 4 is a hydrogen atom, or when R b is a group represented by the following formula (a3), R 4 is optionally a single bond or —O— in combination with R 6 to form a fluorenyl group or a xanthenyl group together with ring B;
each R 5 in the number of k is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
k is an integer of 1 to 4;
ring A optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a is a hydrogen atom or a phenyl group optionally substituted by a halogen atom; and
R b is a hydrogen atom, or a group represented by the formula (a3):
wherein * is the bonding position;
j is an integer of 0 to 4;
each R 7 in the number of j is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
R 6 is a hydrogen atom, or is optionally a single bond or —O— in combination with R 4 to form a fluorenyl group or a xanthenyl group together with ring A; and
ring B optionally has, in addition to OR 7 in the number of j, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a and R b are optionally joined to form a single carbonyl group;
a group represented by the formula (a2′):
wherein * is the bonding position to Y L ; and
other symbols are each as defined for the formula (a2), or a group represented by the formula (a2″):
wherein * is the bonding position to Y L ;
ring A′ optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
each symbol is as defined for the formula (a2), or
a protecting group represented by the formula: —Z′
wherein** is the bonding position to nucleic acid; and
each symbol is as defined for the formula (a2″).
34 . The method according to claim 31 , wherein said functional group is derived from at least one kind member selected from the group consisting of an oligonucleotide, a mononucleoside, cholesterol, GalNac3, PEG, low molecule medicament, biotin, peptide, and a labeled compound.
35 . The method according to claim 31 , wherein said functional group is n′-mer oligonucleotide, n′ is any integer of two or more, in which the 3′-position hydroxyl group or 3′-position amino group or 3′-position phosphoric acid group is protected and the 5′-hydroxyl group is not protected.
36 . The method according to claim 31 , wherein said functional group is n′-mer oligonucleotide, n′ is any integer of two or more, in which the 5′-position hydroxyl group is protected and a 3′-position hydroxyl group or 3′-position amino group is not protected.
37 . The method according to claim 35 , wherein said n′-mer oligonucleotide has the following structure (Ib):
wherein:
each A 1 in the number of r and A 1 outside r is each independently an oxygen atom or NH,
each Base B in the number of r and Base B outside r is independently an optionally protected nucleic acid base,
each P 2b in the number of r is independently a phosphoric acid-protecting group,
each R 40b in the number of r is independently an oxygen atom or a sulfur atom,
P 3b is a hydroxyl- or an amino-protecting group or a phosphoric acid group as -A 1 -P 3b in which one of hydroxyl groups is replaced by —OL n1 -OH wherein L n1 is an organic group and hydroxyl group is protected,
each Y b in the number of r and Y b outside r is independently a hydrogen atom, an optionally protected hydroxyl group, halogen atom, or an organic group that crosslinks to the 4-position carbon atom, and
r is any integer of one or more.
38 . The method according to claim 36 , wherein said n′-mer oligonucleotide has the following structure (Ib′):
wherein:
each A 1 in the number of r and A 1 outside r is each independently an oxygen atom or NH,
each Base B in the number of r and Base B outside r is independently an optionally protected nucleic acid base,
each P 2b in the number of r is independently a phosphoric acid-protecting group,
each R 40b in the number of r is independently an oxygen atom or a sulfur atom,
each Y b in the number of r and Y b outside r is independently a hydrogen atom, an optionally protected hydroxyl group, halogen atom, or an organic group that crosslinks to the 4-position carbon atom,
r is any integer of one or more, and
P 3b′ is a hydroxyl-protecting group or a phosphoric acid group as —O—P 3b′ in which one of hydroxyl groups is replaced by —OL n1 -OH wherein L n1 is an organic group and hydroxyl group is protected.
39 . The method according to claim 37 , wherein at least one of Base B in the number of r+1 is protected by a protecting group represented by the formula: -L-Y L —Z, wherein:
L is a group (linker) represented by the formula (a1):
wherein ** is the bonding position to nucleic acid;
* is the bonding position to Y L ;
L 1 is an optionally substituted divalent C 1-22 hydrocarbon group, an oxygen atom or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group); and
L 2 is a single bond or a group represented by the formula: *C(R 3a )(R 3b )—O—R 1 **, formula: *C(═O) N(R 2 )—R 1 —N(R 3a )** or formula: *C(═O)N(R 2 )—R 1 —C(R 3a )(R 3b )** wherein * is the bonding position to L 1 , ** is the bonding position to CR c R d , R 1 is an optionally substituted C 1 -22 alkylene group, R 2 and R 3a are each independently a hydrogen atom or an optionally substituted C 1-22 alkyl group, or R 2 and R 3a are optionally joined to form an optionally substituted C 1-22 alkylene bond, R 3b is a hydrogen atom or an optionally substituted C 1-22 alkyl group;
R c and R d are each independently a hydrogen atom, an optionally substituted C 1-22 alkyl group or R c and R d are optionally joined to form a single carbonyl group;
Y L is a single bond, an oxygen atom, or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group), a sulfur atom; and
Z is a group represented by the formula (a2):
wherein * is the bonding position to Y L ;
R 4 is a hydrogen atom, or when R b is a group represented by the following formula (a3), R 4 is optionally a single bond or —O— in combination with R 6 to form a fluorenyl group or a xanthenyl group together with ring B;
each R 5 in the number of k is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
k is an integer of 1 to 4;
ring A optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a is a hydrogen atom or a phenyl group optionally substituted by a halogen atom; and
R b is a hydrogen atom, or a group represented by the formula (a3):
wherein * is the bonding position;
j is an integer of 0 to 4;
each R 7 in the number of j is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
R 6 is a hydrogen atom, or is optionally a single bond or —O— in combination with R 4 to form a fluorenyl group or a xanthenyl group together with ring A; and
ring B optionally has, in addition to OR 7 in the number of j, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a and R b are optionally joined to form a single carbonyl group;
a group represented by the formula (a2′):
wherein * is the bonding position to Y L ; and
other symbols are each as defined for the formula (a2), or a group represented by the formula (a2″):
wherein * is the bonding position to Y L ;
ring A′ optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
each symbol is as defined for the formula (a2), or
a protecting group represented by the formula: —Z′
wherein ** is the bonding position to nucleic acid; and
each symbol is as defined for the formula (a2″).
40 . The method according to claim 37 , wherein said hydroxyl-protecting group for P 3b or P 3b′ is represented by the formula: -L-Y L —Z, wherein:
L is a group (linker) represented by the formula (a1):
wherein ** is the bonding position to nucleic acid;
* is the bonding position to Y L ;
L 1 is an optionally substituted divalent C 1-22 hydrocarbon group, an oxygen atom or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group); and
L 2 is a single bond or a group represented by the formula: *C(R 3a )(R 3b )—O—R 1 **, formula: *C(═O) N(R 2 )—R 1 —N(R 3a )** or formula: *C(═O) N(R 2 )—R 1 —C(R 3a )(R 3b )** wherein * is the bonding position to L 1 , ** is the bonding position to CR c R d , R 1 is an optionally substituted C 1-22 alkylene group, R 2 and R 3a are each independently a hydrogen atom or an optionally substituted C 1-22 alkyl group, or R 2 and R 3a are optionally joined to form an optionally substituted C 1-22 alkylene bond, R 3b is a hydrogen atom or an optionally substituted C 1-22 alkyl group;
R c and R d are each independently a hydrogen atom, an optionally substituted C 1-22 alkyl group or R c and R d are optionally joined to form a single carbonyl group;
Y L is a single bond, an oxygen atom, or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group), a sulfur atom; and
Z is a group represented by the formula (a2):
wherein * is the bonding position to Y L ;
R 4 is a hydrogen atom, or when R b is a group represented by the following formula (a3), R 4 is optionally a single bond or —O— in combination with R 6 to form a fluorenyl group or a xanthenyl group together with ring B;
each R 5 in the number of k is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
k is an integer of 1 to 4;
ring A optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a is a hydrogen atom or a phenyl group optionally substituted by a halogen atom; and
R b is a hydrogen atom, or a group represented by the formula (a3):
wherein * is the bonding position;
j is an integer of 0 to 4;
each R 7 in the number of j is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
R 6 is a hydrogen atom, or is optionally a single bond or —O— in combination with R 4 to form a fluorenyl group or a xanthenyl group together with ring A; and
ring B optionally has, in addition to OR 7 in the number of j, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a and R b are optionally joined to form a single carbonyl group;
a group represented by the formula (a2′):
wherein * is the bonding position to Y L ; and
other symbols are each as defined for the formula (a2), or a group represented by the formula (a2″):
wherein * is the bonding position to
ring A′ optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
each symbol is as defined for the formula (a2), or
a protecting group represented by the formula: —Z′
wherein ** is the bonding position to nucleic acid; and
each symbol is as defined for the formula (a2″).
41 . The method according to claim 40 , wherein L is a succinyl group.
42 . A method for producing an oligonucleotide having a functional group at the 3′-terminal and represented by formula (II):
wherein
each Base′ in the number of q and Base′ outside q is independently an unprotected nucleic acid base,
each A 1 in the number of q and A 1 outside q is independently an oxygen atom or NH,
P 1a is a hydroxyl-protecting group or a phosphoric acid group as —O—P 1a in which one of hydroxyl groups is replaced by —OL n1 -OH wherein L n1 is an organic group and hydroxyl group is protected,
each R 40a in the number of q is independently an oxygen atom or a sulfur atom,
each Y a in the number of q and Y a outside q is independently a hydrogen atom, an optionally protected hydroxyl group, halogen atom, or an organic group that crosslinks to the 4-position carbon atom,
q is any integer of one or more,
Lx is a single bond or linker, and
G is a functional group,
said method comprising:
(a) linking, directly or via a linker, a functional group to a 3′-terminal of a 3′-terminal phosphoramidited oligonucleotide represented by formula (Ia-1′):
wherein
each Base A′ in the number of q and Base A′ outside q is is independently protected by a protecting group represented by the formula: -L-Y L —Z, wherein:
L is a group (linker) represented by the formula (a1):
wherein ** is the bonding position to nucleic acid;
is the bonding position to Y L ;
L 1 is an optionally substituted divalent C 1-22 hydrocarbon group, an oxygen atom or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group); and
L 2 is a single bond or a group represented by the formula: *C(R 3a )(R 3b )—O—R 1 **, formula: *C(═O)N(R 2 )—R 1 —N(R 3a )** or formula: *C(═O)N(R 2 )—R 1 —C(R 3a )(R 3b )** wherein * is the bonding position to L 1 , ** is the bonding position to CR c R d , R 1 is an optionally substituted C 1-22 alkylene group, R 2 and R 3a are each independently a hydrogen atom or an optionally substituted C 1-22 alkyl group, or R 2 and R 3a are optionally joined to form an optionally substituted C 1-22 alkylene bond, R 3b is a hydrogen atom or an optionally substituted C 1-22 alkyl group;
R c and R d are each independently a hydrogen atom, an optionally substituted C 1-22 alkyl group or R c and R d are optionally joined to form a single carbonyl group;
Y L is a single bond, an oxygen atom, or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group), a sulfur atom; and
Z is a group represented by the formula (a2):
wherein * is the bonding position to Y L ;
R 4 is a hydrogen atom, or when R b is a group represented by the following formula (a3), R 4 is optionally a single bond or —O— in combination with R 6 to form a fluorenyl group or a xanthenyl group together with ring B;
each R 5 in the number of k is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
k is an integer of 1 to 4;
ring A optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a is a hydrogen atom or a phenyl group optionally substituted by a halogen atom; and
R b is a hydrogen atom, or a group represented by the formula (a3):
wherein * is the bonding position;
j is an integer of 0 to 4;
each R 7 in the number of j is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
R 6 is a hydrogen atom, or is optionally a single bond or —O— in combination with R 4 to form a fluorenyl group or a xanthenyl group together with ring A; and
ring B optionally has, in addition to OR 7 in the number of j, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a and R b are optionally joined to form a single carbonyl group;
a group represented by the formula (a2′):
wherein * is the bonding position to Y L ; and
other symbols are each as defined for the formula (a2), or a group represented by the formula (a2″):
wherein * is the bonding position to Y L ;
ring A′ optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
each symbol is as defined for the formula (a2), or
a protecting group represented by the formula: —Z′
wherein ** is the bonding position to nucleic acid; and
each symbol is as defined for the formula (a2″),
P 2a in the number of q are each independently a phosphoric acid-protecting group,
X is an oxygen atom or a sulfur atom,
R 10 is an aromatic ring, a hydroxy-protecting group or a thiol-protecting group,
each R 30 are each independently an alkyl group, and each of other symbols is as defined above, to obtain an oligonucleotide having a functional group at a 3′-terminal and represented by formula (Ia-2′):
wherein each of other symbols is as defined above, and removing the protecting group.
43 . The method according to claim 42 , wherein said 3′-terminal phosphoramidited oligonucleotide is prepared by a method according to claim 17 .
44 . The method according to claim 42 , wherein said functional group is derived from at least one member selected from the group consisting of an oligonucleotide, a mononucleoside, cholesterol, GalNac3, PEG, low molecule medicament, biotin, peptide, and a labeled compound.
45 . The method according to claim 42 , wherein said functional group is an n′-mer oligonucleotide, wherein n′ is any integer of two or more, in which the 3′-position hydroxyl group or 3′-position amino group or 3′-position phosphoric acid group is protected and the 5′-hydroxyl group is not protected.
46 . The method according to claim 45 , wherein said n′-mer oligonucleotide has the following structure (Ib):
wherein
each A 1 in the number of r and A 1 outside r is independently an oxygen atom or NH,
each Base B in the number of r and Base B outside r is independently an optionally protected nucleic acid base,
each P 2b in the number of r are each a phosphoric acid-protecting group,
each R 40b in the number of r are each an oxygen atom or a sulfur atom,
P 3b is a hydroxyl- or amino-protecting group or a phosphoric acid group as -A 1 -P 3b in which one of hydroxyl groups is replaced by —OL n1 -OH wherein L n1 is an organic group and hydroxyl group is protected,
each Y b in the number of r and Y b outside r is independently a hydrogen atom, an optionally protected hydroxyl group, halogen atom, or an organic group that crosslinks to the 4-position carbon atom, and
r is any integer of one or more.
47 . The method according to claim 46 , wherein at least one of Base B in the number of r+1 is protected by a protecting group represented by the formula: -L-Y L —Z, wherein:
L is a group (linker) represented by the formula (a1):
wherein ** is the bonding position to nucleic acid;
* is the bonding position to Y L ;
L 1 is an optionally substituted divalent C 1-22 hydrocarbon group, an oxygen atom or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group); and
L 2 is a single bond or a group represented by the formula: *C(R 3a )(R 3b )—O—R 1 **, formula: *C(═O)N(R 2 )—R 1 —N(R 3a )** or formula: *C(═O)N(R 2 )—R 1 —C(R 3a )(R 3b )** is the bonding position to L 1 , ** is the bonding position to CR c R d , R 1 is an optionally substituted C 1-22 alkylene group, R 2 and R 3a are each independently a hydrogen atom or an optionally substituted C 1-22 alkyl group, or R 2 and R 3a are optionally joined to form an optionally substituted C 1-22 alkylene bond, R 3b is a hydrogen atom or an optionally substituted C 1-22 alkyl group;
R c and R d are each independently a hydrogen atom, an optionally substituted C 1-22 alkyl group or R c and R d are optionally joined to form a single carbonyl group;
Y L is a single bond, an oxygen atom, or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group), a sulfur atom; and
Z is a group represented by the formula (a2):
wherein * is the bonding position to Y L ;
R 4 is a hydrogen atom, or when R b is a group represented by the following formula (a3), R 4 is optionally a single bond or —O— in combination with R 6 to form a fluorenyl group or a xanthenyl group together with ring B;
each R 5 in the number of k is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
k is an integer of 1 to 4;
ring A optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a is a hydrogen atom or a phenyl group optionally substituted by a halogen atom; and
R b is a hydrogen atom, or a group represented by the formula (a3):
wherein * is the bonding position;
j is an integer of 0 to 4;
each R 7 in the number of j is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
R 6 is a hydrogen atom, or is optionally a single bond or —O— in combination with R 4 to form a fluorenyl group or a xanthenyl group together with ring A; and
ring B optionally has, in addition to OR 7 in the number of j, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a and R b are optionally joined to form a single carbonyl group;
a group represented by the formula (a2′):
wherein * is the bonding position to Y L ; and
other symbols are each as defined for the formula (a2), or a group represented by the formula (a2″):
wherein * is the bonding position to Y L ;
ring A′ optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
each symbol is as defined for the formula (a2), or
a protecting group represented by the formula: —Z′
wherein ** is the bonding position to nucleic acid; and
each symbol is as defined for the formula (a2″).
48 . The method according to claim 46 , wherein the hydroxyl-protecting group for P 3b is represented by the formula: -L-Y L —Z, wherein:
L is a group (linker) represented by the formula (a1):
wherein ** is the bonding position to nucleic acid;
* is the bonding position to Y L ;
L 1 is an optionally substituted divalent C 1-22 hydrocarbon group, an oxygen atom or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group); and
L 2 is a single bond or a group represented by the formula: *C(R 3a )(R 3b )—O—R 1 **, formula: *C(═O) N(R 2 )—R 1 —N(R 3a )** or formula: *C(═O)N(R 2 )—R 1 —C(R 3a )(R 3b )** wherein * is the bonding position to L 1 , ** is the bonding position to CR c R d , R 1 is an optionally substituted C 1-22 alkylene group, R 2 and R 3a are each independently a hydrogen atom or an optionally substituted C 1-22 alkyl group, or R 2 and R 3a are optionally joined to form an optionally substituted C 1-22 alkylene bond, R 3b is a hydrogen atom or an optionally substituted C 1-22 alkyl group;
R c and R d are each independently a hydrogen atom, an optionally substituted C 1-22 alkyl group or R c and R d are optionally joined to form a single carbonyl group;
Y L is a single bond, an oxygen atom, or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group), a sulfur atom; and
Z is a group represented by the formula (a2):
wherein * is the bonding position to Y L ;
R 4 is a hydrogen atom, or when R b is a group represented by the following formula (a3), R 4 is optionally a single bond or —O— in combination with R 6 to form a fluorenyl group or a xanthenyl group together with ring B;
each R 5 in the number of k is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
k is an integer of 1 to 4;
ring A optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a is a hydrogen atom or a phenyl group optionally substituted by a halogen atom; and
R b is a hydrogen atom, or a group represented by the formula (a3):
wherein * is the bonding position;
j is an integer of 0 to 4;
each R 7 in the number of j is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
R 6 is a hydrogen atom, or is optionally a single bond or —O— in combination with R 4 to form a fluorenyl group or a xanthenyl group together with ring A; and
ring B optionally has, in addition to OR 7 in the number of j, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a and R b are optionally joined to form a single carbonyl group;
a group represented by the formula (a2′):
wherein * is the bonding position to Y L ; and
other symbols are each as defined for the formula (a2), or a group represented by the formula (a2″):
wherein * is the bonding position to Y L ;
ring A′ optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
each symbol is as defined for the formula (a2), or
a protecting group represented by the formula: —Z′
wherein ** is the bonding position to nucleic acid; and
each symbol is as defined for the formula (a2″).
49 . The method according to claim 48 , wherein L is a succinyl group.
50 . A compound represented by the following formula:
wherein
each A 1 in the number of q and A 1 outside q is independently an oxygen atom or NH,
each Base in the number of q and Base outside q is independently an optionally protected nucleic acid base,
P 1 is a hydroxyl-protecting group or a phosphoric acid group as —O—P 1 in which one of hydroxyl groups is replaced by —OL n1 -OH wherein L n1 is an organic group and hydroxyl group is protected,
each P 2 in the number of q is independently a phosphoric acid-protecting group,
each R 40 in the number of q is independently an oxygen atom or a sulfur atom,
each Y in the number of q and Y outside q is independently a hydrogen atom, an optionally protected hydroxyl group, halogen atom, or an organic group that crosslinks to the 4-position carbon atom,
P 3 is a silyl-protecting group, and
q is any integer of one or more.
51 . The compound according to claim 50 , wherein at least one of Base in the number of q+1 is protected by a protecting group represented by the formula: -L-Y L —Z, wherein:
L is a group (linker) represented by the formula (a1):
wherein ** is the bonding position to nucleic acid;
* is the bonding position to Y L ;
L 1 is an optionally substituted divalent C 1-22 hydrocarbon group, an oxygen atom or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group); and
L 2 is a single bond or a group represented by the formula: *C(R 3a )(R 3b )—O—R 1 **, formula: *C(═O)N(R 2 )—R 1 —N(R 3a )** or formula: *C(═O)N(R 2 )—R 1 —C(R 3a )(R 3b )** wherein * is the bonding position to L 1 , ** is the bonding position to CR c R d , R 1 is an optionally substituted C 1-22 alkylene group, R 2 and R 3a are each independently a hydrogen atom or an optionally substituted C 1-22 alkyl group, or R 2 and R 3a are optionally joined to form an optionally substituted C 1-22 alkylene bond, R 3b is a hydrogen atom or an optionally substituted C 1-22 alkyl group;
R c and R d are each independently a hydrogen atom, an optionally substituted C 1-22 alkyl group or R c and R d are optionally joined to form a single carbonyl group;
Y L is a single bond, an oxygen atom, or —NR— (R is a hydrogen atom, an alkyl group or an aralkyl group), a sulfur atom; and
Z is a group represented by the formula (a2):
wherein * is the bonding position to Y L ;
R 4 is a hydrogen atom, or when R b is a group represented by the following formula (a3), R 4 is optionally a single bond or —O— in combination with R 6 to form a fluorenyl group or a xanthenyl group together with ring B;
each R 5 in the number of k is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
k is an integer of 1 to 4;
ring A optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a is a hydrogen atom or a phenyl group optionally substituted by a halogen atom; and
R b is a hydrogen atom, or a group represented by the formula (a3):
wherein * is the bonding position;
j is an integer of 0 to 4;
each R 7 in the number of j is independently an organic group having an aliphatic hydrocarbon group having 10 or more carbon atoms;
R 6 is a hydrogen atom, or is optionally a single bond or —O— in combination with R 4 to form a fluorenyl group or a xanthenyl group together with ring A; and
ring B optionally has, in addition to OR′ in the number of j, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a C 1-6 alkoxy group optionally substituted by a halogen atom;
R a and R b are optionally joined to form a single carbonyl group;
a group represented by the formula (a2′):
wherein * is the bonding position to Y L ; and
other symbols are each as defined for the formula (a2), or a group represented by the formula (a2″):
wherein * is the bonding position to Y L ;
ring A′ optionally has, in addition to OR 5 in the number of k, a substituent selected from the group consisting of a halogen atom, a C 1-6 alkyl group optionally substituted by a halogen atom, and a alkoxy group optionally substituted by a halogen atom;
each symbol is as defined for the formula (a2), or
a protecting group represented by the formula: —Z′
wherein ** is the bonding position to nucleic acid; and
each symbol is as defined for the formula (a2″).Join the waitlist — get patent alerts
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