Nucleotide compound, nucleotide block oligonucleotide, and method for producing them
First Claim
1. A nucleotide compound represented by the following formula (I):
-
wherein R1 represents a protective group or an organic group represented by the formula —
C(═
O)—
A′
—
(OCH2CH2)kOCH3 in which k represents an integer of 3 or more, and A′
is a divalent organic group;
R2, R2′
, R3 and R3′
each represents a hydrogen atom or an alkyl, cycloalkyl, aryl or aralkyl group which may contain a hetero-atom and R2, R2′
, R3 and R3′
may be the same or different;
B1 and B2 each represents a base, optionally, protected by a protective group common in nucleotide chemistry or B′
which represents —
B1′
—
C(═
O)—
A—
(OCH2CH2)kOCH3 in which B1′
represents one of the groups represented by the k represents an integer of 3 or more, A is a divalent group and represents an arylene group or an alkylene group having a straight or branched chain which may contain a heteroatom;
X represents an oxygen atom or a sulfur atom;
Y represents an azolyl group, a monoalkylamino group represented by HNR5 in which R5 is an alkyl group or a cycloalkyl group, a dialkylamino group or a saturated nitrogenous heterocyclic ring;
A1 and A2 each represents a hydrogen atom, a hydroxyl group, an alkoxy group or a trialkylsilyloxy group; and
n represents 0 or an integer of 1 to 100;
excluding the case wherein at least one of the combinations of R2 and R3 and of R2′
and R3′
being a hydrogen atom and hydrogen atom, a hydrogen atom and a methyl group, a hydrogen atom and an ethyl group, a methyl group and a methyl group, a methyl group and an ethyl group or an ethyl group and an ethyl group.
1 Assignment
0 Petitions
Accused Products
Abstract
Novel nucleotide compounds represented by the formula (I)
wherein R1 represents a protective group or a PEG bearing organic group; R2, R2′, R2″, R3, R3′ and R3″ each represents a hydrogen atom or an alkyl, cycloalkyl, aryl or aralkyl group which may contain a hetero-atom; B1, B2, B3 and B4 each represents a base, if necessary, protected by a protective group common in nucleotide chemistry or by a PEG bearing organic group; X, X′ and X″ each represents an oxygen atom or a sulfur atom; Y represents an azolyl group, a mono- or di-alkylamino group or a saturated nitrogenous heterocyclic ring; A1, A2, A3 and A4 each represents a hydrogen atom, a hydroxyl group, an alkoxy group or a trialkylsilyloxy group; and m and n each represents 0 or an integer of 1 to 100. The nucleotide of the formula (I) can be used as it is in a reaction mixture for further reaction with 3′-O- and 5′-O-unprotected nucleoside or nucleotide of the formula (II) to yield a nucleotide block or oligonucleotide, and thus is useful as in situ DNA synthesis reagents.
-
Citations
21 Claims
-
1. A nucleotide compound represented by the following formula (I):
-
wherein R1 represents a protective group or an organic group represented by the formula —
C(═
O)—
A′
—
(OCH2CH2)kOCH3 in which k represents an integer of 3 or more, and A′
is a divalent organic group;
R2, R2′
, R3 and R3′
each represents a hydrogen atom or an alkyl, cycloalkyl, aryl or aralkyl group which may contain a hetero-atom and R2, R2′
, R3 and R3′
may be the same or different;
B1 and B2 each represents a base, optionally, protected by a protective group common in nucleotide chemistry or B′
which represents —
B1′
—
C(═
O)—
A—
(OCH2CH2)kOCH3 in which B1′
represents one of the groups represented by thek represents an integer of 3 or more, A is a divalent group and represents an arylene group or an alkylene group having a straight or branched chain which may contain a heteroatom;
X represents an oxygen atom or a sulfur atom;
Y represents an azolyl group, a monoalkylamino group represented by HNR5 in which R5 is an alkyl group or a cycloalkyl group, a dialkylamino group or a saturated nitrogenous heterocyclic ring;
A1 and A2 each represents a hydrogen atom, a hydroxyl group, an alkoxy group or a trialkylsilyloxy group; and
n represents 0 or an integer of 1 to 100;
excluding the case wherein at least one of the combinations of R2 and R3 and of R2′
and R3′
being a hydrogen atom and hydrogen atom, a hydrogen atom and a methyl group, a hydrogen atom and an ethyl group, a methyl group and a methyl group, a methyl group and an ethyl group or an ethyl group and an ethyl group.- View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 16, 18, 21)
wherein B1 represents a base, optionally, protected by a protective group common in nucleotide chemistry; and
Y represents an azolyl group.
-
-
4. A compound according to claim 3, wherein the sum of van der Waals volumes of R2′
- and R3′
in formula (I-1) is at least 49 cubic angstroms and Y is an imidazolyl group, a 2-methylimidazolyl group or a 4-methylimidazolyl group.
- and R3′
-
5. A compound according to claim 1, wherein said compound is represented by the following formula (I-2):
-
wherein B1 represents a base, optionally, protected by a protective group common in nucleotide chemistry; and
Y represents either a monoalkylamino group represented by HNR5 in which R5 represents an alkyl group or a cycloalkyl group or a dialkylamino group.
-
-
6. A monoalkylamino type phosphoramidite compound according to claim 5, wherein the sum of van der Waals volumes of R2′
- and R3′
in formula (I-2) is at least 49 cubic angstroms.
- and R3′
-
7. A compound according to claim 1, wherein said compound is represented by the following formula (I-3):
-
8. A compound according to claim 7, wherein the sum of Van der Waals volumes of R2′
- and R3′
in formula (I-3) is at least 49 cubic angstroms.
- and R3′
-
16. A nucleotide compound according to claim 1, wherein said nucleotide excludes the combination of R2 and R3 representing a hydrogen atom and a hydrogen atom, a hydrogen atom and a methyl group, a hydrogen atom and an ethyl group, a methyl group and a methyl group, a methyl group and an ethyl group or an ethyl group and an ethyl group.
-
18. A nucleotide compound according to claim 1, wherein the nucleotide excludes the combination of R2′
- and R3′
from representing a hydrogen atom and a hydrogen atom, a hydrogen atom and a methyl group, a hydrogen atom and an ethyl group, a methyl group and a methyl group, a methyl group and an ethyl group or an ethyl group and an ethyl group.
- and R3′
-
21. A nucleotide according to claim 1, wherein said nucleotide R2′
- and R3′
are selected from the group consisting of a hydrogen atom, a methyl group, an ethyl group, an n-propyl group, an isopropyl group, an isobutyl group, a sec-butyl group, a tert-butyl group, an n-pentyl group, a 1-methylbutyl group, a 1-ethylpropyl group, a cyclohexyl group, a n-nonyl group, 2-phenyletayl group, a 2-(methylthio)ethyl group, a phenyl group, a 1,1-diethyl-3-butenyl group and 1,1-dimethyl-2-phenylethyl group, provided that the combination of R2′
and R3′
does not represent a hydrogen atom and hydrogen atom, a hydrogen atom and a methyl group, a hydrogen atom and an ethyl group, a methyl group and a methyl group, a methyl group and an ethyl group or an ethyl group and an ethyl group.
- and R3′
-
9. A nucleoside compound represented by the following formula (I-3′
- );
wherein R1 represents a protective group or an organic group represented by the formula —
C(═
O)—
A′
—
(OCH2CH2)kOCH3 in which k represents an integer of 3 or more, R4 represents a hydrogen atom or a protective group commonly used in nucleotide chemistry, A is a divalent group and represents an arylene group or an alkylene group having a straight or branched chain which may contain a hetero-atom;
A1 represents a hydrogen atom, a hydroxyl group, an alkoxy group or a trialkylsilyloxy group; and
B1′
represents one of the groups represented by one of the following formula (1);
- );
-
10. A method for producing a nucleotide block oligonucleotide represented by the following formula (IV) which comprises reacting a nucleotide derivative represented by formula (I-4) with a 3′
- -O- and 5′
-O-unprotected nucleoside derivative or nucleotide derivative represented by formula (II) or reacting them in the presence of an optionally selected activating agent and oxidizing or sulfurizing a trivalent phosphorus atom of the resulting nucleotide represented by the following formula (III) to a pentavalent phosphorus atom;
wherein the above formulas (I-4), (II), (III) and (IV), R1 represents a protective group or an organic group represented by the formula —
C(═
O)—
A′
—
(OCH2CH2)kOCH3 in which k represents an integer of 3 or more, and A′
represents a divalent organic group;
R2, R2′
, R2″
, R3, R3′
and R3″
each represents a hydrogen atom or an alkyl, cycloalkyl, aryl or aralkyl group which may contain a hetero-atom and R2, R2′
, R2″
, R3, R3′
and R3″
may be the same or different;
B1, B2, B3 and B4 each represents a base, optionally, protected by a protective group common in nucleotide chemistry or B′
which represents —
B1′
—
C(═
O)—
A—
(OCH2CH2)kOCH3 in which B1′
represents one of the groups represented by the formula (1);
k represents an integer of 3 or more, A is a divalent group and represents an arylene group or an alkylene group having a straight or branched chain which may contain a hetero-atom;
X, X1 and X″
each represents an oxygen atom or a sulfur atom;
Y represents an azolyl group;
A1, A2, A3 and A4 each represents a hydrogen atom, a hydroxyl group, an alkoxy group or a trialkylsilyloxy group; and
m and n each represents 0 or an integer of 1 to 100;
excluding the case wherein at least one of the combinations of R2 and R3, of R2′
and R3′
and of R2″
and R3″
being a hydrogen atom and a hydrogen atom, a hydrogen atom and a methyl group, a hydrogen atom and an ethyl group, a methyl group and a methyl group, a methyl group and an ethyl group or a ethyl group and ethyl group.- View Dependent Claims (11, 12, 13, 14, 15, 17, 19, 20)
- -O- and 5′
Specification