Oligonucleotide analogues
First Claim
1. An oligomer comprising at least one LNA nucleoside of the general formula I whereinX is selected from —
- O—
;
B is selected from hydrogen, hydroxy, optionally substituted C1-4-alkoxy, optionally substituted C1-4-alkyl, optionally substituted C1-4-acyloxy, nucleobases, DNA intercalators, photochemically active groups, thermochemically active groups, chelating groups, reporter groups, and ligands;
P designates the radical position for an internucleoside linkage to a succeeding monomer, or a 5′
-terminal group, such internucleoside linkage or 5′
-terminal group optionally including the substituent R5;
one of the substituents R2, R2*, R3, and R3* is a group P* which designates an internucleoside linkage to a preceding monomer, or a 3′
-terminal group, one pair of non-geminal substituents R4*, and R2*, designating a biradical consisting of 2-5 groups/atoms selected from —
(CR*R*)r—
Y—
(CR*R*)s—
, —
(CR*R*)r—
Y—
(CR*R*)s—
Y—
, —
Y—
(CR*R*)r+s—
Y—
, —
Y—
(CR*R*)r—
Y—
(CR*R*)s—
, —
(CR*R*)r+s—
, each R* is independently selected from hydrogen, halogen, hydroxy, mercapto, amino, optionally substituted C1-6-alkoxy, optionally substituted C1-6-alkyl, DNA intercalators, photochemically active groups, thermochemically active groups, chelating groups, reporter groups, and ligands, Y is —
O—
, —
S—
, 0 (zero) or —
N(RN)—
, and each of r and s is 0-4 with the proviso that the sum r+s is 1-4, and provided that when the biradical is —
(CR*R*)r—
Y—
(CR*R*)s—
, then Y is —
S—
or —
N(RN′
)—
; and
each of the substituents R1*, R2, R3, R5, and R5*, which are present and not involved in P, P* is independently selected from hydrogen, optionally substituted C1-12-alkyl, optionally substituted C2-12-alkenyl, optionally substituted C2-12-alkynyl, hydroxy, C1-12-alkoxy, C2-12-alkenyloxy, carboxy, C1-12-alkoxycarbonyl, C1-12-alkylcarbonyl, formyl, aryl, aryloxy-carbonyl, aryloxy, arylcarbonyl, heteroaryl, heteroaryloxy-carbonyl, heteroaryloxy, heteroarycarbonyl, amino, mono- and di(C1-6-alkyl)amino, carbamoyl, mono- and di(C1-6-alkyl)-amino-carbonyl, amino-C1-6-alkyl-aminocarbonyl, mono- and di(C1-6-alkyl)amino-C1-6-alkyl-aminocarbonyl, C1-6-alkyl-carbonylamino, carbamido, C1-6-alkanoyloxy, sulphono, C1-6-alkylsulphonyloxy, nitro, azido, sulphanyl, C1-6-alkylthio, halogen, DNA intercalators, photochemically active groups, thermochemically active groups, chelating groups, reporter groups, and ligands, where aryl and heteroaryl may be optionally substituted;
and basic salts and acid addition salts thereof.
1 Assignment
0 Petitions
Accused Products
Abstract
Novel oligomers, and synthesis thereof, comprising one or more bi-, tri, or polycyclic nucleoside analogues are disclosed herein. The nucleoside analogues have a “locked” structure, termed Locked Nucleoside Analogues (LNA). LNA'"'"'s exhibit highly desirable and useful properties. LNA'"'"'s are capable of forming nucleobase specific duplexes and triplexes will single and double stranded nucleic acids. These complexes exhibit higher thermostability than the corresponding complexes formed with normal nucleic acids. The properties of LNA'"'"'s allow for a wide range of uses such as diagnostic agents and therapeutic agents in a mammal suffering from or susceptible to, various diseases.
-
Citations
33 Claims
-
1. An oligomer comprising at least one LNA nucleoside of the general formula I
wherein X is selected from — - O—
;
B is selected from hydrogen, hydroxy, optionally substituted C1-4-alkoxy, optionally substituted C1-4-alkyl, optionally substituted C1-4-acyloxy, nucleobases, DNA intercalators, photochemically active groups, thermochemically active groups, chelating groups, reporter groups, and ligands;
P designates the radical position for an internucleoside linkage to a succeeding monomer, or a 5′
-terminal group, such internucleoside linkage or 5′
-terminal group optionally including the substituent R5;
one of the substituents R2, R2*, R3, and R3* is a group P* which designates an internucleoside linkage to a preceding monomer, or a 3′
-terminal group,one pair of non-geminal substituents R4*, and R2*, designating a biradical consisting of 2-5 groups/atoms selected from —
(CR*R*)r—
Y—
(CR*R*)s—
, —
(CR*R*)r—
Y—
(CR*R*)s—
Y—
, —
Y—
(CR*R*)r+s—
Y—
, —
Y—
(CR*R*)r—
Y—
(CR*R*)s—
, —
(CR*R*)r+s—
, each R* is independently selected from hydrogen, halogen, hydroxy, mercapto, amino, optionally substituted C1-6-alkoxy, optionally substituted C1-6-alkyl, DNA intercalators, photochemically active groups, thermochemically active groups, chelating groups, reporter groups, and ligands, Y is —
O—
, —
S—
, 0 (zero) or —
N(RN)—
, and each of r and s is 0-4 with the proviso that the sum r+s is 1-4, and provided that when the biradical is —
(CR*R*)r—
Y—
(CR*R*)s—
, then Y is —
S—
or —
N(RN′
)—
; and
each of the substituents R1*, R2, R3, R5, and R5*, which are present and not involved in P, P* is independently selected from hydrogen, optionally substituted C1-12-alkyl, optionally substituted C2-12-alkenyl, optionally substituted C2-12-alkynyl, hydroxy, C1-12-alkoxy, C2-12-alkenyloxy, carboxy, C1-12-alkoxycarbonyl, C1-12-alkylcarbonyl, formyl, aryl, aryloxy-carbonyl, aryloxy, arylcarbonyl, heteroaryl, heteroaryloxy-carbonyl, heteroaryloxy, heteroarycarbonyl, amino, mono- and di(C1-6-alkyl)amino, carbamoyl, mono- and di(C1-6-alkyl)-amino-carbonyl, amino-C1-6-alkyl-aminocarbonyl, mono- and di(C1-6-alkyl)amino-C1-6-alkyl-aminocarbonyl, C1-6-alkyl-carbonylamino, carbamido, C1-6-alkanoyloxy, sulphono, C1-6-alkylsulphonyloxy, nitro, azido, sulphanyl, C1-6-alkylthio, halogen, DNA intercalators, photochemically active groups, thermochemically active groups, chelating groups, reporter groups, and ligands, where aryl and heteroaryl may be optionally substituted;
and basic salts and acid addition salts thereof. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33)
wherein P, P*, B, X, R1*,R2, R2*, R1, R4*, R5 and R5* are as defined in claim 1. -
6. An oligomer of claim 5 wherein R3* designates P*.
-
7. An oligomer of claim 6 wherein the oligomer comprises one biradical constituted by two non-geminal substituents.
-
8. An oligomer of claim 1 wherein R3* designates P*.
-
9. An oligomer of claim 8 wherein, R2 is selected from hydrogen, hydroxy, and optionally substituted C1-4-alkoxy, and R3*, R3, R5, and R5* designate hydrogen.
-
10. An oligomer of claim 9 wherein B is selected from nucleobases.
-
11. An oligomer of claim 10 wherein the oligomer comprises at least one LNA nucleoside wherein B is selected from adenine, guanine, thymine, cytosine, uracil, purine, xanthine, diaminopurine, 8-oxo-N6-methyladenine, 7-deazaxanthine, 7-deazaguanine, N4, N6-ethanocytosin, N6,N6-ethano-2,6-diaminopurine, 5-methylcytosine, 5-(C3-C6)-alkynylcytosine, 2,6-diaminopyrimidino,2,6-diaminopyrazine,1-methyl-pyrazolo[4,3-d]pyrimidino-5,7(4H,6H)-dione, 1-methyl-pyrazolo[4,3-d]pyrimidine-5,7(4H,6H)-dione, 5-fluorouracil, 5-bromouracil, pseudoisocytosine, 2-hydroxy-5-methyl-4-triazolopyridin, isocytosine, isoguanin, and inosine.
-
12. An oligomer according to claim 1 wherein any internucleoside linkage of the one or more LNA nucleosides is selected from linkages consisting of 2 to 4 groups/atoms selected from —
- CH2—
, —
O—
, —
S—
, —
NRH—
, >
C═
O, >
NRH, >
C═
S, —
Si(R″
)2—
—
SO—
, —
S(O)2—
, —
P(O)2—
, —
P(O,S)—
, —
P(S)2—
, —
PO(R″
)—
, —
PO(OCH2)—
, and —
PO(NHRH)—
, where RH is selected form hydrogen and C1-4-alkyl, and R″
is selected from C1-6-alkyl and phenyl.
- CH2—
-
13. An oligomer of claim 12 wherein any internucleoside linkage of the one or more LNA nucleosides is selected from —
- CH2—
CH2—
CH2—
, —
CH2—
CO—
CH2—
CH2—
CHOH—
CH2—
, —
O—
CH2—
O—
, —
O—
CH2—
CH2—
, —
O—
CH2—
CH═
, —
CH2—
CH2—
O—
, —
NRH—
CH2—
, —
CH2—
CH2—
NRH—
, —
CH2—
NRH—
CH2—
, —
O—
CH2—
CH2NRH—
, —
NRH—
CO—
O—
, —
NRH—
CO—
NRH—
, —
NRH—
CS—
NRH—
, —
NRH—
C(═
NRH)—
NRH—
, —
NRH—
CO—
CH2—
NRH—
, —
O—
CO—
O—
, —
O—
CO—
CH2—
O—
, —
O—
CH2—
CO—
O—
, —
CH2—
CO—
NRH—
, —
O—
CO—
NRH—
, —
NRH—
CO—
CH2—
, —
O—
CH2—
CO—
NRH—
, —
O—
CH2—
CH2—
NRH—
, —
CH═
N—
O—
, —
CH2—
NRH—
O—
, —
CH2—
O—
N═
, —
CH2—
O—
NRH—
, —
CO—
NRH—
CH2—
, —
CH2—
NRH—
O—
, —
CH2—
NRH—
CO—
, —
O—
NRH—
CH2—
, —
O—
NRH—
, —
O—
CH2—
S—
, —
S—
CH2—
O—
, —
CH2—
CH2—
S—
, —
O—
CH2—
CH2—
S—
, —
S—
CH2—
CH═
, —
S—
CH2—
CH2—
, —
CH2—
CH2—
O—
, —
S—
CH2—
CH2—
S—
, —
CH2—
S—
CH2—
, —
CH2—
SO—
CH2—
, —
CH2—
SO2—
CH2—
, —
O—
SO—
O—
, —
S(O)2—
O—
, —
O—
S(O)2—
CH2—
, —
O—
S(O)2—
NRH—
, —
NRH—
S(O)2—
CH2—
, —
O—
S(O)2—
CH2—
, —
O—
P(O)2—
O—
, —
O—
P(O,S)—
O—
, —
O—
P(S)2—
O—
, —
S—
P(O)2—
O—
, —
S—
P(O,S)—
O—
, —
S—
P(S)2—
O—
, —
O—
P(O)2—
S—
, —
O—
P(O,S)—
S—
, —
O—
P(S)2—
S—
, —
S—
P(O)2—
S—
, —
S—
P(O,S)—
S—
, —
S—
P(S)2—
S—
, —
O—
PO(R″
)—
O—
, —
O—
PO(OCH3)—
O—
, —
O—
PO(BH3)—
O—
, —
O—
PO(NHRH)—
O—
, —
O—
P(O)2—
NRH—
, —
NRH—
P(O)2—
O—
, —
O—
P(O,NRH)—
O—
, and —
O—
Si(R″
)2—
O—
.
- CH2—
-
14. An oligomer of claim 13 wherein any internucleoside linkage of the one or more LNA nucleosides is selected from —
- CH2—
CO—
NRH—
, —
CH2—
NRH—
O—
, —
S—
CH2—
O—
, —
O—
P(O)2—
, —
O—
P(O,S)—
O—
, —
O—
P(S)2—
O—
, —
NRH—
P(O)2—
O—
, —
O—
P(O,NRH)—
O—
, —
O—
PO(R″
)—
O—
, —
O—
PO(CH2)—
O—
, and —
O—
PO(NHRN)—
O—
, where RH is selected form hydrogen and C1-4-alkyl, and R″
is selected from C1-6-alkyl and phenyl.
- CH2—
-
15. An oligomer of claim 1 wherein each of the substituents R1*, R2, R3, R3*, R5, and R5*, of the one or more LNA nucleosides, which are present and not involved in P, P* is independently selected from hydrogen, optionally substituted C1-6-alkyl, optionally substituted C2-6-alkenyl), hydroxy, C1-6-alkoxy, C2-6-alkenyloxy, carboxy, C1-6-alkoxycarbonyl, C1-6-alkylcarbonyl, formyl, amino, mono- and di(C1-6-alkyl)amino, carbamoyl, mono- and di(C1-6-alkyl)-amino-carbonyl, C1-6-alkyl-carbonylamino, cabamido, azido, C1-6-alkanoyloxy, sulphono, sulphanyl, C1-6-alkylthio, DNA intercalators, photochemically active groups, thermochemically active groups, chelating groups, reporter groups, and ligands, and halogen, where two geminal substituents together may designate oxo, and where RN*, when present and not involved in a biradical, is selected from hydrogen and C1-4-alkyl.
-
16. An oligomer of claim 1 wherein each of the substituents R1*, R2, R1, R3*, R5, and R5*, of the LNA(s), which are present and not involved in P, P* designate hydrogen.
-
17. An oligomer of claim 1 wherein P is a 5′
- -terminal group selected from hydrogen, hydroxy, optionally substituted C1-6-alkyl, optionally substituted C1-6-alkoxy, optionally substituted C1-6-alkylcarbonyloxy, optionally substituted aryloxy, monophosphate, diphosphate, triphosphate, and —
W—
A′
, wherein W is selected from —
O—
, —
S—
, and —
N(RH)—
where RH is selected from hydrogen and C1-6-alkyl, and where A′
is selected from DNA intercalators, photochemically active groups, thermochemically active groups, chelating groups, reporter groups, and ligands.
- -terminal group selected from hydrogen, hydroxy, optionally substituted C1-6-alkyl, optionally substituted C1-6-alkoxy, optionally substituted C1-6-alkylcarbonyloxy, optionally substituted aryloxy, monophosphate, diphosphate, triphosphate, and —
-
18. An oligomer of claim 1 wherein P* is a 3′
- -terminal group selected from hydrogen, hydroxy, optionally substituted C1-6-alkoxy, optionally substituted C1-6-alkylcarbonyloxy, optionally substituted aryloxy, and —
W—
A′
, wherein W is selected from —
O—
, —
S—
, and —
N(RH)—
where RH is selected from hydrogen and C1-6-alkyl, and where A′
is selected from DNA intercalators, photochemically active groups, thermochemically active groups, chelating groups, reporter groups, and ligands.
- -terminal group selected from hydrogen, hydroxy, optionally substituted C1-6-alkoxy, optionally substituted C1-6-alkylcarbonyloxy, optionally substituted aryloxy, and —
-
19. An oligomer of claim 1 wherein the oligomer corresponds to the following formula V:
-
20. An oligomer of claim 1 further comprising a PNA mono- or oligomer segment of the formula
wherein B is a defined above for the formula I, AASC designates hydrogen or an amino acid side chain, t is b 1-5, and w is 1-50. -
21. An oligomer of claim 1 which has an increased specificity towards complementary ssRNA or ssDNA compared to a corresponding reference oligonucleotide which does not contain any LNA units.
-
22. An oligomer of claim 1 which has an increased affinity towards complementary ssRNA or ssDNA compared to a corresponding reference oligonucleotide which does not contain any LNA units.
-
23. An oligomer of claim 1 which is capable of binding to a target sequence in a dsDNA or dsRNA molecule by of strand displacement or by triple helix formation.
-
24. An oligomer of claim 1 which is more resistant to nucleases than a corresponding reference oligonucleotide which does not contain any LNA units.
-
25. An oligomer according to claim 1 which has nucleic acid catalytic activity.
-
26. A diagnostic or analysis kit comprising an oligonucleotide of claim 1.
-
27. A kit of claim 26 wherein the oligonucleotide is immobilized on a solid support.
-
28. A diagnostic or analysis kit comprising a reaction body and one or more oligonucleotides of claim 1.
-
29. The kit of claim 28 wherein the one or more oligonucleotides are immobilized on the reaction body.
-
30. A diagnostic or analysis kit comprising a reaction body and one or more oligonucleotides of claim 1.
-
31. The kit of claim 30 wherein the one or more oligonucleotides are immobilized on the reaction body.
-
32. A diagnostic or analysis kit comprising a reaction body and one or more oligonucleotides of claim 9.
-
33. The kit of claim 32 wherein the one or more oligonucleotides are immobilized on the reaction body.
- O—
Specification