Oligoribonucleotides and ribonucleases for cleaving rna
Abstract
Oligomeric compounds including oligoribonucleotides and oligoribonucleosides are provided that have subsequences of 2′-pentoribofuranosyl nucleosides that activate dsRNase. The oligoribonucleotides and oligoribonucleosides can include substituent groups for increasing binding affinity to complementary nucleic acid strand as well as substituent groups for increasing nuclease resistance. The oligomeric compounds are useful for diagnostics and other research purposes, for modulating the expression of a protein in organisms, and for the diagnosis, detection and treatment of other conditions susceptible to oligonucleotide therapeutics. Also included in the invention are mammalian ribonucleases, i.e., enzymes that degrade RNA, and substrates for such ribonucleases. Such a ribonuclease is referred to herein as a dsRNase, wherein “ds” indicates the RNase's specificity for certain double-stranded RNA substrates. The artificial substrates for the dsRNases described herein are useful in preparing affinity matrices for purifying mammalian ribonuclease as well as non-degradative RNA-binding proteins.
Claims
exact text as granted — not AI-modified1 . A composition comprising a duplex consisting of a first chemically synthesized oligomeric compound and a second chemically synthesized oligomeric compound, wherein:
each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound independently consists of 17 to 25 linked nucleosides; at least 17 contiguous nucleobases of the first chemically synthesized oligomeric compound are 100% complementary to at least 17 contiguous nucleobases of the second chemically synthesized oligomeric compound and to a target messenger RNA; at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a plurality of nucleosides comprising a 2′-hydroxyl pentofuranosyl sugar moiety; at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a 2′-fluoro sugar modification; and the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound are not covalently linked to each other.
2 . The composition of claim 1 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a central gap region flanked by at least two wing regions.
3 . The composition of claim 1 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a central gap region flanked by at least two wing regions.
4 . The composition of claim 1 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least 4 contiguous nucleosides that comprise 2′-hydroxyl pentofuranosyl sugar moieties.
5 . (canceled)
6 . (canceled)
7 . (canceled)
8 . The composition of claim 1 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a 2′ sugar modification selected from, alkoxy, amino-alkoxy, allyloxy, imidazolylalkoxy, polyethylene glycol, and methoxyethoxy.
9 . The composition of claim 1 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound independently comprises at least one nucleoside comprising a 2′ sugar modification.
10 . The composition of claim 9 wherein at least one of the 2′ sugar modifications is selected from, alkoxy, amino-alkoxy, allyloxy, imidazolylalkoxy, polyethylene glycol, and methoxyethoxy.
11 . The compound of claim 1 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a plurality of nucleoside subunits comprising a 2′-hydroxyl pentofuranosyl sugar moiety and at least one nucleoside comprising a 2′ sugar modification.
12 . The compound of claim 1 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a plurality of nucleoside subunits comprising a 2′-hydroxyl pentofuranosyl sugar moiety and at least one nucleoside comprising a 2′ sugar modification.
13 . (canceled)
14 . (canceled)
15 . The composition of claim 1 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides each comprising a sugar comprising a 2′-fluoro.
16 . The composition of claim 1 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides each comprising a sugar comprising a 2′-fluoro.
17 . The composition of claim 1 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a sugar comprising a 2′-fluoro and at least one nucleoside comprising a sugar comprising a 2′-O-alkyl.
18 . The composition of claim 1 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a sugar comprising a 2′-fluoro and at least one nucleoside comprising a sugar comprising a 2′-O-alkyl.
19 . The composition of claim 1 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides each comprising a sugar comprising a 2′-OCH 3 .
20 . The composition of claim 19 wherein the 5′ terminal nucleoside of at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a sugar comprising a 2′-OCH 3 .
21 . The composition of claim 1 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides each comprising a sugar comprising a 2′-OCH 3 .
22 . The composition of claim 21 wherein the 5′ terminal nucleoside of at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a sugar comprising a 2′-OCH 3 .
23 . The composition of claim 1 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides comprising different 2′ sugar modifications.
24 . The composition of claim 1 wherein the first chemically synthesized oligomeric compound comprises at least one nucleoside comprising a 2′ sugar modification and the second chemically synthesized oligomeric compound comprises at least one nucleoside that comprises a different 2′ sugar modification.
25 . The composition of claim 1 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a sugar surrogate.
26 . The composition of claim 1 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a sugar surrogate.
27 . The composition of claim 1 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one chemically modified internucleoside linkage.
28 . The composition of claim 27 wherein at least one chemically modified internucleoside linkage is a phosphorothioate linkage.
29 . The composition of claim 1 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one chemically modified internucleoside linkage.
30 . The composition of claim 29 wherein at least one chemically modified internucleoside linkage is a phosphorothioate linkage.
31 . A composition comprising a duplex consisting of a first chemically synthesized oligomeric compound and a second chemically synthesized oligomeric compound, wherein:
each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound independently consists of 17 to 25 linked nucleoside subunits; at least 17 contiguous nucleobases of the first chemically synthesized oligomeric compound are 100% complementary to at least 17 contiguous nucleobases of the second chemically synthesized oligomeric compound and to a target messenger RNA; each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a plurality of nucleoside subunits comprising a 2′-hydroxyl pentofuranosyl sugar moiety; at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a 2′-fluoro sugar modification; and the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound are not covalently linked to each other.
32 . The composition of claim 31 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a central gap region flanked by at least two wing regions.
33 . The composition of claim 31 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a central gap region flanked by at least two wing regions.
34 . The composition of claim 31 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least 4 contiguous nucleosides that comprise 2′-hydroxyl pentofuranosyl sugar moieties.
35 . The composition of claim 31 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least 4 contiguous nucleosides that comprise 2′-hydroxyl pentofuranosyl sugar moieties.
36 . The composition of claim 35 wherein the at least 4 contiguous nucleosides comprising 2′-hydroxyl pentofuranosyl sugar moieties of the first chemically synthesized oligomeric compound and the at least 4 contiguous nucleosides comprising 2′-hydroxyl pentofuranosyl sugar moieties of the second chemically synthesized oligomeric compound hybridize to each other in the duplex.
37 . (canceled)
38 . The composition of claim 31 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a 2′ sugar modification selected from, alkoxy, amino-alkoxy, allyloxy, imidazolylalkoxy, polyethylene glycol, and methoxyethoxy.
39 . The composition of claim 31 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound independently comprises at least one nucleoside comprising a 2′ sugar modification.
40 . The composition of claim 39 wherein at least one of the 2′ sugar modifications is selected from, alkoxy, amino-alkoxy, allyloxy, imidazolylalkoxy, polyethylene glycol, and methoxyethoxy.
41 . (canceled)
42 . (canceled)
43 . The composition of claim 31 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides each comprising a sugar comprising a 2′-fluoro.
44 . The composition of claim 31 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides each comprising a sugar comprising a 2′-fluoro.
45 . The composition of claim 31 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a sugar comprising a 2′-fluoro and at least one nucleoside comprising a sugar comprising a 2′-O-alkyl.
46 . The composition of claim 31 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a sugar comprising a 2′-fluoro and at least one nucleoside comprising a sugar comprising a 2′-O-alkyl.
47 . The composition of claim 31 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides each comprising a sugar comprising a 2′-OCH 3 .
48 . The composition of claim 47 wherein the 5′ terminal nucleoside of at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a sugar comprising a 2′-OCH 3 .
49 . The composition of claim 31 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides each comprising a sugar comprising a 2′-OCH 3 .
50 . The composition of claim 49 wherein the 5′ terminal nucleoside of at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a sugar comprising a 2′-OCH 3 .
51 . The composition of claim 31 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides comprising different 2′ sugar modifications.
52 . The composition of claim 31 wherein the first chemically synthesized oligomeric compound comprises at least one nucleoside comprising a 2′ sugar modification and the second chemically synthesized oligomeric compound comprises at least one nucleoside that comprises a different 2′ sugar modification.
53 . The composition of claim 31 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a sugar surrogate.
54 . The composition of claim 31 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a sugar surrogate.
55 . The composition of claim 31 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one chemically modified internucleoside linkage.
56 . The composition of claim 31 wherein at least one chemically modified internucleoside linkage is a phosphorothioate linkage.
57 . The composition of claim 31 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one chemically modified internucleoside linkage.
58 . The composition of claim 31 wherein at least one chemically modified internucleoside linkage is a phosphorothioate linkage.
59 . A composition comprising a duplex consisting of a first chemically synthesized oligomeric compound and a second chemically synthesized oligomeric compound, wherein:
each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound independently consists of 17 to 25 linked nucleoside subunits; at least 17 contiguous nucleobases of the first chemically synthesized oligomeric compound are 100% complementary to at least 17 contiguous nucleobases of the second chemically synthesized oligomeric compound and to a target messenger RNA; at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a plurality of nucleoside subunits comprising a 2′-hydroxyl pentofuranosyl sugar moiety; each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound independently comprises at least one nucleoside comprising a 2′-fluoro sugar modification; and the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound are not covalently linked to each other.
60 . The composition of claim 59 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a central gap region flanked by at least two wing regions.
61 . The composition of claim 59 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a central gap region flanked by at least two wing regions.
62 . The composition of claim 59 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least 4 contiguous nucleosides that comprise 2′-hydroxyl pentofuranosyl sugar moieties.
63 . (canceled)
64 . (canceled)
65 . (canceled)
66 . The composition of claim 59 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a 2′ sugar modification selected from, alkoxy, amino-alkoxy, allyloxy, imidazolylalkoxy, polyethylene glycol, and methoxyethoxy
67 . (canceled)
68 . The composition of claim 59 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a 2′ sugar modification selected from, alkoxy, amino-alkoxy, allyloxy, imidazolylalkoxy, polyethylene glycol, and methoxyethoxy.
69 . The compound of claim 59 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a plurality of nucleoside subunits comprising a 2′-hydroxyl pentofuranosyl sugar moiety and at least one nucleoside comprising a 2′ sugar modification.
70 . (canceled)
71 . (canceled)
72 . (canceled)
73 . (canceled)
74 . (canceled)
75 . (canceled)
76 . (canceled)
77 . The composition of claim 59 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides each comprising a sugar comprising a 2′-OCH 3 .
78 . The composition of claim 77 wherein the 5′ terminal nucleoside of at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a sugar comprising a 2′-OCH 3 .
79 . The composition of claim 59 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides each comprising a sugar comprising a 2′-OCH 3 .
80 . The composition of claim 79 wherein the 5′ terminal nucleoside of at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a sugar comprising a 2′-OCH 3 .
81 . The composition of claim 59 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides comprising different 2′ sugar modifications.
82 . The composition of claim 59 wherein the first chemically synthesized oligomeric compound comprises at least one nucleoside comprising a 2′ sugar modification and the second chemically synthesized oligomeric compound comprises at least one nucleoside that comprises a different 2′ sugar modification.
83 . The composition of claim 59 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a sugar surrogate.
84 . The composition of claim 59 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a sugar surrogate.
85 . The composition of claim 59 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one chemically modified internucleoside linkage.
86 . The composition of claim 85 wherein at least one chemically modified internucleoside linkage is a phosphorothioate linkage.
87 . The composition of claim 59 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one chemically modified internucleoside linkage.
88 . The composition of claim 87 wherein at least one chemically modified internucleoside linkage is a phosphorothioate linkage.
89 . A composition comprising a duplex consisting of a first chemically synthesized oligomeric compound and a second chemically synthesized oligomeric compound, wherein:
each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound independently consists of 17 to 25 linked nucleoside subunits; at least 17 contiguous nucleobases of the first chemically synthesized oligomeric compound are 100% complementary to at least 17 contiguous nucleobases of the second chemically synthesized oligomeric compound and to a target messenger RNA; each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a plurality of nucleoside subunits comprising a 2′-hydroxyl pentofuranosyl sugar moiety; each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound independently comprises at least one nucleoside comprising a 2′-fluoro sugar modification; and the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound are not covalently linked to each other.
90 . The composition of claim 89 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a central gap region flanked by at least two wing regions.
91 . The composition of claim 89 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a central gap region flanked by at least two wing regions.
92 . The composition of claim 89 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least 4 contiguous nucleosides that comprise 2′-hydroxyl pentofuranosyl sugar moieties.
93 . The composition of claim 89 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least 4 contiguous nucleosides that comprise 2′-hydroxyl pentofuranosyl sugar moieties.
94 . The composition of claim 93 wherein the at least 4 contiguous nucleosides comprising 2′-hydroxyl pentofuranosyl sugar moieties of the first chemically synthesized oligomeric compound and the at least 4 contiguous nucleosides comprising 2′-hydroxyl pentofuranosyl sugar moieties of the second chemically synthesized oligomeric compound hybridize to each other in the duplex.
95 . (canceled)
96 . The composition of claim 89 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a 2′ sugar modification selected from, alkoxy, amino-alkoxy, allyloxy, imidazolylalkoxy, polyethylene glycol, and methoxyethoxy.
97 . (canceled)
98 . The composition of claim 89 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one 2′ sugar modification selected from, alkoxy, amino-alkoxy, allyloxy, imidazolylalkoxy, polyethylene glycol, and methoxyethoxy.
99 . (canceled)
100 . (canceled)
101 . The composition of claim 89 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides each comprising a sugar comprising a 2′-fluoro.
102 . (canceled)
103 . (canceled)
104 . (canceled)
105 . The composition of claim 89 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides each comprising a sugar comprising a 2′-OCH 3 .
106 . The composition of claim 105 wherein the 5′ terminal nucleoside of at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a sugar comprising a 2′-OCH 3 .
107 . The composition of claim 89 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides comprising a sugar comprising a 2′-OCH 3 .
108 . The composition of claim 107 wherein the 5′ terminal nucleoside of at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises a sugar comprising a 2′-OCH 3 .
109 . The composition of claim 89 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least two nucleosides comprising different 2′ sugar modifications.
110 . The composition of claim 89 wherein the first chemically synthesized oligomeric compound comprises at least one nucleoside comprising a 2′ sugar modification and the second chemically synthesized oligomeric compound comprises at least one nucleoside that comprises a different 2′ sugar modification.
111 . The composition of claim 89 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a sugar surrogate.
112 . The composition of claim 89 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one nucleoside comprising a sugar surrogate.
113 . The composition of claim 89 wherein at least one of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one chemically modified internucleoside linkage.
114 . The composition of claim 113 wherein at least one chemically modified internucleoside linkage is a phosphorothioate linkage.
115 . The composition of claim 89 wherein each of the first chemically synthesized oligomeric compound and the second chemically synthesized oligomeric compound comprises at least one chemically modified internucleoside linkage.
116 . The composition of claim 115 wherein at least one chemically modified internucleoside linkage is a phosphorothioate linkage.Join the waitlist — get patent alerts
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