Signal activated RNA interference
First Claim
1. A signal-activated polynucleotide construct, comprising:
- (1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with;
(a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and,(b) one or more regions comprising part of the guide sequence and/or part of the sense sequence;
wherein,(i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited;
(ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and,wherein the signal polynucleotides are calculated to lack sequence identity with other sequences in the human genome.
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Accused Products
Abstract
The invention provides compositions and methods for signal activated RNA interference (saRNAi), preferably in vivo. The invention provides polynucleotides that switches between an inactive form and an active form upon covalent or non-covalent interaction with one or more specific chemical signals, such as disease-specific mRNA, miRNA, or other cellular RNA products with sequences that characterize diseased states of the cell. The interaction between the subject polynucleotides and the signals is preferably mediated by hybridization, which exposes, facilitates the formation, and/or allows the formation of a substrate that can be processed by proteins of the RNAi pathway (such as Dicer). The input and output of multiple different polynucleotides of the invention can form an in vivo signaling network. In addition, the multiple input signals can be integrated to modulate the activity of the subject polynucleotides.
96 Citations
44 Claims
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1. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein the signal polynucleotides are calculated to lack sequence identity with other sequences in the human genome. - View Dependent Claims (2, 3, 4, 5, 6, 7, 10, 24, 25, 27, 28, 29, 30, 31, 44)
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8. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein said part of the guide sequence is a continuous stretch of about 3 nucleotides or less.
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9. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein said part of the sense sequence is a continuous stretch of about 5 nucleotides or less.
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11. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein in the presence of the signal polynucleotides, an extension duplex region extends said duplex region formed by said guide sequence and said sense sequence. - View Dependent Claims (12)
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13. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein in the absence of the signal polynucleotides, a first part of the signal detecting sequence hybridizes with said region comprising said part of the guide sequence to form a first additional duplex region. - View Dependent Claims (14, 15, 16, 17, 18, 19, 20, 21, 22, 23)
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26. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein the signal-activated polynucleotide construct comprises one or more chemical modifications that are largely/mostly present on the sense sequence but are absent on the guide sequence.
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32. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein the signal polynucleotides comprise an mRNA, an miRNA, an siRNA, a ribozyme, or a non-coding RNA. - View Dependent Claims (36)
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33. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein the signal polynucleotides comprise two independent/unrelated signal polynucleotides.
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34. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein at least one of said signal polynucleotides is not a transcript of the target gene.
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35. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein the target gene is a wild-type gene with normal expression.
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37. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein the signal polynucleotides are within a 3′
-UTR region.
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38. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein the signal polynucleotides are within an evolutionary conserved site for miRNA binding.
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39. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein the signal polynucleotides comprise a viral RNA, or mutations associated with a disease or cellular process.
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40. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and part of the sense sequence, and comprises a 3-4 nucleotide single-stranded region between the sequences that hybridize to said part of the guide sequence and said part of the sense sequence.
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41. A signal-activated polynucleotide construct, comprising:
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(1) a guide sequence and a sense sequence capable of forming a duplex region that can either become, or be cleaved by Dicer or RNase III to generate, an siRNA or an miRNA comprising the guide sequence, wherein the guide sequence is substantially complementary to a transcript of a target gene; and
,(2) a signal detecting sequence capable of hybridizing with; (a) one or more signal polynucleotides that are not linked to said signal-activated polynucleotide construct, and, (b) one or more regions comprising part of the guide sequence and/or part of the sense sequence; wherein, (i) in the absence of the signal polynucleotides, the signal detecting sequence hybridizes with said one or more regions comprising part of the guide sequence and/or part of the sense sequence, wherein generation of the siRNA or miRNA is inhibited, and/or productive incorporation of said siRNA or miRNA into RISC is inhibited; (ii) in the presence of the signal polynucleotides, the signal detecting sequence hybridizes with said signal polynucleotides, and allows the formation of said duplex region for the generation of said siRNA or said miRNA, and, wherein two or more signal polynucleotides bind simultaneously or sequentially to different portions of said signal detecting sequence. - View Dependent Claims (42, 43)
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Specification