U.S. patent application number 12/704256 was filed with the patent office on 2010-09-30 for multiplex dicer substrate rna interference molecules having joining sequences.
This patent application is currently assigned to Dicerna Pharmaceuticals. Invention is credited to Bob Dale Brown.
Application Number | 20100249214 12/704256 |
Document ID | / |
Family ID | 42562275 |
Filed Date | 2010-09-30 |
United States Patent
Application |
20100249214 |
Kind Code |
A1 |
Brown; Bob Dale |
September 30, 2010 |
MULTIPLEX DICER SUBSTRATE RNA INTERFERENCE MOLECULES HAVING JOINING
SEQUENCES
Abstract
The present invention is based, at least in part, upon the
insight that compound DsiRNA agents can be generated using
site-specific RNase H-cleavable double stranded nucleic acid double
stranded nucleic acid regions to attach, e.g., one DsiRNA moiety to
another DsiRNA moiety and/or one DsiRNA moiety to a functional
group and/or payload. Because such double stranded nucleic acid
joining sequences are site-specifically RNase H-cleavable, the
bifunctional molecule is cleaved into DsiRNAs which bear terminal
ends that orient dicer cleavage. The detrimental impact of
administering a single double stranded nucleic acid RNAi agent of
longer than 30-35 nucleotides in length (e.g., provocation of
interferon response) can be minimized, as once administered or
delivered to a subject or RNase H-containing cell, RNase H cleavage
produces a shortened, active DsiRNA agent(s). The invention also
provides bifunctional DsiRNA agents that are joined by double
stranded DNA extension joining sequences--such bifunctional DsiRNA
agents joined by dsDNA sequences do not provoke RNase H
cleavage.
Inventors: |
Brown; Bob Dale;
(Millington, NJ) |
Correspondence
Address: |
EDWARDS ANGELL PALMER & DODGE LLP
P.O. BOX 55874
BOSTON
MA
02205
US
|
Assignee: |
Dicerna Pharmaceuticals
|
Family ID: |
42562275 |
Appl. No.: |
12/704256 |
Filed: |
February 11, 2010 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
61151841 |
Feb 11, 2009 |
|
|
|
Current U.S.
Class: |
514/44A ;
435/367; 536/24.5 |
Current CPC
Class: |
C12N 2310/11 20130101;
C12N 15/113 20130101; C12N 2320/53 20130101; A61P 31/20 20180101;
C12N 15/1137 20130101; C12N 15/1135 20130101; C12N 2310/51
20130101; C12N 15/111 20130101; A61P 35/00 20180101; A61P 37/06
20180101; A61P 31/14 20180101; C12N 2310/533 20130101; A61P 31/22
20180101; A61K 31/713 20130101; C12N 2310/14 20130101 |
Class at
Publication: |
514/44.A ;
536/24.5; 435/367 |
International
Class: |
A61K 31/713 20060101
A61K031/713; C12N 15/113 20100101 C12N015/113; C12N 5/02 20060101
C12N005/02; A61P 31/14 20060101 A61P031/14 |
Claims
1. An isolated nucleic acid duplex comprising: a first region
comprising first and second oligonucleotide strands comprising
ribonucleotides, each strand having 5' and 3' termini, wherein said
first region forms a duplex of 23 and 35 ribonucleotides in length;
a second region comprising first and second oligonucleotide strands
and comprising a RNA:DNA duplex having a length of DNA sufficient
to activate a detectable amount of RNase H cleavage of said second
region in an RNase H cleavage assay; and a third region comprising
first and second oligonucleotide strands comprising
ribonucleotides, each strand having 5' and 3' termini, wherein said
third region forms a duplex of 23 and 35 ribonucleotides in length;
and wherein said isolated duplex comprises a nick, wherein the
position of said nick between immediately adjacent nucleotides is
selected from the group consisting of: (a) within said second
region in one of said first and second oligonucleotide strands, (b)
between said first region and said second region on one strand, and
c) between said second region and said third region on one
strand.
2. The isolated nucleic acid duplex of claim 1, wherein said second
region first oligonucleotide strand comprises deoxynucleotides.
3. The isolated nucleic acid duplex of claim 1, wherein said second
region second oligonucleotide strand comprises
deoxyribonucleotides.
4. The isolated nucleic acid duplex of claim 2 or 3, wherein said
oligonucleotide strand consists of deoxyribonucleotides.
5. The isolated nucleic acid duplex of claim 1, wherein each of
said first and third regions, independently, form a duplex of 23
and 30 ribonucleotides in length.
6. The isolated nucleic acid duplex of claim 1, wherein said nick
is positioned within said second region on the strand that
comprises deoxyribonucleotides.
7. The isolated nucleic acid duplex of claim 1, wherein said nick
is positioned between one of said first and second regions or said
second and third regions, and wherein said nick is positioned
between a deoxyribonucleotide of a second region strand and a
ribonucleotide of one of said first or third region strands.
8. The nucleic acid duplex of claim 1, wherein said RNase H
cleavage assay is an in vitro or a mammalian cell RNase H cleavage
assay.
9. The nucleic acid duplex of claim 1, wherein DNA of said RNA:DNA
duplex of said second region consists of 4-40 deoxyribonucleotides
that base pair with ribonucleotides, and wherein said nick is
positioned on one of said first oligonucleotide strand or said
second oligonucleotide strand between immediately adjacent
deoxyribonucleotides.
10. The nucleic acid duplex of claim 1, wherein DNA of said RNA:DNA
duplex of said second region consists of 4-40 deoxyribonucleotides
that base pair with ribonucleotides, and wherein said nick is
positioned on one of said first oligonucleotide strand or said
second oligonucleotide strand between a deoxyribonucleotide that is
immediately adjacent to a ribonucleotide.
11. The isolated nucleic acid duplex of claim 9 or 10, wherein DNA
said RNA:DNA duplex
12. The nucleic acid duplex of claim 1, wherein DNA of said RNA:DNA
duplex of said second region consists of 4-20 deoxyribonucleotides
that base pair with ribonucleotides, and wherein said nick is
positioned on one of said first oligonucleotide strand or said
second oligonucleotide strand between immediately adjacent
deoxyribonucleotides.
13. The nucleic acid duplex of claim 1, wherein DNA of said RNA:DNA
duplex of said second region consists of 4-20 deoxyribonucleotides
that base pair with ribonucleotides, and wherein said nick is
positioned on one of said first oligonucleotide strand or said
second oligonucleotide strand between a deoxyribonucleotide that is
immediately adjacent to a ribonucleotide.
14. The nucleic acid of claim 1, wherein said first region
comprises a duplex of at least 25 nucleotides in length.
15. The nucleic acid of claim 1, wherein said third region
comprises a duplex of at least 25 nucleotides in length.
16. The isolated nucleic acid duplex of claim 1, wherein said
second oligonucleotide strand of said first region is sufficiently
complementary to a first target RNA along at least 19 nucleotides
of said second oligonucleotide strand length to reduce target gene
expression when said nucleic acid duplex is introduced into a
mammalian cell.
17. The isolated nucleic acid duplex of claim 16, wherein said
first target RNA is selected from the group consisting of K-RAS,
HPRT1, VEGF, VEGFR, EGF, EGFR and an HCV target RNA sequence.
18. The isolated nucleic acid duplex of claim 1, wherein said
second oligonucleotide strand of said third region is sufficiently
complementary to a second target RNA along at least 19 nucleotides
of said second oligonucleotide strand length to reduce target gene
expression when said nucleic acid duplex is introduced into a
mammalian cell.
19. The isolated nucleic acid duplex of claim 1, wherein said first
oligonucleotide strand of said third region is sufficiently
complementary to a second target RNA along at least 19 nucleotides
of said first oligonucleotide strand length to reduce target gene
expression when said nucleic acid duplex is introduced into a
mammalian cell.
20. The isolated nucleic acid duplex of claim 18 or claim 19,
wherein said second target RNA is selected from the group
consisting of K-RAS, HPRT1, VEGF, VEGFR, EGF, EGFR and an HCV
target RNA sequence.
21. The isolated nucleic acid duplex of claim 20, wherein pairs of
first and second target RNAs are selected from the group consisting
of HPRT1 and K-RAS; VEGF and VEGFR; and EGF and EGFR.
22. The isolated nucleic acid duplex of claim 16, wherein said
nucleic acid duplex reduces target gene expression in a mammalian
cell in vitro by an amount (expressed by %) selected from the group
consisting of at least 10%, at least 50% and at least 80-90%.
23. The isolated nucleic acid duplex of claim 18 or claim 19,
wherein said nucleic acid duplex reduces expression of said first
target gene and said second target gene in a mammalian cell in
vitro by an amount (expressed by %) selected from the group
consisting of at least 10%, at least 50% and at least 80-90%.
24. The isolated nucleic acid duplex of claim 1, wherein said
second oligonucleotide strand of said first region possesses a 3'
overhang of 1-4 nucleotides in length.
25. The isolated nucleic acid duplex of claim 1, wherein said first
oligonucleotide strand of said third region possesses a 3' overhang
of 1-4 nucleotides in length.
26. The isolated nucleic acid duplex of claim 24 or claim 25,
wherein said 3' overhang is 1-3 nucleotides in length.
27. The isolated nucleic acid duplex of claim 26, wherein said 3'
overhang is 1-2 nucleotides in length.
28. The isolated nucleic acid duplex of claim 24 or claim 25,
wherein said nucleotides of said 3' overhang comprise a modified
nucleotide.
29. The isolated nucleic acid duplex of claim 28, wherein said
modified nucleotide residue is selected from the group consisting
of 2'-O-methyl, 2'-methoxyethoxy, 2'-fluoro, 2'-allyl, 2'-O
-[2-(methylamino)-2-oxoethyl], 4'-thio, 4'-CH.sub.2--O-2'-bridge,
4'-(CH2)2-O-2'-bridge, 2'-LNA, 2'-amino and
2'-O-(N-methlycarbamate).
30. The isolated nucleic acid duplex of claim 28, wherein said
modified nucleotide of said 3' overhang is a 2'-O-methyl
ribonucleotide.
31. The isolated nucleic acid duplex of claim 28, wherein all
nucleotides of said 3' overhang are modified nucleotides.
32. The isolated nucleic acid duplex of claim 28, wherein said 3'
overhang is two nucleotides in length and wherein said modified
nucleotide of said 3' overhang is a 2'-O-methyl modified
ribonucleotide.
33. The isolated nucleic acid duplex of claim 1, wherein said
second oligonucleotide strand of said first region, starting from
the nucleotide residue of said second oligonucleotide strand of
said first region that is complementary to the 5' terminal
nucleotide residue of said first oligonucleotide strand of said
first region, comprises unmodified nucleotide residues at all
positions from position 20 to the most 5' residue of said second
oligonucleotide strand of said first region.
34. The isolated nucleic acid duplex of claim 1, wherein said first
oligonucleotide strand of said third region, starting from the
nucleotide residue of said first oligonucleotide strand of said
third region that is complementary to the 5' terminal nucleotide
residue of said second oligonucleotide strand of said third region,
comprises unmodified nucleotide residues at all positions from
position 20 to the most 5' residue of said first oligonucleotide
strand of said third region.
35. The isolated nucleic acid duplex of claim 1, wherein the second
oligonucleotide strand of said first region comprises modified
nucleotides at positions 1, 2, and 3 from the 3' terminus of said
second oligonucleotide strand of said first region.
36. The isolated nucleic acid duplex of claim 1, wherein the first
oligonucleotide strand of said third region comprises modified
nucleotides at positions 1, 2, and 3 from the 3' terminus of said
first oligonucleotide strand of said third region.
37. The isolated nucleic acid duplex of claim 1, wherein at least
the two most 3' nucleotide residues of said first oligonucleotide
strand of said first region are deoxyribonucleotides that base pair
with two deoxyribonucleotides of said second oligonucleotide strand
of said first region.
38. The isolated nucleic acid duplex of claim 1, wherein at least
the two most 5' nucleotide residues of said first oligonucleotide
strand of said third region are deoxyribonucleotides that base pair
with two deoxyribonucleotides of said second oligonucleotide strand
of said third region.
39. The isolated nucleic acid duplex of claim 1, wherein the two
most 3' nucleotide residues of said second oligonucleotide strand
of said second region are modified ribonucleotides.
40. The isolated nucleic acid duplex of claim 1, wherein the two
most 5' nucleotide residues of said second oligonucleotide strand
of said second region are modified ribonucleotides.
41. The isolated nucleic acid duplex of claim 1, wherein said
second oligonucleotide strand of said third region, starting from
the most 3' nucleotide residue of said second oligonucleotide
strand of said third region, comprises alternating modified and
unmodified nucleotide residues.
42. The isolated nucleic acid duplex of claim 3, wherein the two
most 5' nucleotide residues of said first oligonucleotide strand of
said second region are modified ribonucleotides.
43. The isolated nucleic acid duplex of claim 3, wherein the two
most 3' nucleotide residues of said first oligonucleotide strand of
said second region are modified ribonucleotides.
44. The isolated nucleic acid duplex of claim 3, wherein said first
oligonucleotide strand of said third region, starting from the 3'
terminus of said first oligonucleotide strand of said third region,
comprises alternating modified and unmodified nucleotide
residues.
45. The isolated nucleic acid duplex of claim 1, wherein the 3'
terminus of said first oligonucleotide strand of said third region
and the 5' terminus of said second oligonucleotide strand of said
third region form a blunt end.
46. The isolated nucleic acid duplex of claim 1, wherein at least
one of positions 1, 2 or 3 from the 3' terminus of said 3' terminus
of said first oligonucleotide strand of said third region is a
deoxyribonucleotide.
47. The isolated nucleic acid duplex of claim 1, wherein said
deoxynucleotide residues of said second region that comprise said
RNA:DNA duplex are unmodified deoxyribonucleotides.
48. The isolated nucleic acid duplex of claim 1, wherein at least
50% of all deoxyribonucleotides of said nucleic acid duplex are
unmodified deoxyribonucleotides.
49. The isolated nucleic acid duplex of claim 1, wherein said first
oligonucleotide strand of said third region is attached to said
second oligonucleotide strand of said third region by a nucleotide
sequence, wherein said nucleotide sequence attaches the most 3'
nucleotide of said first oligonucleotide strand of said third
region that base pairs with a nucleotide of said second
oligonucleotide strand of said third region to said second
oligonucleotide strand nucleotide of said third region that base
pairs with said most 3' nucleotide of said first oligonucleotide
strand of said third region.
50. The isolated nucleic acid duplex of claim 49, wherein said
nucleotide sequence that attaches said first oligonucleotide strand
of said third region and said second oligonucleotide strand of said
third region comprises a tetraloop.
51. The isolated nucleic acid duplex of claim 49, wherein said
nucleotide sequence that attaches said first oligonucleotide strand
of said third region and said second oligonucleotide strand of said
third region comprises a hairpin, a chemical linker or an extended
loop.
52. The isolated nucleic acid duplex of claim 1, wherein one or
both of the first and second oligonucleotide strands of any of said
first, second or third regions comprises a 5' phosphate.
53. The isolated nucleic acid duplex of claim 1, wherein said
nucleic acid duplex is cleaved endogenously in a mammalian cell by
RNase H.
54. The isolated nucleic acid duplex of claim 53, wherein said
endogenous RNase H cleavage generates a nucleic acid duplex that is
cleaved endogenously in said mammalian cell by Dicer.
55. The isolated nucleic acid of claim 53, wherein said endogenous
RNase H cleavage generates two nucleic acid duplexes that are each
cleaved endogenously in said mammalian cell by Dicer.
56. The isolated nucleic acid duplex of claim 1, wherein said
nucleic acid duplex is cleaved endogenously in a mammalian cell by
Dicer.
57. The isolated nucleic acid duplex of claim 1, wherein said
nucleic acid duplex is cleaved endogenously in a mammalian cell to
produce a double-stranded nucleic acid of 19-23 nucleotides in
length that reduces target gene expression.
58. The isolated nucleic acid duplex of claim 1, wherein a
nucleotide of said second or first oligonucleotide strand of any of
said first, second or third regions is substituted with a modified
nucleotide that directs the orientation of Dicer cleavage.
59. The isolated nucleic acid duplex of claim 1 comprising a
phosphate backbone modification selected from the group consisting
of a phosphonate, a phosphorothioate and a phosphotriester.
60. The isolated nucleic acid duplex of claim 1, wherein at least
50% of said ribonucleotide residues of positions 1 to 23 of said
first oligonucleotide strand that base pair with ribonucleotides of
said second oligonucleotide strand to form a duplex are unmodified
ribonucleotides.
61. The isolated nucleic acid duplex of claim 1, wherein at least
50% of all ribonucleotides of said nucleic acid duplex are
unmodified ribonucleotides.
62. The isolated nucleic acid duplex of claim 1, wherein the first
and second oligonucleotide strands of said third region are joined
by a chemical linker.
63. The isolated nucleic acid duplex of claim 62, wherein said 3'
terminus of said first oligonucleotide strand of said third region
and said 5' terminus of said second oligonucleotide strand of said
third region are joined by a chemical linker.
64. The isolated nucleic acid duplex of claim 1, wherein positions
24 and greater of said first oligonucleotide strand of said first
region comprise between one and 12 deoxyribonucleotide residues,
wherein each of said deoxynucleotide residues of said first
oligonucleotide strand of said first region base pairs with a
deoxyribonucleotide of said second oligonucleotide strand of said
first region to form a duplex.
65. The isolated nucleic acid duplex of claim 1, wherein the first
oligonucleotide strand of said first or third regions has a
nucleotide sequence that is at least 60%, 70%, 80%, 90%, 95% or
100% complementary to the second oligonucleotide strand nucleotide
sequence of said respective first or third regions.
66. An isolated nucleic acid duplex comprising: a first region
comprising first and second oligonucleotide strands comprising
ribonucleotides, each strand having 5' and 3' termini, wherein said
first region forms a duplex of 23 and 35 ribonucleotides in length;
a second region comprising first and second oligonucleotide
strands, said second region comprising a DNA:DNA duplex having a
length of DNA of 2-40 base pairs; and a third region comprising
first and second oligonucleotide strands comprising
ribonucleotides, each strand having 5' and 3' termini, wherein said
third region forms a duplex of 23 and 35 ribonucleotides in
length.
67. The nucleic acid of claim 66, wherein said first region
comprises a duplex of at least 25 nucleotides in length.
68. The nucleic acid of claim 66, wherein said first region
comprises a duplex of between 26 and 35 nucleotides in length.
69. The nucleic acid of claim 66, wherein said first region
comprises a duplex of between 26 and 30 nucleotides in length.
70. The nucleic acid of claim 66, wherein said third region
comprises a duplex of at least 25 nucleotides in length.
71. The nucleic acid of claim 66, wherein said third region
comprises a duplex of between 26 and 35 nucleotides in length.
72. The nucleic acid of claim 66, wherein said third region
comprises a duplex of between 26 and 30 nucleotides in length.
73. The isolated nucleic acid duplex of claim 66, wherein said
second oligonucleotide strand of said first region is sufficiently
complementary to a first target RNA along at least 19 nucleotides
of said second oligonucleotide strand length to reduce target gene
expression when said nucleic acid duplex is introduced into a
mammalian cell.
74. The isolated nucleic acid duplex of claim 73, wherein said
first target RNA is selected from the group consisting of K-RAS,
HPRT1, VEGF, VEGFR, EGF, EGFR and an HCV target RNA sequence.
75. The isolated nucleic acid duplex of claim 66, wherein said
second oligonucleotide strand of said third region is sufficiently
complementary to a second target RNA along at least 19 nucleotides
of either said first or said second oligonucleotide strand length
to reduce target gene expression when said nucleic acid duplex is
introduced into a mammalian cell.
76. The isolated nucleic acid duplex of claim 73, wherein said
first oligonucleotide strand of said third region is sufficiently
complementary to a second target RNA along at least 19 nucleotides
of either said first or said second oligonucleotide strand length
to reduce target gene expression when said nucleic acid duplex is
introduced into a mammalian cell.
77. The isolated nucleic acid duplex of claim 75 or claim 76,
wherein said second target RNA is selected from the group
consisting of K-RAS, HPRT1, VEGF, VEGFR, EGF, EGFR and an HCV
target RNA sequence.
78. The isolated nucleic acid duplex of claim 77, wherein pairs of
first and second target RNAs are selected from the group consisting
of HPRT1 and K-RAS; VEGF and VEGFR; and EGF and EGFR.
79. The isolated nucleic acid duplex of claim 66, wherein said
nucleic acid duplex reduces target gene expression in a mammalian
cell in vitro by an amount (expressed by %) selected from the group
consisting of at least 10%, at least 50% and at least 80-90%.
80. The isolated nucleic acid duplex of claim 75 or claim 76,
wherein said nucleic acid duplex reduces expression of said first
target gene and said second target gene in a mammalian cell in
vitro by an amount (expressed by %) selected from the group
consisting of at least 10%, at least 50% and at least 80-90%.
81. The isolated nucleic acid duplex of claim 66, wherein said
second oligonucleotide strand of said first region possesses a 3'
overhang of 1-4 nucleotides in length.
82. The isolated nucleic acid duplex of claim 66, wherein said
first oligonucleotide strand of said third region possesses a 3'
overhang of 1-4 nucleotides in length.
83. The isolated nucleic acid duplex of claim 81 or claim 82,
wherein said 3' overhang is 1-3 nucleotides in length.
84. The isolated nucleic acid duplex of claim 83, wherein said 3'
overhang is 1-2 nucleotides in length.
85. The isolated nucleic acid duplex of claim 81 or claim 82,
wherein said nucleotides of said 3' overhang comprise a modified
nucleotide.
86. The isolated nucleic acid duplex of claim 85, wherein said
modified nucleotide residue is selected from the group consisting
of 2'-O-methyl, 2'-methoxyethoxy, 2'-fluoro, 2'-allyl, 2'-O
-[2-(methylamino)-2-oxoethyl], 4'-thio, 4'-CH.sub.2--O-2'-bridge,
4'-(CH2)2-O-2'-bridge, 2'-LNA, 2'-amino and
2'-O-(N-methlycarbamate).
87. The isolated nucleic acid duplex of claim 85, wherein said
modified nucleotide of said 3' overhang is a 2'-O-methyl
ribonucleotide.
88. The isolated nucleic acid duplex of claim 85, wherein all
nucleotides of said 3' overhang are modified nucleotides.
89. The isolated nucleic acid duplex of claim 85, wherein said 3'
overhang is two nucleotides in length and wherein said modified
nucleotide of said 3' overhang is a 2'-O-methyl modified
ribonucleotide.
90. The isolated nucleic acid duplex of claim 66, wherein said
second oligonucleotide strand of said first region, starting from
the nucleotide residue of said second oligonucleotide strand of
said first region that is complementary to the 5' terminal
nucleotide residue of said first oligonucleotide strand of said
first region, comprises unmodified nucleotide residues at all
positions from position 20 to the most 5' residue of said second
oligonucleotide strand of said first region.
91. The isolated nucleic acid duplex of claim 66, wherein said
first oligonucleotide strand of said third region, starting from
the nucleotide residue of said first oligonucleotide strand of said
third region that is complementary to the 5' terminal nucleotide
residue of said second oligonucleotide strand of said third region,
comprises unmodified nucleotide residues at all positions from
position 20 to the most 5' residue of said first oligonucleotide
strand of said third region.
92. The isolated nucleic acid duplex of claim 66, wherein the
second oligonucleotide strand of said first region comprises
modified nucleotides at positions 1, 2, and 3 from the 3' terminus
of said second oligonucleotide strand of said first region.
93. The isolated nucleic acid duplex of claim 66, wherein the first
oligonucleotide strand of said third region comprises modified
nucleotides at positions 1, 2, and 3 from the 3' terminus of said
first oligonucleotide strand of said third region.
94. The isolated nucleic acid duplex of claim 66, wherein at least
the two most 3' nucleotide residues of said first oligonucleotide
strand of said first region are deoxyribonucleotides that base pair
with two deoxyribonucleotides of said second oligonucleotide strand
of said first region.
95. The isolated nucleic acid duplex of claim 66, wherein at least
the two most 5' nucleotide residues of said first oligonucleotide
strand of said third region are deoxyribonucleotides that base pair
with two deoxyribonucleotides of said second oligonucleotide strand
of said third region.
96. The isolated nucleic acid duplex of claim 66, wherein the two
most 3' nucleotide residues of said second oligonucleotide strand
of said second region are modified ribonucleotides.
97. The isolated nucleic acid duplex of claim 66, wherein the two
most 5' nucleotide residues of said second oligonucleotide strand
of said second region are modified ribonucleotides.
98. The isolated nucleic acid duplex of claim 66, wherein said
second oligonucleotide strand of said third region, starting from
the most 3' nucleotide residue of said second oligonucleotide
strand of said third region, comprises alternating modified and
unmodified nucleotide residues.
99. The isolated nucleic acid duplex of claim 66, wherein the 3'
terminus of said first oligonucleotide strand of said third region
and the 5' terminus of said second oligonucleotide strand of said
third region form a blunt end.
100. The isolated nucleic acid duplex of claim 66, wherein at least
one of positions 1, 2 or 3 from the 3' terminus of said 3' terminus
of said first oligonucleotide strand of said third region is a
deoxyribonucleotide.
101. The isolated nucleic acid duplex of claim 66, wherein said
deoxynucleotide residues of said second region that comprise said
DNA:DNA duplex are unmodified deoxyribonucleotides.
102. The isolated nucleic acid duplex of claim 66, wherein at least
50% of all deoxyribonucleotides of said nucleic acid duplex are
unmodified deoxyribonucleotides.
103. The isolated nucleic acid duplex of claim 66, wherein said
first oligonucleotide strand of said third region is attached to
said second oligonucleotide strand of said third region by a
nucleotide sequence, wherein said nucleotide sequence attaches the
most 3' nucleotide of said first oligonucleotide strand of said
third region that base pairs with a nucleotide of said second
oligonucleotide strand of said third region to said second
oligonucleotide strand nucleotide of said third region that base
pairs with said most 3' nucleotide of said first oligonucleotide
strand of said third region.
104. The isolated nucleic acid duplex of claim 103, wherein said
nucleotide sequence that attaches said first oligonucleotide strand
of said third region and said second oligonucleotide strand of said
third region comprises a tetraloop.
105. The isolated nucleic acid duplex of claim 103, wherein said
nucleotide sequence that attaches said first oligonucleotide strand
of said third region and said second oligonucleotide strand of said
third region comprises a hairpin, a chemical linker or an extended
loop.
106. The isolated nucleic acid duplex of claim 66, wherein one or
both of the first and second oligonucleotide strands of any of said
first, second or third regions comprises a 5' phosphate.
107. The isolated nucleic acid duplex of claim 66, wherein said
nucleic acid duplex is cleaved endogenously in a mammalian cell by
Dicer.
108. The isolated nucleic acid duplex of claim 107, wherein said
nucleic acid duplex is cleaved twice endogenously in a mammalian
cell by Dicer.
109. The isolated nucleic acid duplex of claim 66, wherein said
nucleic acid duplex is cleaved endogenously in a mammalian cell to
produce a double-stranded nucleic acid of 19-23 nucleotides in
length that reduces target gene expression.
110. The isolated nucleic acid duplex of claim 66, wherein a
nucleotide of said second or first oligonucleotide strand of any of
said first, second or third regions is substituted with a modified
nucleotide that directs the orientation of Dicer cleavage.
111. The isolated nucleic acid duplex of claim 66 comprising a
phosphate backbone modification selected from the group consisting
of a phosphonate, a phosphorothioate and a phosphotriester.
112. The isolated nucleic acid duplex of claim 66, wherein at least
50% of said ribonucleotide residues of positions 1 to 23 of said
first oligonucleotide strand that base pair with ribonucleotides of
said second oligonucleotide strand to form a duplex are unmodified
ribonucleotides.
113. The isolated nucleic acid duplex of claim 66, wherein at least
50% of all ribonucleotides of said nucleic acid duplex are
unmodified ribonucleotides.
114. The isolated nucleic acid duplex of claim 66, wherein the
first and second oligonucleotide strands of said third region are
joined by a chemical linker.
115. The isolated nucleic acid duplex of claim 114, wherein said 3'
terminus of said first oligonucleotide strand of said third region
and said 5' terminus of said second oligonucleotide strand of said
third region are joined by a chemical linker.
116. The isolated nucleic acid duplex of claim 66, wherein
positions 24 and greater of said first oligonucleotide strand of
said first region comprise between one and 12 deoxyribonucleotide
residues, wherein each of said deoxynucleotide residues of said
first oligonucleotide strand of said first region base pairs with a
deoxyribonucleotide of said second oligonucleotide strand of said
first region to form a duplex.
117. The isolated nucleic acid duplex of claim 66, wherein the
first oligonucleotide strand of said first or third regions has a
nucleotide sequence that is at least 60%, 70%, 80%, 90%, 95% or
100% complementary to the second oligonucleotide strand nucleotide
sequence of said respective first or third regions.
118. The isolated nucleic acid duplex of any of claims 1 or 66,
wherein said isolated nucleic acid duplex is at least 50% more
effective at target gene inhibition in a mammalian cell contacted
with a fixed concentration of said nucleic acid duplex than a
corresponding bifunctional siRNA agent at the same
concentration.
119. The isolated nucleic acid duplex of any of claims 1 or 66,
wherein said isolated nucleic acid duplex possesses a duration of
target gene inhibition in a mammalian cell contacted with a fixed
concentration of said nucleic acid duplex that is at least 25%
longer than a corresponding bifunctional siRNA agent at the same
concentration.
120. A method for reducing expression of a first target gene and a
second target gene in a cell, comprising: contacting a cell with an
isolated nucleic acid duplex as claimed in any one of claims 1 or
66 in an amount effective to reduce expression of a first target
gene and a second target gene in a cell more than two unattached
reference dsRNAs.
121. A method for reducing expression of a first target gene and a
second target gene in an animal, comprising: administering to an
animal an isolated nucleic acid duplex as claimed in any one of
claims 1 or 66 in an amount effective to reduce expression of a
first target gene and a second target gene in a cell of the animal
more than two unattached reference dsRNAs.
122. A pharmaceutical composition for reducing expression of a
first target gene and a second target gene in a cell of a subject
comprising an isolated nucleic acid duplex as claimed in any one of
claims 1 or 66 in an amount effective to reduce expression of a
first target gene and a second target gene in a cell, and a
pharmaceutically acceptable carrier.
123. A pharmaceutical composition for reducing expression of a
first target gene and a second target gene in a cell of a subject
comprising an isolated nucleic acid duplex as claimed in any one of
claims 1 or 66 in an amount effective to reduce expression of a
first target gene and a second target gene in a cell more than two
unattached reference dsRNAs, and a pharmaceutically acceptable
carrier.
124. An isolated nucleic acid duplex comprising: a first region
comprising first and second oligonucleotide strands comprising
ribonucleotides, said first strand having a 5' terminus and said
second strand having a 3' terminus, wherein the nucleotides of said
first and second oligonucleotide strands form a duplex of between
23 and 30 nucleotides in length; and a second region comprising a
first oligonucleotide strand and a second oligonucleotide strand
comprising a RNA:DNA duplex having a length of DNA sufficient to
activate a detectable amount of RNase H cleavage of said second
region in an RNase H cleavage assay, wherein said second region is
covalently attached to said first region; wherein the 5' terminal
residue of said second oligonucleotide strand or the 3' terminal
residue of said first oligonucleotide strand of said second region
is covalently attached to a functional group.
125. An isolated nucleic acid duplex comprising: a first region
comprising a first oligonucleotide strand comprising
ribonucleotides and having a 5' terminus and a second
oligonucleotide strand comprising ribonucleotides and having a 3'
terminus, wherein the nucleotides of said first and second
oligonucleotide strands form a duplex of between 23 and 30
nucleotides in length; and a second region comprising a RNA:DNA
duplex, wherein said RNA:DNA duplex comprises a first
oligonucleotide strand having a 3' terminus, wherein the most 5'
nucleotide of said first oligonucleotide strand of said second
region is covalently attached to the most 3' nucleotide of said
first oligonucleotide strand of said first region, and a second
oligonucleotide strand having a 5' terminus, wherein the most 3'
nucleotide of said second oligonucleotide strand of said second
region is covalently attached to the most 5' nucleotide of said
second oligonucleotide strand of said first region, wherein said
first oligonucleotide strand of said second region comprises
between four and twenty deoxyribonucleotides that form a RNA:DNA
duplex with ribonucleotides of said second oligonucleotide strand
of said second region, wherein the 5' terminal residue of said
second oligonucleotide strand of said second region is covalently
attached to a functional group.
126. An isolated nucleic acid duplex comprising: a first region
comprising a first oligonucleotide strand comprising
ribonucleotides and having a 5' terminus and a second
oligonucleotide strand comprising ribonucleotides and having a 3'
terminus, wherein the nucleotides of said first and second
oligonucleotide strands form a duplex of between 23 and 30
nucleotides in length; and a second region comprising a RNA:DNA
duplex, wherein said RNA:DNA duplex comprises a first
oligonucleotide strand having a 3' terminus, wherein the most 5'
nucleotide of said first oligonucleotide strand of said second
region is covalently attached to the most 3' nucleotide of said
first oligonucleotide strand of said first region, and a second
oligonucleotide strand having a 5' terminus, wherein the most 3'
nucleotide of said second oligonucleotide strand of said second
region is covalently attached to the most 5' nucleotide of said
second oligonucleotide strand of said first region, wherein said
second oligonucleotide strand of said second region comprises
between four and twenty deoxyribonucleotides that form a RNA:DNA
duplex with ribonucleotides of said first oligonucleotide strand of
said second region, wherein the 3' terminal residue of said first
oligonucleotide strand of said second region is covalently attached
to a functional group.
127. The isolated nucleic acid duplex of claims 124-126, wherein
said second oligonucleotide strand of said first region is
sufficiently complementary to a target RNA along at least 19
nucleotides of said second oligonucleotide strand length to reduce
target gene expression when said nucleic acid duplex is introduced
into a mammalian cell.
128. The isolated nucleic acid duplex of claims 124-126, wherein
said functional group is selected from the group consisting of a
ligand for a cellular receptor, a protein localization sequence, an
antibody; a nucleic acid aptamer, a vitamin or other co-factor, a
polymer, a phospholipid, cholesterol, a polyamine, an intercalator,
a reporter molecule, a polyamine, a polyamide, polyethylene glycol,
polyether, a group that enhances a pharmacodynamic property of a
nucleic acid agent, a group that enhances a pharmacokinetic
property of a nucleic acid agent and an active drug substance.
129. The isolated nucleic acid duplex of claim 128, wherein said
functional group is attached to said second region by a linking
moiety.
130. The isolated nucleic acid duplex of claim 129, wherein said
linking moiety is selected from the group consisting of a chemical
linker and an extended loop.
131. The isolated nucleic acid duplex of claims 124-126, wherein
said functional group improves formulation, biodistribution,
adsorption, metabolism, pharmacodynamics or cellular uptake of said
nucleic acid duplex.
132. A method for reducing expression of a target gene in a cell,
comprising: contacting a cell with an isolated nucleic acid duplex
as claimed in any one of claims 1, 6, and 124 in an amount
effective to reduce expression of a target gene in a cell in
comparison to a reference dsRNA.
133. A method for reducing expression of a target gene in an
animal, comprising: administering to an animal an isolated nucleic
acid duplex as claimed in any one of claims 1, 6, and 124 in an
amount effective to reduce expression of a target gene in a cell of
the animal in comparison to a reference dsRNA.
134. A pharmaceutical composition for reducing expression of a
target gene in a cell of a subject comprising an isolated nucleic
acid duplex as claimed in any one of claims 1, 6, and 124 in an
amount effective to reduce expression of a target gene in a cell in
comparison to a reference dsRNA and a pharmaceutically acceptable
carrier.
135. A method of synthesizing an isolated nucleic acid duplex as
claimed in any one of claims 1, 6, and 124, comprising chemically
or enzymatically synthesizing said nucleic acid duplex.
136. A kit comprising the isolated nucleic acid duplex of any one
of claims 1, 6, and 124 and instructions for its use.
Description
RELATED APPLICATIONS
[0001] This present invention is a U.S. Utility patent application
which claims the benefit of U.S. provisional patent application
61/151,841, filed on Feb. 11, 2009, the entirety of which is herein
incorporated by reference.
BACKGROUND OF THE INVENTION
[0002] It has recently been discovered that dsRNA agents possessing
strand lengths longer than 21-23 nucleotide siRNAs--specifically
dsRNA agents wherein each strand is of 25 to 30, or even 35
nucleotides in length--are surprisingly effective at reducing
target gene expression in mammalian cells (Rossi et al., U.S.
Patent Application Nos. 2005/0244858 and US 2005/0277610). Such
Dicer substrate siRNA ("DsiRNA") agents have been shown to possess
enhanced potency as compared to 21-23 nucleotide siRNAs directed at
the same target, e.g., DsiRNAs have been shown to be active at
concentrations less than 1 nM. Certain preferred structures for
DsiRNA agents have recently been described (Rossi et al., U.S.
Patent Application No. 2007/0265220).
[0003] While the synthesis and use of combination RNAi therapies
has been previously described (see, e.g., WO 2005/076999), such
combination RNAi therapies have largely described co-delivered,
unlinked RNAi agents. Indeed, in view of the immune responses
associated with administration of longer dsRNAs (Stark et al., 1998
Annu Rev Biochem 67:227-264), the skilled artisan would generally
not view a combination RNAi therapy composition comprising multiple
RNAi agents that are joined by double-stranded nucleotides as an
attractive therapeutic agent.
[0004] A tandem siRNA agent (within which each siRNA moiety is of
19 nucleotides in length) featuring an RNA:DNA linker sequence was
recently disclosed (Aygun and Feinstein, U.S. Patent Application
No. 2008/0293655). However, while inhibitory activity was reported
for such an agent, the inhibitory efficacy observed for such a
tandem siRNA agent against its best-inhibited target RNA was less
than 60% at a concentration of 10 nanomolar and less than 80% at a
concentration of 20 nanomolar, respectively. Such efficacy was
lower than what is commonly observed for unlinked siRNA agents.
[0005] At least in view of the above, a need exists for combination
RNAi therapy agents that possess enhanced efficacy and duration of
effect relative to previously described tandem siRNA agents.
BRIEF SUMMARY OF THE INVENTION
[0006] The present invention is based, at least in part, upon the
insight that compound DsiRNA agents can be generated using RNase
H-cleavable double stranded nucleic acid regions to attach, e.g.,
one DsiRNA moiety to another DsiRNA moiety and/or one DsiRNA moiety
to a functional group and/or payload. Because such double stranded
nucleic acid joining sequences are RNase H-cleavable, the
detrimental impact of administering a single double stranded
nucleic acid RNAi agent of longer than 30-35 nucleotides in length
(e.g., provocation of interferon response) can be minimized, as
once administered or delivered to a subject or RNase H-containing
cell, RNase H cleavage produces a shortened, active DsiRNA
agent(s).
[0007] The instant invention is also based, at least in part, upon
the insight that effective compound DsiRNA agents can be generated
using double stranded DNA:DNA extension regions, or even a single
stranded DNA region, to attach one DsiRNA moiety to another DsiRNA
moiety.
[0008] In one aspect, the invention provides an isolated nucleic
acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 3' terminus, where the nucleotides of the first and
second oligonucleotide strands form a duplex of between 23 and 35
ribonucleotides in length; a second region possessing a first
oligonucleotide strand and a second oligonucleotide strand having a
RNA:DNA duplex having a length of DNA sufficient to activate a
detectable amount of RNase H cleavage of the second region in an
RNase H cleavage assay, where the second region is covalently
attached to the first region by an attachment that is either a
covalent bond connecting the most 5' nucleotide of the first strand
of the second region to the most 3' nucleotide of the first strand
of the first region or a covalent bond connecting the most 3'
nucleotide of the second oligonucleotide strand of the second
region to the most 5' nucleotide of the second oligonucleotide
strand of the first region, or both; and a third region possessing
a first oligonucleotide strand possessing ribonucleotides and
having a 3' terminus and a second oligonucleotide strand possessing
ribonucleotides and having a 5' terminus, where the third region is
covalently attached to the second region by an attachment that is
either a covalent bond connecting the most 5' nucleotide of the
first strand of the third region to the most 3' nucleotide of the
first strand of the second region or a covalent bond connecting the
most 3' nucleotide of the second oligonucleotide strand of the
third region to the most 5' nucleotide of the second
oligonucleotide strand of the second region, or both, where the
nucleotides of the first and second oligonucleotide strands of the
third region form a duplex of between 23 and 35 ribonucleotides in
length.
[0009] In another aspect, the invention provides an isolated
nucleic acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 3' terminus, where the nucleotides of the first and
second oligonucleotide strands form a duplex of between 23 and 35
ribonucleotides in length; a second region possessing a first
oligonucleotide strand and a second oligonucleotide strand having a
RNA:DNA duplex having a length of DNA sufficient to activate a
detectable amount of RNase H cleavage of the second region in an
RNase H cleavage assay, where the first oligonucleotide strand of
the second region has deoxyribonucleotides and a 3' terminus and
the most 5' nucleotide of the first oligonucleotide strand of the
second region is covalently attached to the most 3' nucleotide of
the first oligonucleotide strand of the first region and the most
3' nucleotide of the second oligonucleotide strand of the second
region is covalently attached to the most 5' nucleotide of the
second oligonucleotide strand of the first region; and a third
region possessing a first oligonucleotide strand having
ribonucleotides and having a 5' terminus and a 3' terminus, where
the 5' terminus of the first oligonucleotide strand of the third
region is located immediately adjacent to the 3' terminus of the
first oligonucleotide strand of the second region, and a second
oligonucleotide strand having ribonucleotides and having a 5'
terminus, where the most 3' nucleotide of the second
oligonucleotide strand of the third region is covalently attached
to the most 5' residue of the second oligonucleotide strand of the
second region, where the nucleotides of the first and second
oligonucleotide strands of the third region form a duplex of
between 23 and 35 ribonucleotides in length.
[0010] In an additional aspect, the invention provides an isolated
nucleic acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 3' terminus, where the nucleotides of the first and
second oligonucleotide strands form a duplex of between 23 and 35
ribonucleotides in length; a second region possessing a first
oligonucleotide strand and a second oligonucleotide strand having a
RNA:DNA duplex having a length of DNA sufficient to activate a
detectable amount of RNase H cleavage of the second region in an
RNase H cleavage assay, where the most 5' nucleotide of the first
oligonucleotide strand of the second region is covalently attached
to the most 3' nucleotide of the first oligonucleotide strand of
the first region and the most 3' nucleotide of the second
oligonucleotide strand of the second region is covalently attached
to the most 5' nucleotide of the second oligonucleotide strand of
the first region and where the second oligonucleotide strand of the
second region has deoxyribonucleotides and a 5' terminus; and a
third region possessing a first oligonucleotide strand having
ribonucleotides and having a 3' terminus, where the most 5'
nucleotide of the first oligonucleotide strand of the third region
is covalently attached to the most 3' residue of the first
oligonucleotide strand of the second region, and a second
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a 3' terminus, where the 3' terminus of the second
oligonucleotide strand of the third region is located immediately
adjacent to the 5' terminus of the second oligonucleotide strand of
the second region, where the nucleotides of the first and second
oligonucleotide strands of the third region form a duplex of
between 23 and 35 ribonucleotides in length.
[0011] In another aspect, the invention provides an isolated
nucleic acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a 3' terminus and a second oligonucleotide strand
having ribonucleotides and having a 3' terminus, where the
nucleotides of the first and second oligonucleotide strands form a
duplex of between 23 and 30 nucleotides in length; a second region
possessing a RNA:DNA duplex having a length of DNA sufficient to
activate a detectable amount of RNase H cleavage of the second
region in an RNase H cleavage assay, where the RNA:DNA duplex has a
first oligonucleotide strand having deoxyribonucleotides and a 5'
terminus, where the 5' terminus of the first oligonucleotide strand
of the second region is located immediately adjacent to the 3'
terminus of the first oligonucleotide strand of the first region,
and a second oligonucleotide strand, where the most 3' nucleotide
of the second oligonucleotide strand of the second region is
covalently attached to the most 5' nucleotide of the second
oligonucleotide strand of the first region; and a third region
possessing a first oligonucleotide strand having ribonucleotides
and having a 3' terminus, where the most 5' nucleotide of the first
oligonucleotide strand of the third region is covalently attached
to the most 3' nucleotide of the first oligonucleotide strand of
the second region, and a second oligonucleotide strand having
ribonucleotides and having a 5' terminus, where the most 3'
nucleotide of the second oligonucleotide strand of the third region
is covalently attached to the most 5' residue of the second
oligonucleotide strand of the second region, where the nucleotides
of the first and second oligonucleotide strands of the third region
form a duplex of between 23 and 30 ribonucleotides in length.
[0012] In a further aspect, the invention provides an isolated
nucleic acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 5' terminus and a 3' terminus, where the nucleotides
of the first and second oligonucleotide strands form a duplex of
between 23 and 30 nucleotides in length; a second region possessing
a RNA:DNA duplex having a length of DNA sufficient to activate a
detectable amount of RNase H cleavage of the second region in an
RNase H cleavage assay, where the RNA:DNA duplex has a first
oligonucleotide strand, where the most 5' nucleotide of the first
oligonucleotide strand of the second region is covalently attached
to the most 3' nucleotide of the first oligonucleotide strand of
the first region, and a second oligonucleotide strand having
deoxyribonucleotides and a 3' terminus, where the 3' terminus of
the second oligonucleotide strand of the second region is located
immediately adjacent to but is not covalently attached to the 5'
terminus of the second oligonucleotide strand of the first region;
and a third region possessing a first oligonucleotide strand having
ribonucleotides and having a 3' terminus, where the most 3'
nucleotide of the first oligonucleotide strand of the second region
is covalently attached to the most 5' nucleotide of the first
oligonucleotide strand of the third region, and a second
oligonucleotide strand having ribonucleotides and having a 5'
terminus, where the most 3' nucleotide of the second
oligonucleotide strand of the third region is covalently attached
to the most 5' residue of the second oligonucleotide strand of the
second region, where the nucleotides of the first and second
oligonucleotide strands of the third region form a duplex of
between 23 and 30 ribonucleotides in length.
[0013] In an additional aspect, the invention provides an isolated
nucleic acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 3' terminus, where the nucleotides of the first and
second oligonucleotide strands form a duplex of between 25 and 35
nucleotides in length; a second region possessing a first
oligonucleotide strand and a second oligonucleotide strand having a
RNA:DNA duplex having a length of DNA sufficient to activate a
detectable amount of RNase H cleavage of the second region in an
RNase H cleavage assay, where the second region is covalently
attached to the first region by an attachment that is either a
covalent bond connecting the most 5' nucleotide of the first strand
of the second region to the most 3' nucleotide of the first strand
of the first region or a covalent bond connecting the most 3'
nucleotide of the second oligonucleotide strand of the second
region to the most 5' nucleotide of the second oligonucleotide
strand of the first region, or both; and a third region possessing
a first oligonucleotide strand having ribonucleotides and having a
3' terminus and a second oligonucleotide strand having
ribonucleotides and having a 5' terminus, where the third region is
covalently attached to the second region by an attachment that is
either a covalent bond connecting the most 5' nucleotide of the
first strand of the third region to the most 3' nucleotide of the
first strand of the second region or a covalent bond connecting the
most 3' nucleotide of the second oligonucleotide strand of the
third region to the most 5' nucleotide of the second
oligonucleotide strand of the second region, or both, where the
nucleotides of the first and second oligonucleotide strands of the
third region form a duplex of between 23 and 35 ribonucleotides in
length.
[0014] In one embodiment, the RNase H cleavage assay is an in vitro
RNase H cleavage assay. In another embodiment, the RNase H cleavage
assay is a mammalian cell RNase H cleavage assay.
[0015] In an additional embodiment, the first oligonucleotide
strand of the second region has between four and twenty
deoxyribonucleotides that base pair with ribonucleotides of the
second oligonucleotide strand of the second region to form an
RNA:DNA duplex.
[0016] Another aspect of the invention provides an isolated nucleic
acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 3' terminus, where the nucleotides of the first and
second oligonucleotide strands form a duplex of between 23 and 35
nucleotides in length; a second region possessing a RNA:DNA duplex,
where the RNA:DNA duplex has a first oligonucleotide strand having
a 3' terminus, where the most 5' nucleotide of the first
oligonucleotide strand of the second region is covalently attached
to the most 3' nucleotide of the first oligonucleotide strand of
the first region, and a second oligonucleotide strand, where the
most 3' nucleotide of the second oligonucleotide strand of the
second region is covalently attached to the most 5' nucleotide of
the second oligonucleotide strand of the first region, where the
first oligonucleotide strand of the second region has between four
and forty deoxyribonucleotides that form a RNA:DNA duplex with
ribonucleotides of the second oligonucleotide strand of the second
region; and a third region possessing a first oligonucleotide
strand having ribonucleotides and having a 5' terminus and a 3'
terminus, where the 5' terminus of the first oligonucleotide strand
of the third region is located immediately adjacent to the 3'
terminus of the first oligonucleotide strand of the second region,
and a second oligonucleotide strand having ribonucleotides and
having a 5' terminus, where the most 3' nucleotide of the second
oligonucleotide strand of the third region is covalently attached
to the most 5' residue of the second oligonucleotide strand of the
second region, where the nucleotides of the first and second
oligonucleotide strands of the third region form a duplex of
between 23 and 35 ribonucleotides in length.
[0017] An additional aspect of the invention provides an isolated
nucleic acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 3' terminus, where the nucleotides of the first and
second oligonucleotide strands form a duplex of between 23 and 35
nucleotides in length; a second region possessing a RNA:DNA duplex,
where the RNA:DNA duplex has a first oligonucleotide strand, where
the most 5' nucleotide of the first oligonucleotide strand of the
second region is covalently attached to the most 3' nucleotide of
the first oligonucleotide strand of the first region, and a second
oligonucleotide strand having a 5' terminus, where the most 3'
nucleotide of the second oligonucleotide strand of the second
region is covalently attached to the most 5' nucleotide of the
second oligonucleotide strand of the first region, where the second
oligonucleotide strand of the second region has between four and
twenty deoxyribonucleotides that form a RNA:DNA duplex with
ribonucleotides of the first oligonucleotide strand of the second
region; and a third region possessing a first oligonucleotide
strand having ribonucleotides and having a 3' terminus, where the
most 5' nucleotide of the first oligonucleotide strand of the third
region is covalently attached to the most 3' residue of the first
oligonucleotide strand of the second region, and a second
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a 3' terminus, where the 3' terminus of the second
oligonucleotide strand of the third region is located immediately
adjacent to the 5' terminus of the second oligonucleotide strand of
the second region, where the nucleotides of the first and second
oligonucleotide strands of the third region form a duplex of
between 23 and 35 ribonucleotides in length.
[0018] A further aspect of the invention provides an isolated
nucleic acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a 3' terminus and a second oligonucleotide strand
having ribonucleotides and having a 3' terminus, where the
nucleotides of the first and second oligonucleotide strands form a
duplex of between 23 and 35 nucleotides in length; a second region
possessing a RNA:DNA duplex, where the RNA:DNA duplex has a first
oligonucleotide strand having a 5' terminus, where the 5' terminus
of the first oligonucleotide strand of the second region is located
immediately adjacent to the 3' terminus of the first
oligonucleotide strand of the first region, and a second
oligonucleotide strand, where the most 3' nucleotide of the second
oligonucleotide strand of the second region is covalently attached
to the most 5' nucleotide of the second oligonucleotide strand of
the first region, where the first oligonucleotide strand of the
second region has between four and twenty deoxyribonucleotides that
base pair with ribonucleotides of the second oligonucleotide strand
of the second region to form an RNA:DNA duplex; and a third region
possessing a first oligonucleotide strand having ribonucleotides
and having a 3' terminus, where the most 5' nucleotide of the first
oligonucleotide strand of the third region is covalently attached
to the most 3' nucleotide of the first oligonucleotide strand of
the second region, and a second oligonucleotide strand having
ribonucleotides and having a 5' terminus, where the most 3'
nucleotide of the second oligonucleotide strand of the third region
is covalently attached to the most 5' residue of the second
oligonucleotide strand of the second region, where the nucleotides
of the first and second oligonucleotide strands of the third region
form a duplex of between 23 and 35 ribonucleotides in length.
[0019] Another aspect of the invention provides an isolated nucleic
acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 5' terminus and a 3' terminus, where the nucleotides
of the first and second oligonucleotide strands form a duplex of
between 23 and 35 nucleotides in length; a second region possessing
a RNA:DNA duplex, where the RNA:DNA duplex has a first
oligonucleotide strand, where the most 5' nucleotide of the first
oligonucleotide strand of the second region is covalently attached
to the most 3' nucleotide of the first oligonucleotide strand of
the first region, and a second oligonucleotide strand having a 3'
terminus, where the 3' terminus of the second oligonucleotide
strand of the second region is located immediately adjacent to but
is not covalently attached to the 5' terminus of the second
oligonucleotide strand of the first region, where the second
oligonucleotide strand of the second region has between four and
twenty deoxyribonucleotides that form a RNA:DNA duplex with
ribonucleotides of the first oligonucleotide strand of the second
region; and a third region possessing a first oligonucleotide
strand having ribonucleotides and having a 3' terminus, where the
most 3' nucleotide of the first oligonucleotide strand of the
second region is covalently attached to the most 5' nucleotide of
the first oligonucleotide strand of the third region, and a second
oligonucleotide strand having ribonucleotides and having a 5'
terminus, where the most 3' nucleotide of the second
oligonucleotide strand of the third region is covalently attached
to the most 5' residue of the second oligonucleotide strand of the
second region, where the nucleotides of the first and second
oligonucleotide strands of the third region form a duplex of
between 23 and 35 ribonucleotides in length.
[0020] In one embodiment, the first region possesses a duplex of at
least 25 nucleotides in length. In another embodiment, the third
region possesses a duplex of at least 25 nucleotides in length. In
an additional embodiment, the second oligonucleotide strand of the
first region is sufficiently complementary to a first target RNA
along at least 19 nucleotides of the second oligonucleotide strand
length to reduce target gene expression when the nucleic acid
duplex is introduced into a mammalian cell. In another embodiment,
the first or second strand of the third region is sufficiently
complementary to a second target RNA along at least 19 nucleotides
of the second oligonucleotide strand length to reduce target gene
expression when the nucleic acid duplex is introduced into a
mammalian cell.
[0021] In one embodiment, the first target RNA or the second target
RNA is K-RAS, HPRT1, VEGF, VEGFR, EGF, EGFR or an HCV target RNA
sequence. Optionally, both the first and second target RNAs are
K-RAS, HPRT1, VEGF, VEGFR, EGF, EGFR or an HCV target RNA sequence.
In a related embodiment, paired target RNAs of the first and second
regions are HPRT1 and K-RAS; VEGF and VEGFR; or EGF and EGFR.
[0022] In another embodiment, the nucleic acid duplex reduces
target gene expression (of either the first target RNA, the second
target RNA, or both) in a mammalian cell in vitro by an amount
(expressed by %) of at least 10%, at least 50% or at least
80-90%.
[0023] In one embodiment, the second oligonucleotide strand of the
first region possesses a 3' overhang of 1-4 nucleotides in length.
In another embodiment, the first oligonucleotide strand of the
third region possesses a 3' overhang of 1-4 nucleotides in length.
In an additional embodiment the 3' overhang is 1-3 nucleotides in
length, or, optionally, 1-2 nucleotides in length. In a related
embodiment, the nucleotides of the 3' overhang comprise a modified
nucleotide. Optionally, the modified nucleotide residue is
2'-O-methyl, 2'-methoxyethoxy, 2'-fluoro, 2'-allyl,
2'-O-[2-(methylamino)-2-oxoethyl], 4'-thio, 4'-CH2-O-2'-bridge,
4'-(CH2)2-O-2'-bridge, 2'-LNA, 2'-amino or
2'-O-(N-methlycarbamate). In another embodiment, all nucleotides of
the 3' overhang are modified nucleotides. In an additional
embodiment, the 3' overhang is two nucleotides in length and the
modified nucleotide is a 2'-O-methyl modified ribonucleotide.
[0024] In one embodiment, the second oligonucleotide strand of the
first region, starting from the nucleotide residue of the second
oligonucleotide strand of the first region that is complementary to
the 5' terminal nucleotide residue of the first oligonucleotide
strand of the first region, has unmodified nucleotide residues at
all positions from position 20 to the most 5' residue of the second
oligonucleotide strand of the first region. In another embodiment,
the first oligonucleotide strand of the third region, starting from
the nucleotide residue of the first oligonucleotide strand of the
third region that is complementary to the 5' terminal nucleotide
residue of the second oligonucleotide strand of the third region,
has unmodified nucleotide residues at all positions from position
20 to the most 5' residue of the first oligonucleotide strand of
the third region. In an additional embodiment, the second
oligonucleotide strand of the first region has modified nucleotides
at positions 1, 2, and 3 from the 3' terminus of the second
oligonucleotide strand of the first region. In another embodiment,
the first oligonucleotide strand of the third region has modified
nucleotides at positions 1, 2, and 3 from the 3' terminus of the
first oligonucleotide strand of the third region.
[0025] In an additional embodiment, at least the two most 3'
nucleotide residues of the first oligonucleotide strand of the
first region are deoxyribonucleotides that base pair with two
deoxyribonucleotides of the second oligonucleotide strand of the
first region. In a further embodiment, at least the two most 5'
nucleotide residues of the first oligonucleotide strand of the
third region are deoxyribonucleotides that base pair with two
deoxyribonucleotides of the second oligonucleotide strand of the
third region. In another embodiment, the two most 3' nucleotide
residues of the second oligonucleotide strand of the second region
are modified ribonucleotides.
[0026] In one embodiment, the two most 5' nucleotide residues of
the second oligonucleotide strand of the second region are modified
ribonucleotides. In an additional embodiment, the second
oligonucleotide strand of the third region, starting from the most
3' nucleotide residue of the second oligonucleotide strand of the
third region, has alternating modified and unmodified nucleotide
residues. In another embodiment, the two most 5' nucleotide
residues of the first oligonucleotide strand of the second region
are modified ribonucleotides. In an additional embodiment, the two
most 3' nucleotide residues of the first oligonucleotide strand of
the second region are modified ribonucleotides. In another
embodiment, the first oligonucleotide strand of the third region,
starting from the 3' terminus of the first oligonucleotide strand
of the third region, has alternating modified and unmodified
nucleotide residues.
[0027] In one embodiment, the 3' terminus of the first
oligonucleotide strand of the third region and the 5' terminus of
the second oligonucleotide strand of the third region form a blunt
end. In an additional embodiment, at least one of positions 1, 2 or
3 from the 3' terminus of the 3' terminus of the first
oligonucleotide strand of the third region is a
deoxyribonucleotide. In another embodiment, the deoxynucleotide
residues of the second region that comprise the RNA:DNA duplex are
unmodified deoxyribonucleotides.
[0028] In a further embodiment, at least 50% of all
deoxyribonucleotides of the nucleic acid duplex are unmodified
deoxyribonucleotides. In one embodiment, the first oligonucleotide
strand of the third region is attached to the second
oligonucleotide strand of the third region by a nucleotide
sequence, where the nucleotide sequence attaches the most 3'
nucleotide of the first oligonucleotide strand of the third region
that base pairs with a nucleotide of the second oligonucleotide
strand of the third region to the second oligonucleotide strand
nucleotide of the third region that base pairs with the most 3'
nucleotide of the first oligonucleotide strand of the third region.
In another embodiment, the nucleotide sequence that attaches the
first oligonucleotide strand of the third region and the second
oligonucleotide strand of the third region has a tetraloop. In an
additional embodiment, the nucleotide sequence that attaches the
first oligonucleotide strand of the third region and the second
oligonucleotide strand of the third region includes a hairpin, a
chemical linker or an extended loop.
[0029] In one embodiment, one or both of the first and second
oligonucleotide strands of any of the first, second or third
regions has a 5' phosphate. In another embodiment, the nucleic acid
duplex is cleaved endogenously in a mammalian cell by RNase H. In a
further embodiment, the endogenous RNase H cleavage generates a
nucleic acid duplex that is cleaved endogenously in the mammalian
cell by Dicer. In another embodiment, the endogenous RNase H
cleavage generates two nucleic acid duplexes that are each cleaved
endogenously in the mammalian cell by Dicer.
[0030] In an additional embodiment, the nucleic acid duplex is
cleaved endogenously in a mammalian cell by Dicer. In one
embodiment, the nucleic acid duplex is cleaved endogenously in a
mammalian cell to produce a double-stranded nucleic acid of 19-23
nucleotides in length that reduces target gene expression.
[0031] In another embodiment, a nucleotide of the second or first
oligonucleotide strand of any of the first, second or third regions
is substituted with a modified nucleotide that directs the
orientation of Dicer cleavage.
[0032] In a further embodiment, the isolated nucleic acid duplex
has a phosphate backbone modification that is a phosphonate, a
phosphorothioate or a phosphotriester.
[0033] In one embodiment, at least 50% of the ribonucleotide
residues of positions 1 to 23 of the first oligonucleotide strand
that base pair with ribonucleotides of the second oligonucleotide
strand to form a duplex are unmodified ribonucleotides. In another
embodiment, at least 50% of all ribonucleotides of the nucleic acid
duplex are unmodified ribonucleotides.
[0034] In a further embodiment, the first and second
oligonucleotide strands of the third region are joined by a
chemical linker. In another embodiment, the 3' terminus of the
first oligonucleotide strand of the third region and the 5'
terminus of the second oligonucleotide strand of the third region
are joined by a chemical linker.
[0035] In one embodiment, positions 24 and greater of the first
oligonucleotide strand of the first region comprise between one and
12 deoxyribonucleotide residues, where each of the deoxynucleotide
residues of the first oligonucleotide strand of the first region
base pairs with a deoxyribonucleotide of the second oligonucleotide
strand of the first region to form a duplex.
[0036] In another embodiment, the first oligonucleotide strand of
the first or third regions has a nucleotide sequence that is at
least 60%, 70%, 80%, 90%, 95% or 100% complementary to the second
oligonucleotide strand nucleotide sequence of the respective first
or third regions.
[0037] Another aspect of the invention provides an isolated nucleic
acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 3' terminus, where the nucleotides of the first and
second oligonucleotide strands form a duplex of between 23 and 35
ribonucleotides in length; a second region possessing a first
oligonucleotide strand and a second oligonucleotide strand having a
DNA:DNA duplex having a length of DNA between two and forty base
pairs, where the second region is covalently attached to the first
region by an attachment that is either a covalent bond connecting
the most 5' nucleotide of the first strand of the second region to
the most 3' nucleotide of the first strand of the first region or a
covalent bond connecting the most 3' nucleotide of the second
oligonucleotide strand of the second region to the most 5'
nucleotide of the second oligonucleotide strand of the first
region, or both; and a third region possessing a first
oligonucleotide strand having ribonucleotides and having a 3'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 5' terminus, where the third region is covalently
attached to the second region by an attachment that is either a
covalent bond connecting the most 5' nucleotide of the first strand
of the third region to the most 3' nucleotide of the first strand
of the second region or a covalent bond connecting the most 3'
nucleotide of the second oligonucleotide strand of the third region
to the most 5' nucleotide of the second oligonucleotide strand of
the second region, or both, where the nucleotides of the first and
second oligonucleotide strands of the third region form a duplex of
between 23 and 35 ribonucleotides in length.
[0038] In one embodiment, the first region includes a duplex of at
least 25 nucleotides in length. In another embodiment, the first
region includes a duplex of between 26 and 35 nucleotides in
length. In an additional embodiment, the first region includes a
duplex of between 26 and 30 nucleotides in length. In a further
embodiment, the third region includes a duplex of at least 25
nucleotides in length. In another embodiment, the third region
includes a duplex of between 26 and 35 nucleotides in length. In
one embodiment, the third region includes a duplex of between 26
and 30 nucleotides in length.
[0039] In an additional embodiment, the second oligonucleotide
strand of the first region is sufficiently complementary to a first
target RNA along at least 19 nucleotides of the second
oligonucleotide strand length to reduce target gene expression when
the nucleic acid duplex is introduced into a mammalian cell. In a
further embodiment, the second oligonucleotide strand of the third
region is sufficiently complementary to a second target RNA along
at least 19 nucleotides of the second oligonucleotide strand length
to reduce target gene expression when the nucleic acid duplex is
introduced into a mammalian cell.
[0040] In another embodiment, the first oligonucleotide strand of
the third region is sufficiently complementary to a second target
RNA along at least 19 nucleotides of the first oligonucleotide
strand length to reduce target gene expression when the nucleic
acid duplex is introduced into a mammalian cell. In an additional
embodiment, the second oligonucleotide strand of the first region
possesses a 3' overhang of 1-4 nucleotides in length. In another
embodiment, the first oligonucleotide strand of the third region
possesses a 3' overhang of 1-4 nucleotides in length. In one
embodiment, the 3' overhang is 1-3 nucleotides in length. In
another embodiment, the 3' overhang is 1-2 nucleotides in
length.
[0041] In an additional embodiment, the nucleotides of the 3'
overhang comprise a modified nucleotide. In another embodiment, the
modified nucleotide of the 3' overhang is a 2'-O-methyl
ribonucleotide.
[0042] In a further embodiment, all nucleotides of the 3' overhang
are modified nucleotides. In an additional embodiment, the 3'
overhang is two nucleotides in length and where the modified
nucleotide of the 3' overhang is a 2'-O-methyl modified
ribonucleotide.
[0043] In a further embodiment, the second oligonucleotide strand
of the first region, starting from the nucleotide residue of the
second oligonucleotide strand of the first region that is
complementary to the 5' terminal nucleotide residue of the first
oligonucleotide strand of the first region, has unmodified
nucleotide residues at all positions from position 20 to the most
5' residue of the second oligonucleotide strand of the first
region. In another embodiment, the first oligonucleotide strand of
the third region, starting from the nucleotide residue of the first
oligonucleotide strand of the third region that is complementary to
the 5' terminal nucleotide residue of the second oligonucleotide
strand of the third region, has unmodified nucleotide residues at
all positions from position 20 to the most 5' residue of the first
oligonucleotide strand of the third region.
[0044] In one embodiment, the second oligonucleotide strand of the
first region has modified nucleotides at positions 1, 2, and 3 from
the 3' terminus of the second oligonucleotide strand of the first
region. In an additional embodiment, the first oligonucleotide
strand of the third region has modified nucleotides at positions 1,
2, and 3 from the 3' terminus of the first oligonucleotide strand
of the third region. In another embodiment, at least the two most
3' nucleotide residues of the first oligonucleotide strand of the
first region are deoxyribonucleotides that base pair with two
deoxyribonucleotides of the second oligonucleotide strand of the
first region.
[0045] In one embodiment, at least the two most 5' nucleotide
residues of the first oligonucleotide strand of the third region
are deoxyribonucleotides that base pair with two
deoxyribonucleotides of the second oligonucleotide strand of the
third region. In an additional embodiment, the two most 3'
nucleotide residues of the second oligonucleotide strand of the
second region are modified ribonucleotides. In a further
embodiment, the two most 5' nucleotide residues of the second
oligonucleotide strand of the second region are modified
ribonucleotides.
[0046] In another embodiment, the second oligonucleotide strand of
the third region, starting from the most 3' nucleotide residue of
the second oligonucleotide strand of the third region, has
alternating modified and unmodified nucleotide residues.
[0047] In one embodiment, the 3' terminus of the first
oligonucleotide strand of the third region and the 5' terminus of
the second oligonucleotide strand of the third region form a blunt
end. In another embodiment, at least one of positions 1, 2 or 3
from the 3' terminus of the 3' terminus of the first
oligonucleotide strand of the third region is a
deoxyribonucleotide.
[0048] In an additional embodiment, the deoxynucleotide residues of
the second region that comprise the DNA:DNA duplex are unmodified
deoxyribonucleotides.
[0049] In a further embodiment, at least 50% of all
deoxyribonucleotides of the nucleic acid duplex are unmodified
deoxyribonucleotides. In an additional embodiment, the first
oligonucleotide strand of the third region is attached to the
second oligonucleotide strand of the third region by a nucleotide
sequence, where the nucleotide sequence attaches the most 3'
nucleotide of the first oligonucleotide strand of the third region
that base pairs with a nucleotide of the second oligonucleotide
strand of the third region to the second oligonucleotide strand
nucleotide of the third region that base pairs with the most 3'
nucleotide of the first oligonucleotide strand of the third
region.
[0050] In one embodiment, the nucleotide sequence that attaches the
first oligonucleotide strand of the third region and the second
oligonucleotide strand of the third region has a tetraloop. In
another embodiment, the nucleotide sequence that attaches the first
oligonucleotide strand of the third region and the second
oligonucleotide strand of the third region has a hairpin, a
chemical linker or an extended loop.
[0051] In an additional embodiment, one or both of the first and
second oligonucleotide strands of any of the first, second or third
regions has a 5' phosphate.
[0052] In another embodiment, the nucleic acid duplex is cleaved
endogenously in a mammalian cell by Dicer. In a related embodiment,
the nucleic acid duplex is cleaved twice endogenously in a
mammalian cell by Dicer.
[0053] In a further embodiment, the nucleic acid duplex is cleaved
endogenously in a mammalian cell to produce a double-stranded
nucleic acid of 19-23 nucleotides in length that reduces target
gene expression. In an additional embodiment, a nucleotide of the
second or first oligonucleotide strand of any of the first, second
or third regions is substituted with a modified nucleotide that
directs the orientation of Dicer cleavage.
[0054] In another embodiment, at least 50% of the ribonucleotide
residues of positions 1 to 23 of the first oligonucleotide strand
that base pair with ribonucleotides of the second oligonucleotide
strand to form a duplex are unmodified ribonucleotides. In a
further embodiment, at least 50% of all ribonucleotides of the
nucleic acid duplex are unmodified ribonucleotides.
[0055] In an additional embodiment, the first and second
oligonucleotide strands of the third region are joined by a
chemical linker. In a related embodiment, the 3' terminus of the
first oligonucleotide strand of the third region and the 5'
terminus of the second oligonucleotide strand of the third region
are joined by a chemical linker.
[0056] In an additional embodiment, positions 24 and greater of the
first oligonucleotide strand of the first region comprise between
one and 12 deoxyribonucleotide residues, where each of the
deoxynucleotide residues of the first oligonucleotide strand of the
first region base pairs with a deoxyribonucleotide of the second
oligonucleotide strand of the first region to form a duplex.
[0057] In one embodiment, the first oligonucleotide strand of the
first or third regions has a nucleotide sequence that is at least
60%, 70%, 80%, 90%, 95% or 100% complementary to the second
oligonucleotide strand nucleotide sequence of the respective first
or third regions.
[0058] In another embodiment, the isolated nucleic acid duplex is
at least 50% more effective at target gene inhibition in a
mammalian cell contacted with a fixed concentration of the nucleic
acid duplex than a corresponding bifunctional siRNA agent (e.g., a
bifunctional agent having two 19-21mer siRNAs linked via a RNase H
cleavable sequence) at the same concentration. In a further
embodiment, the isolated nucleic acid duplex possesses a duration
of target gene inhibition in a mammalian cell contacted with a
fixed concentration of the nucleic acid duplex that is at least 25%
longer than a corresponding bifunctional siRNA agent at the same
concentration.
[0059] A further aspect of the invention provides a method for
reducing expression of a first target gene and a second target gene
in a cell, by contacting a cell with an isolated nucleic acid
duplex of the invention in an amount effective to reduce expression
of a first target gene and a second target gene in a cell more than
two unattached reference dsRNAs (optionally, 19-21mer siRNAs).
[0060] Another aspect of the invention provides a method for
reducing expression of a first target gene and a second target gene
in an animal, involving administering to an animal an isolated
nucleic acid duplex of the invention in an amount effective to
reduce expression of a first target gene and a second target gene
in a cell of the animal more than two unattached reference
dsRNAs.
[0061] In an additional aspect, the invention provides a
pharmaceutical composition for reducing expression of a first
target gene and a second target gene in a cell of a subject
including an isolated nucleic acid duplex of the invention in an
amount effective to reduce expression of a first target gene and a
second target gene in a cell, and a pharmaceutically acceptable
carrier.
[0062] Another aspect of the invention provides a pharmaceutical
composition for reducing expression of a first target gene and a
second target gene in a cell of a subject that includes an isolated
nucleic acid duplex of the invention in an amount effective to
reduce expression of a first target gene and a second target gene
in a cell more than two unattached reference dsRNAs (optionally,
19-21mer siRNAs), and a pharmaceutically acceptable carrier.
[0063] A further aspect of the invention provides an isolated
nucleic acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 3' terminus, where the nucleotides of the first and
second oligonucleotide strands form a duplex of between 23 and 30
nucleotides in length; and a second region possessing a first
oligonucleotide strand and a second oligonucleotide strand having a
RNA:DNA duplex having a length of DNA sufficient to activate a
detectable amount of RNase H cleavage of the second region in an
RNase H cleavage assay, where the second region is covalently
attached to the first region by an attachment that is either a
covalent bond connecting the most 5' nucleotide of the first strand
of the second region to the most 3' nucleotide of the first strand
of the first region or a covalent bond connecting the most 3'
nucleotide of the second oligonucleotide strand of the second
region to the most 5' nucleotide of the second oligonucleotide
strand of the first region, or both, where the 5' terminal residue
of the second oligonucleotide strand or the 3' terminal residue of
the first oligonucleotide strand of the second region is covalently
attached to a functional group.
[0064] An additional aspect of the invention provides an isolated
nucleic acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 3' terminus, where the nucleotides of the first and
second oligonucleotide strands form a duplex of between 23 and 30
nucleotides in length; and a second region possessing a RNA:DNA
duplex, where the RNA:DNA duplex has a first oligonucleotide strand
having a 3' terminus, where the most 5' nucleotide of the first
oligonucleotide strand of the second region is covalently attached
to the most 3' nucleotide of the first oligonucleotide strand of
the first region, and a second oligonucleotide strand having a 5'
terminus, where the most 3' nucleotide of the second
oligonucleotide strand of the second region is covalently attached
to the most 5' nucleotide of the second oligonucleotide strand of
the first region, where the first oligonucleotide strand of the
second region has between four and twenty deoxyribonucleotides that
form a RNA:DNA duplex with ribonucleotides of the second
oligonucleotide strand of the second region, where the 5' terminal
residue of the second oligonucleotide strand of the second region
is covalently attached to a functional group.
[0065] Another aspect of the invention provides an isolated nucleic
acid duplex having a first region possessing a first
oligonucleotide strand having ribonucleotides and having a 5'
terminus and a second oligonucleotide strand having ribonucleotides
and having a 3' terminus, where the nucleotides of the first and
second oligonucleotide strands form a duplex of between 23 and 30
nucleotides in length; and a second region possessing a RNA:DNA
duplex, where the RNA:DNA duplex has a first oligonucleotide strand
having a 3' terminus, where the most 5' nucleotide of the first
oligonucleotide strand of the second region is covalently attached
to the most 3' nucleotide of the first oligonucleotide strand of
the first region, and a second oligonucleotide strand having a 5'
terminus, where the most 3' nucleotide of the second
oligonucleotide strand of the second region is covalently attached
to the most 5' nucleotide of the second oligonucleotide strand of
the first region, where the second oligonucleotide strand of the
second region has between four and forty deoxyribonucleotides that
form a RNA:DNA duplex with ribonucleotides of the first
oligonucleotide strand of the second region, where the 3' terminal
residue of the first oligonucleotide strand of the second region is
covalently attached to a functional group.
[0066] In one embodiment, the second oligonucleotide strand of the
first region is sufficiently complementary to a target RNA along at
least 19 nucleotides of the second oligonucleotide strand length to
reduce target gene expression when the nucleic acid duplex is
introduced into a mammalian cell.
[0067] In another embodiment, the functional group is a ligand for
a cellular receptor, a protein localization sequence, an antibody;
a nucleic acid aptamer, a vitamin or other co-factor, a polymer, a
phospholipid, cholesterol, a polyamine, an intercalator, a reporter
molecule, a polyamine, a polyamide, polyethylene glycol, polyether,
a group that enhances a pharmacodynamic property of a nucleic acid
agent, a group that enhances a pharmacokinetic property of a
nucleic acid agent or an active drug substance. In an additional
embodiment, the functional group is attached to the second region
by a linking moiety. In another embodiment, the functional group
improves formulation, biodistribution, adsorption, metabolism,
pharmacodynamics or cellular uptake of the nucleic acid duplex.
[0068] A further aspect of the invention provides a method for
reducing expression of a target gene in a cell by contacting a cell
with an isolated nucleic acid duplex of the invention in an amount
effective to reduce expression of a target gene in a cell in
comparison to a reference dsRNA.
[0069] An additional aspect of the invention provides a method for
reducing expression of a target gene in an animal, involving
administering to an animal an isolated nucleic acid duplex of the
invention in an amount effective to reduce expression of a target
gene in a cell of the animal in comparison to a reference
dsRNA.
[0070] In another aspect, the invention provides a pharmaceutical
composition for reducing expression of a target gene in a cell of a
subject that includes an isolated nucleic acid duplex of the
invention in an amount effective to reduce expression of a target
gene in a cell in comparison to a reference dsRNA, and a
pharmaceutically acceptable carrier.
[0071] In an additional aspect, the invention provides a method of
synthesizing an isolated nucleic acid duplex of the invention by
chemically or enzymatically synthesizing the nucleic acid
duplex.
[0072] In a further aspect, the invention provides a kit having an
isolated nucleic acid duplex of the invention, with instructions
for its use.
BRIEF DESCRIPTION OF THE DRAWINGS
[0073] FIG. 1 shows the structure of an exemplary bifunctional
DsiRNA agent of the invention, with the two DsiRNA agents that may
be liberated via RNase H cleavage oriented in tandem within the
uncleaved bifunctional DsiRNA agent shown.
[0074] FIG. 2 shows the structure of an exemplary bifunctional
DsiRNA agent of the invention, with the two DsiRNA agents that may
be liberated via RNase H cleavage oriented in opposite directions
to one another within the uncleaved bifunctional DsiRNA agent
shown.
[0075] FIG. 3 shows the structure of an exemplary RNase H-cleavable
agent designed to release both a DsiRNA agent and a functional
group upon RNase H cleavage.
[0076] FIG. 4 shows a bifunctional DsiRNA agent having two DsiRNA
agents directed to independent RNA targets that are joined by a
tract of double stranded DNA. Such agents are not reliant upon
RNase H for cleavage, but instead rely upon Dicer cleavage to
produce effective inhibitory products.
DETAILED DESCRIPTION
[0077] The invention provides compositions and methods for reducing
expression of one or more target genes in a cell, involving
contacting a cell with an isolated double stranded nucleic acid
double stranded nucleic acid in an amount effective to reduce
expression of one or more target genes in a cell. In certain
embodiments, the double stranded nucleic acids of the invention
comprise RNase H-cleavable double stranded nucleic acid regions,
which are employed to attach DsiRNA agents to one another within
one compound (precursor) agent (termed a "bifunctional DsiRNA"
herein). Alternatively, such RNase H-cleavable double stranded
nucleic acid double stranded nucleic acid regions are used to
attach a DsiRNA agent to a functional group (e.g., a functional
group of any type suitable to improve a desired property of DsiRNA
in vivo, such as improvement of formulation, biodistribution,
adsorption, metabolism, pharmacodynamics, cellular uptake, etc.;
such agents are also referred to herein as "functional
group-tethered DsiRNA agents"). In additional embodiments, DsiRNA
moieties can also be joined by a double stranded DNA joining
sequence, which allows for construction of another form of
bifunctional DsiRNA of the instant invention that is not reliant
upon/does not provoke RNase H-mediated cleavage.
DEFINITIONS
[0078] Unless defined otherwise, all technical and scientific terms
used herein have the meaning commonly understood by a person
skilled in the art to which this invention belongs. The following
references provide one of skill with a general definition of many
of the terms used in this invention: Singleton et al., Dictionary
of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge
Dictionary of Science and Technology (Walker ed., 1988); The
Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer
Verlag (1991); and Hale & Marham, The Harper Collins Dictionary
of Biology (1991). As used herein, the following terms have the
meanings ascribed to them below, unless specified otherwise.
[0079] As used herein, the term "nucleic acid" refers to
deoxyribonucleotides, ribonucleotides, or modified nucleotides, and
polymers thereof in single- or double-stranded form. The term
encompasses nucleic acids containing known nucleotide analogs or
modified backbone residues or linkages, which are synthetic,
naturally occurring, and non-naturally occurring, which have
similar binding properties as the reference nucleic acid, and which
are metabolized in a manner similar to the reference nucleotides.
Examples of such analogs include, without limitation,
phosphorothioates, phosphoramidates, methyl phosphonates,
chiral-methyl phosphonates, 2-O-methyl ribonucleotides,
peptide-nucleic acids (PNAs).
[0080] As used herein, "nucleotide" is used as recognized in the
art to include those with natural bases (standard), and modified
bases well known in the art. Such bases are generally located at
the 1' position of a nucleotide sugar moiety. Nucleotides generally
comprise a base, sugar and a phosphate group. The nucleotides can
be unmodified or modified at the sugar, phosphate and/or base
moiety, (also referred to interchangeably as nucleotide analogs,
modified nucleotides, non-natural nucleotides, non-standard
nucleotides and other; see, e.g., Usman and McSwiggen, supra;
Eckstein, et al., International PCT Publication No. WO 92/07065;
Usman et al, International PCT Publication No. WO 93/15187; Uhlman
& Peyman, supra, all are hereby incorporated by reference
herein). There are several examples of modified nucleic acid bases
known in the art as summarized by Limbach, et al, Nucleic Acids
Res. 22:2183, 1994. Some of the non-limiting examples of base
modifications that can be introduced into nucleic acid molecules
include, hypoxanthine, purine, pyridin-4-one, pyridin-2-one,
phenyl, pseudouracil, 2,4,6-trimethoxy benzene, 3-methyl uracil,
dihydrouridine, naphthyl, aminophenyl, 5-alkylcytidines (e.g.,
5-methylcytidine), 5-alkyluridines (e.g., ribothymidine),
5-halouridine (e.g., 5-bromouridine) or 6-azapyrimidines or
6-alkylpyrimidines (e.g. 6-methyluridine), propyne, and others
(Burgin, et al., Biochemistry 35:14090, 1996; Uhlman & Peyman,
supra). By "modified bases" in this aspect is meant nucleotide
bases other than adenine, guanine, cytosine and uracil at 1'
position or their equivalents.
[0081] As used herein, a "double-stranded nucleic acid" is a
molecule comprising two oligonucleotide strands which form a
duplex. A double stranded nucleic acid may contain ribonucleotides,
deoxyribonucleotides, modified nucleotides, and combinations
thereof. The double-stranded NAs of the instant invention are
substrates for proteins and protein complexes in the RNA
interference pathway, e.g., Dicer and RISC. Structures of double
stranded nucleic acids of the invention are shown in FIG. 1, and
characteristically comprise an RNA duplex in a region that is
capable of functioning as a Dicer substrate siRNA (DsiRNA) and a
DNA duplex comprising at least one deoxyribonucleotide, which is
located at a position 3' of the projected Dicer cleavage site of
the first strand of the DsiRNA/DNA agent, base paired with a
cognate deoxyribonucleotide of the second strand, which is located
at a position 5' of the projected Dicer cleavage site of the second
strand of the DsiRNA/DNA agent.
[0082] As used herein, "duplex" refers to a double helical
structure formed by the interaction of two single stranded nucleic
acids. According to the present invention, a duplex may contain
first and second strands which are sense and antisense, or which
are target and antisense. A duplex is typically formed by the
pairwise hydrogen bonding of bases, i.e., "base pairing", between
two single stranded nucleic acids which are oriented antiparallel
with respect to each other. Base pairing in duplexes generally
occurs by Watson-Crick base pairing, e.g., guanine (G) forms a base
pair with cytosine (C) in DNA and RNA (thus, the cognate nucleotide
of a guanine deoxyribonucleotide is a cytosine deoxyribonucleotide,
and vice versa), adenine (A) forms a base pair with thymine (T) in
DNA, and adenine (A) forms a base pair with uracil (U) in RNA.
Conditions under which base pairs can form include physiological or
biologically relevant conditions (e.g., intracellular: pH 7.2, 140
mM potassium ion; extracellular pH 7.4, 145 mM sodium ion).
Furthermore, duplexes are stabilized by stacking interactions
between adjacent nucleotides. As used herein, a duplex may be
established or maintained by base pairing or by stacking
interactions. A duplex is formed by two complementary nucleic acid
strands, which may be substantially complementary or fully
complementary (see below).
[0083] By "complementary" or "complementarity" is meant that a
nucleic acid can form hydrogen bond(s) with another nucleic acid
sequence by either traditional Watson-Crick or Hoogsteen base
pairing. In reference to the nucleic acid molecules of the present
disclosure, the binding free energy for a nucleic acid molecule
with its complementary sequence is sufficient to allow the relevant
function of the nucleic acid to proceed, e.g., RNAi activity.
Determination of binding free energies for nucleic acid molecules
is well known in the art (see, e.g., Turner, et al., CSH Symp.
Quant. Biol. LII, pp. 123-133, 1987; Frier, et al., Proc. Nat.
Acad. Sci. USA 83:9373-9377, 1986; Turner, et al., J. Am. Chem.
Soc. 109:3783-3785, 1987). A percent complementarity indicates the
percentage of contiguous residues in a nucleic acid molecule that
can form hydrogen bonds (e.g., Watson-Crick base pairing) with a
second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, or 10
nucleotides out of a total of 10 nucleotides in the first
oligonucleotide being based paired to a second nucleic acid
sequence having 10 nucleotides represents 50%, 60%, 70%, 80%, 90%,
and 100% complementary, respectively). To determine that a percent
complementarity is of at least a certain percentage, the percentage
of contiguous residues in a nucleic acid molecule that can form
hydrogen bonds (e.g., Watson-Crick base pairing) with a second
nucleic acid sequence is calculated and rounded to the nearest
whole number (e.g., 12, 13, 14, 15, 16, or 17 nucleotides out of a
total of 23 nucleotides in the first oligonucleotide being based
paired to a second nucleic acid sequence having 23 nucleotides
represents 52%, 57%, 61%, 65%, 70%, and 74%, respectively; and has
at least 50%, 50%, 60%, 60%, 70%, and 70% complementarity,
respectively). As used herein, "substantially complementary" refers
to complementarity between the strands such that they are capable
of hybridizing under biological conditions. Substantially
complementary sequences have 60%, 70%, 80%, 90%, 95%, or even 100%
complementarity. Additionally, techniques to determine if two
strands are capable of hybridizing under biological conditions by
examining their nucleotide sequences are well known in the art.
[0084] Single-stranded nucleic acids that base pair over a number
of bases are said to "hybridize." Hybridization is typically
determined under physiological or biologically relevant conditions
(e.g., intracellular: pH 7.2, 140 mM potassium ion; extracellular
pH 7.4, 145 mM sodium ion). Hybridization conditions generally
contain a monovalent cation and biologically acceptable buffer and
may or may not contain a divalent cation, complex anions, e.g.
gluconate from potassium gluconate, uncharged species such as
sucrose, and inert polymers to reduce the activity of water in the
sample, e.g. PEG. Such conditions include conditions under which
base pairs can form.
[0085] Hybridization is measured by the temperature required to
dissociate single stranded nucleic acids forming a duplex, i.e.,
(the melting temperature; Tm). Hybridization conditions are also
conditions under which base pairs can form. Various conditions of
stringency can be used to determine hybridization (see, e.g., Wahl,
G. M. and S. L. Berger (1987) Methods Enzymol. 152:399; Kimmel, A.
R. (1987) Methods Enzymol. 152:507). Stringent temperature
conditions will ordinarily include temperatures of at least about
30.degree. C., more preferably of at least about 37.degree. C., and
most preferably of at least about 42.degree. C. The hybridization
temperature for hybrids anticipated to be less than 50 base pairs
in length should be 5-10.degree. C. less than the melting
temperature (Tm) of the hybrid, where Tm is determined according to
the following equations. For hybrids less than 18 base pairs in
length, Tm(.degree. C.)=2(# of A+T bases)+4(# of G+C bases). For
hybrids between 18 and 49 base pairs in length, Tm(.degree.
C.)=81.5+16.6(log 10[Na+])+0.41 (% G+C)-(600/N), where N is the
number of bases in the hybrid, and [Na+] is the concentration of
sodium ions in the hybridization buffer ([Na+] for
1.times.SSC=0.165 M). For example, a hybridization determination
buffer is shown in Table 1.
TABLE-US-00001 TABLE 1 To make 50 final conc. Vender Cat# Lot#
m.w./Stock ml solution NaCl 100 mM Sigma S-5150 41K8934 5M 1 mL KCl
80 mM Sigma P-9541 70K0002 74.55 0.298 g MgCl.sub.2 8 mM Sigma
M-1028 120K8933 1M 0.4 mL sucrose 2% w/v Fisher BP220-212 907105
342.3 1 g Tris-HCl 16 mM Fisher BP1757-500 12419 1M 0.8 mL
NaH.sub.2PO.sub.4 1 mM Sigma S-3193 52H-029515 120.0 0.006 g EDTA
0.02 mM Sigma E-7889 110K89271 0.5M 2 .mu.L H.sub.2O Sigma W4502
51K2359 to 50 mL pH = 7.0 adjust with at 20.degree. C. HCl
[0086] Useful variations on hybridization conditions will be
readily apparent to those skilled in the art. Hybridization
techniques are well known to those skilled in the art and are
described, for example, in Benton and Davis (Science 196:180,
1977); Grunstein and Hogness (Proc. Natl. Acad. Sci., USA 72:3961,
1975); Ausubel et al. (Current Protocols in Molecular Biology,
Wiley Interscience, New York, 2001); Berger and Kimmel (Antisense
to Molecular Cloning Techniques, 1987, Academic Press, New York);
and Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold
Spring Harbor Laboratory Press, New York.
[0087] As used herein, "oligonucleotide strand" is a single
stranded nucleic acid molecule. An oligonucleotide may comprise
ribonucleotides, deoxyribonucleotides, modified nucleotides (e.g.,
nucleotides with 2' modifications, synthetic base analogs, etc.) or
combinations thereof. Such modified oligonucleotides can be
preferred over native forms because of properties such as, for
example, enhanced cellular uptake and increased stability in the
presence of nucleases.
[0088] Certain nucleic acid duplex agents of this invention are
chimeric double stranded nucleic acids. "Chimeric double stranded
nucleic acids" or "chimeras", in the context of this invention, are
double stranded nucleic acids which contain two or more chemically
distinct regions, each made up of at least one nucleotide. These
double stranded nucleic acids typically contain at least one region
primarily comprising ribonucleotides (optionally including modified
ribonucleotides) that form a Dicer substrate siRNA ("DsiRNA")
molecule. This DsiRNA region is covalently attached (at one or both
strands) to a second region comprising a RNA:DNA duplex that forms
an RNase H substrate. This RNA:DNA duplex region is, in turn,
covalently attached to a third region comprising a DsiRNA moiety,
or is covalently attached to a moiety comprising a functional
group. Any of the above-described chimeric double stranded nucleic
acid regions may also include modified or synthetic nucleotides
and/or modified or synthetic deoxyribonucleotides.
[0089] As used herein, the term "ribonucleotide" encompasses
natural and synthetic, unmodified and modified ribonucleotides.
Modifications include changes to the sugar moiety, to the base
moiety and/or to the linkages between ribonucleotides in the
oligonucleotide. As used herein, the term "ribonucleotide"
specifically excludes a deoxyribonucleotide, which is a nucleotide
possessing a single proton group at the 2' ribose ring
position.
[0090] As used herein, the term "deoxyribonucleotide" encompasses
natural and synthetic, unmodified and modified
deoxyribonucleotides. Modifications include changes to the sugar
moiety, to the base moiety and/or to the linkages between
deoxyribonucleotide in the oligonucleotide.
[0091] As used herein, the term "RNAse H" refers to an enzyme that
cleaves RNA that is part of a RNA:DNA heteroduplex. Incorporation
of one or more DNA residues within a first strand of a duplex RNA
agent allows the oligoribonucleotide region of a second strand,
within the oligoribonucleotide region that anneals to the one or
more DNA residues of the first strand to be cleaved at the
hybridized RNA residues. In certain non-mammalian animals, some
RNAse H enzymes require only one ribonucleotide in an
oligonucleotide as substrate. However, mammalian RNase H enzymes
require a segment of at lease four ribonucleotides. RNAse H
activity can be found in some polymerases, including reverse
transcriptase. RNAse H can also be a separate enzyme. Suitable
RNAse H enzymes include human and E. coli RNAse Hs. The human RNase
H family includes the following: RNase H1 (GenBank Accession No.
NM.sub.--002936.3); RNase H2A (GenBank Accession No.
NM.sub.--006397.2); RNase H.sub.2B (GenBank Accession No.
NM.sub.--024570.1); and RNase H.sub.2C (GenBank Accession No.
NM.sub.--032193.3). RNase H activity is also observed in human EXO1
(GenBank Accession Nos. NM.sub.--130398.2, NM.sub.--006027.3 and
NM.sub.--003686.3 isoforms). An additional RNAse H that can be used
is Thermus thermophilus, or Tth, RNAse H.
[0092] RNase H cleavage of an agent of the instant invention can be
assessed by any art-recognized method. Exemplary methods for
detecting RNase H cleavage of a candidate substrate (e.g., where
the RNase H substrate is a DsiRNA agent joined to a region
comprising a DNA:RNA duplex sequence) include, e.g., detection of
RNase H cleavage product(s) based upon the appearance of
appropriately-sized bands on a gel (e.g., gel
electrophoresis/electrophoretic mobility test and, if necessary,
associated nucleic acid hybridization techniques known in the art).
In addition, RNase H cleavage products also can be assessed via
performance of mass spectroscopy (e.g., time of flight) upon a
candidate substrate solution that has been exposed to RNase H
(e.g., cleavage products derived from mammalian cell culture or
lysate, and/or cleavage products found in an appropriate in vitro
assay for RNase H cleavage.
[0093] In certain embodiments, the detectability of an RNase H
cleavage product in a solution is assessed. The lower limit at
which an RNase H cleavage product becomes detectable is likely to
depend upon the nature of the RNase H cleavage assay employed
(e.g., mass spectroscopy approaches will tend to detect cleavage
product at a lower threshold than gel electrophoresis methods). The
skilled artisan will recognize how to set appropriate limits in
performing such assays to classify a product as detectable or not
detectable. In certain embodiments, e.g., a cleavage product is
considered detectable if at least 1% of input agent is cleaved in a
given time (e.g., 30 minute treatment) at a given concentration of
RNase H enzyme (e.g., 1 unit/mL). In related embodiments, at least
2%, at least 3%, at least 4%, at least 5%, at least 10%, at least
20%, at least 30%, at least 40%, at least 50%, at least 60%, at
least 70%, at least 80%, or even at least 90% of input agent must
yield an appropriate cleavage product for the product to be
considered detectable or for the input agent to be classified as an
RNase H cleavable agent.
[0094] RNase H hydrolyzes RNA in RNA-DNA hybrids. This enzyme was
first identified in calf thymus but has subsequently been described
in a variety of organisms (Stein, H. and Hausen, P., Science, 1969,
166, 393-395; Hausen, P. and Stein, H., Eur. J. Biochem., 1970, 14,
278-283). RNase H activity appears to be ubiquitous in eukaryotes
and bacteria (Itaya, M. and Kondo K. Nucleic Acids Res., 1991, 19,
4443-4449; Itaya et al., Mol. Gen. Genet., 1991 227, 438-445;
Kanaya, S., and Itaya, M., J. Biol. Chem., 1992, 267, 10184-10192;
Busen, W., J. Biol. Chem., 1980, 255, 9434-9443; Rong, Y. W. and
Carl, P. L., 1990, Biochemistry 29, 383-389; Eder et al.,
Biochimie, 1993 75, 123-126). Although RNase Hs constitute a family
of proteins of varying molecular weight, nucleolytic activity and
substrate requirements appear to be similar for the various
isotypes. For example, all RNase Hs studied to date function as
endonucleases, exhibiting limited sequence specificity and
requiring divalent cations (e.g., Mg.sup.2+, Mn.sup.2+) to produce
cleavage products with 5' phosphate and 3' hydroxyl termini
(Crouch, R. J., and Dirksen, M. L., Nuclease, Linn, S, M., &
Roberts, R. J., Eds., Cold Spring Harbor Laboratory Press,
Plainview, N.Y. 1982, 211-241).
[0095] To evaluate the binding affinity (and specificity) of a
human RNase H1 for a substrate, a competitive cleavage assay in
which increasing concentrations of noncleavable substrates are
added can also be used. Using this approach, the Ki is formally
equivalent to the Kd for the competing substrates. Such assays have
been described in greater detail, e.g., in U.S. Application No.
2007/0292875.
[0096] As used herein, the term "functional group" refers to a
moiety that improves any desired property of a DsiRNA-containing
agent in vivo. Such properties include, but are not limited to,
improvement of formulation, biodistribution, adsorption,
metabolism, pharmacodynamics, and cellular uptake. In certain
embodiments, such a "functional group" is selected from the
following: ligands for cellular receptors, such as peptides derived
from naturally occurring protein ligands; protein localization
sequences, including cellular ZIP code sequences; antibodies;
nucleic acid aptamers; vitamins and other co-factors, such as
folate and N-acetylgalactosamine; polymers, such as
polyethyleneglycol (PEG); phospholipids; cholesterol; polyamines,
such as spermine or spermidine; intercalators; reporter molecules;
polyamines; polyamides; polyethylene glycols; polyethers; groups
that enhance the pharmaco-dynamic properties of nucleic acid
agents, such as cholesterols, lipids, phospholipids, biotin,
phenazine, folate, phenanthridine, anthraquinone, acridine,
fluoresceins, rhodamines, coumarins and dyes; groups that enhance
the pharmacodynamic properties, such as groups that improve uptake,
enhance resistance to degradation, enhance RISC residency and/or
strengthen sequence-specific hybridization with the target nucleic
acid; groups that enhance the pharmacokinetic properties, such as
groups that improve uptake, distribution, metabolism or excretion
of the compounds of the present invention. Functional group
moieties include but are not limited to lipid moieties such as a
cholesterol moiety, cholic acid, a thioether, e.g.,
hexyl-S-tritylthiol, a thiocholesterol, an aliphatic chain, e.g.,
dodecandiol or undecyl residues, a phospholipid, e.g.,
di-hexadecyl-rac-glycerol or triethylammonium
1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a polyamine or a
polyethylene glycol chain, or adamantane acetic acid, a palmityl
moiety, or an octadecylamine or hexylamino-carbonyl-oxycholesterol
moiety. Nucleic acid agents of the invention may also be attached
to active drug substances, for example, aspirin, warfarin,
phenylbutazone, ibuprofen, suprofen, fenbufen, ketoprofen,
(S)-(+)-pranoprofen, carprofen, dansylsarcosine,
2,3,5-triiodobenzoic acid, flufenamic acid, folinic acid, a
benzothiadiazide, chlorothiazide, a diazepine, indomethicin, a
barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an
antibacterial or an antibiotic.
[0097] In certain embodiments, a nucleic acid duplex of the
invention comprises at least one duplex region of at least 23
nucleotides in length, within which at least 50% of all nucleotides
are unmodified ribonucleotides. As used herein, the term
"unmodified ribonucleotide" refers to a ribonucleotide possessing a
hydroxyl (--OH) group at the 2' position of the ribose sugar.
[0098] In certain embodiments, a nucleic acid duplex of the
invention comprises at least one region, located 3' of the
projected Dicer cleavage site on the first strand and 5' of the
projected Dicer cleavage site on the second strand, having a length
of at least 4 base paired nucleotides that form an RNA:DNA duplex,
wherein at least 50% of all deoxynucleotides within this region of
at least 4 base paired nucleotides in length are unmodified
deoxyribonucleotides. As used herein, the term "unmodified
deoxyribonucleotide" refers to a ribonucleotide possessing a single
proton at the 2' position of the ribose sugar.
[0099] As used herein, "antisense strand" refers to a single
stranded nucleic acid molecule which has a sequence complementary
to that of a target RNA. When the antisense strand contains
modified nucleotides with base analogs, it is not necessarily
complementary over its entire length, but must at least duplex with
a target RNA.
[0100] As used herein, "sense strand" refers to a single stranded
nucleic acid molecule which has a sequence complementary to that of
an antisense strand. When the antisense strand contains modified
nucleotides with base analogs, the sense strand need not be
complementary over the entire length of the antisense strand, but
must at least duplex with the antisense strand.
[0101] As used herein, "guide strand" refers to a single stranded
nucleic acid molecule of a dsRNA, which has a sequence
complementary to that of a target RNA, and results in RNA
interference by binding to a target RNA. After cleavage of the
dsRNA by Dicer, a fragment of the guide strand remains associated
with RISC, binds a target RNA as a component of the RISC complex,
and promotes cleavage of a target RNA by RISC. As used herein, the
guide strand does not necessarily refer to a continuous single
stranded nucleic acid and may comprise a discontinuity (e.g., a
"nick" referring to the absence of solely a single phosphodiester
bond between adjacent nucleotides, a "gap" referring to the absence
of at least one internal nucleotide from a length of duplex
sequence), preferably at a site that is cleaved by Dicer. A guide
strand is an antisense strand.
[0102] As used herein, "target RNA" refers to an RNA that would be
subject to modulation guided by the antisense strand, such as
targeted cleavage or steric blockage. The target RNA could be, for
example genomic viral RNA, mRNA, a pre-mRNA, or a non-coding RNA.
The preferred target is mRNA, such as the mRNA encoding a disease
associated protein, such as ApoB, Bcl2, Hif-1alpha, Survivin or a
p21 ras, such as Ha. ras, K-ras or N-ras.
[0103] As used herein, "passenger strand" refers to an
oligonucleotide strand of a dsRNA, which has a sequence that is
complementary to that of the guide strand. As used herein, the
passenger strand does not necessarily refer to a continuous single
stranded nucleic acid and may comprise a discontinuity (e.g., a
"nick" referring to the absence of solely a single phosphodiester
bond between adjacent nucleotides, a "gap" referring to the absence
of at least one internal nucleotide from a length of duplex
sequence), preferably at a site that is cleaved by Dicer. A
passenger strand is a sense strand.
[0104] As used herein, "Dicer" refers to an endoribonuclease in the
RNase III family that cleaves a dsRNA, e.g., double-stranded RNA
(dsRNA) or pre-microRNA (miRNA), into double-stranded nucleic acid
fragments about 20-25 nucleotides long, usually with a two-base
overhang on the 3' end. With respect to the dsRNAs of the
invention, the duplex formed by a dsRNA is recognized by Dicer and
is a Dicer substrate on at least one strand of the duplex. Dicer
catalyzes the first step in the RNA interference pathway, which
consequently results in the degradation of a target RNA. The
protein sequence of human Dicer is provided at the NCBI database
under accession number NP.sub.--085124, hereby incorporated by
reference.
[0105] Dicer "cleavage" is determined as follows (e.g., see
Collingwood et al., Oligonucleotides 18:187-200 (2008)). In a Dicer
cleavage assay, RNA duplexes (100 .mu.mol) are incubated in 20
.mu.L of 20 mM Tris pH 8.0, 200 mM NaCl, 2.5 mM MgCl2 with or
without 1 unit of recombinant human Dicer (Genlantis, San Diego,
Calif.) at 37.degree. C. for 18-24 hours. Samples are desalted
using a Performa SR 96-well plate (Edge Biosystems, Gaithersburg,
Md.). Electrospray-ionization liquid chromatography mass
spectroscopy (ESI-LCMS) of duplex RNAs pre- and post-treatment with
Dicer is done using an Oligo HTCS system (Novatia, Princeton, N.J.;
Hail et al., 2004), which consists of a ThermoFinnigan TSQ7000,
Xcalibur data system, ProMass data processing software and Paradigm
MS4 HPLC (Michrom BioResources, Auburn, Calif.). In this assay,
Dicer cleavage occurs where at least 5%, 10%, 20%, 30%, 40%, 50%,
60%, 70%, 80%, 90%, 95%, or even 100% of the Dicer substrate dsRNA,
(i.e., 25-30 bp, dsRNA, preferably 26-30 by dsRNA) is cleaved to a
shorter dsRNA (e.g., 19-23 by dsRNA, preferably, 21-23 by dsRNA).
The orientation of Dicer cleavage may also be determined in such an
assay, or can be determined via evaluation of the functional
efficacy of resultant RNAi agents post-Dicer cleavage. In a
scenario in which Dicer exhibited no end preference, the
orientation of Dicer cleavage of a given agent would be split
equally between the two orientations of a given double-stranded
nucleic acid, e.g., 50% of molecules releasing one orientation of
cleavage product, while 50% of resultant molecules show the
opposite orientation. However, in view of art-recognized end
structures believed to orient Dicer cleavage, one orientation of
DsiRNA cleavage may be favored over another, resulting in, e.g., at
least 60%, at least 70%, at least 80%, at least 90%, at least 95%,
etc. of Dicer-cleaved products resulting from a given DsiRNA being
the cleavage product of a single preferred orientation of DsiRNA
agent, to the corresponding reduction or exclusion of the cleavage
product that would result/results from Dicer cleavage of the input
DsiRNA agent in the opposite orientation. Thus, the orientation of
Dicer cleavage of a given agent can be tested using a functional
(e.g., target RNA inhibition measurement) and/or marker- or
label-based readout, or can be assessed using any other
art-recognized means of such detection (e.g., mass spectroscopy may
also be used to assess the identity of Dicer cleavage
products).
[0106] As used herein, "Dicer cleavage site" refers to the sites at
which Dicer cleaves a dsRNA (e.g., the dsRNA region of a double
stranded nucleic acid of the invention). Dicer contains two RNase
III domains which typically cleave both the sense and antisense
strands of a dsRNA. The average distance between the RNase III
domains and the PAZ domain determines the length of the short
double-stranded nucleic acid fragments it produces and this
distance can vary (Macrae I, et al. (2006). "Structural basis for
double-stranded RNA processing by Dicer". Science 311 (5758):
195-8.). For the RNase H-cleavable double stranded nucleic acid
agents of the invention, the most prominent Dicer cleavage site of
the first DsiRNA agent is generally positioned about 21 nucleotides
from the 5' terminus of the first strand (though certain
modifications of the double stranded nucleic acid are capable of
shifting the location and distribution of Dicer cleavage products
within such first region DsiRNA agent). While dependent upon the
length of this first region DsiRNA, DNA:RNA hybrid sequences of the
double stranded nucleic acid agents of the invention generally
commence at a position between about position 24 and 36 of the
first strand (where position 1 is the 5' terminal residue of the
first strand).
[0107] As used herein, "overhang" refers to unpaired nucleotides,
in the context of a duplex having two or four free ends at either
the 5' terminus or 3' terminus of a dsRNA. In certain embodiments,
the overhang is a 3' or 5' overhang on the antisense strand or
sense strand.
[0108] As used herein, "target" refers to any nucleic acid sequence
whose expression or activity is to be modulated. In particular
embodiments, the target refers to an RNA which duplexes to a single
stranded nucleic acid that is an antisense strand in a RISC
complex. Hybridization of the target RNA to the antisense strand
results in processing by the RISC complex. Consequently, expression
of the RNA or proteins encoded by the RNA, e.g., mRNA, is
reduced.
[0109] As used herein, "reference" is meant a standard or control.
As is apparent to one skilled in the art, an appropriate reference
is where only one element is changed in order to determine the
effect of the one element.
[0110] By the term "antisense agent" is meant a polynucleotide
fragment (comprising either deoxyribonucleotides, ribonucleotides,
synthetic nucleotides or a mixture thereof) having inhibitory
antisense activity, said activity causing a decrease in the
expression of the endogenous genomic copy of the corresponding
gene. The sequence of the antisense agent is designed to complement
a target mRNA of interest and form an RNA:antisense agent duplex.
This duplex formation can prevent processing, splicing, transport
or translation of the relevant mRNA. Moreover, certain antisense
agents can elicit cellular RNase H activity when hybridized with
the target mRNA, resulting in mRNA degradation (Calabretta et al,
1996: Antisense strategies in the treatment of leukemias. Semin
Oncol. 23(1):78-87). In that case, RNase H will cleave the RNA
component of the duplex and can potentially release the antisense
agent to further hybridize with additional molecules of the target
RNA. An additional mode of action results from the interaction of
an antisense agent with genomic DNA to form a triple helix, which
can be transcriptionally inactive.
[0111] As used herein, "modified nucleotide" refers to a nucleotide
that has one or more modifications to the nucleoside, the
nucleobase, pentose ring, or phosphate group. For example, modified
nucleotides exclude ribonucleotides containing adenosine
monophosphate, guanosine monophosphate, uridine monophosphate, and
cytidine monophosphate and deoxyribonucleotides containing
deoxyadenosine monophosphate, deoxyguanosine monophosphate,
deoxythymidine monophosphate, and deoxycytidine monophosphate.
Modifications include those naturally occurring that result from
modification by enzymes that modify nucleotides, such as
methyltransferases. Modified nucleotides also include synthetic or
non-naturally occurring nucleotides. Synthetic or non-naturally
occurring modifications in nucleotides include those with 2'
modifications, e.g., 2'-methoxyethoxy, 2'-fluoro, 2'-allyl,
2'-O-[2-(methylamino)-2-oxoethyl], 4'-thio,
4'-CH.sub.2--O-2'-bridge, 4'-(CH.sub.2).sub.2--O-2'-bridge, 2'-LNA,
and 2'-O--(N-methylcarbamate) or those comprising base analogs. In
connection with 2'-modified nucleotides as described for the
present disclosure, by "amino" is meant 2'--NH.sub.2 or
2'-O--NH.sub.2, which can be modified or unmodified. Such modified
groups are described, e.g., in Eckstein, et al., U.S. Pat. No.
5,672,695 and Matulic-Adamic, et al., U.S. Pat. No. 6,248,878.
[0112] In reference to the nucleic acid molecules of the present
disclosure, the modifications may exist in patterns on a strand of
the double stranded nucleic acid. As used herein, "alternating
positions" refers to a pattern where every other nucleotide is a
modified nucleotide or there is an unmodified nucleotide (e.g., an
unmodified ribonucleotide) between every modified nucleotide over a
defined length of a strand of the dsRNA (e.g., 5'-MNMNMN-3';
3'-MNMNMN-5'; where M is a modified nucleotide and N is an
unmodified nucleotide). The modification pattern starts from the
first nucleotide position at either the 5' or 3' terminus according
to any of the position numbering conventions described herein. The
pattern of modified nucleotides at alternating positions may run
the full length of the strand, but preferably includes at least 4,
6, 8, 10, 12, 14 nucleotides containing at least 2, 3, 4, 5, 6 or 7
modified nucleotides, respectively. As used herein, "alternating
pairs of positions" refers to a pattern where two consecutive
modified nucleotides are separated by two consecutive unmodified
nucleotides over a defined length of a strand of the dsRNA (e.g.,
5'-MMNNMMNNMMNN-3'; 3'-MMNNMMNNMMNN-5'; where M is a modified
nucleotide and N is an unmodified nucleotide). The modification
pattern starts from the first nucleotide position at either the 5'
or 3' terminus according to any of the position numbering
conventions described herein. The pattern of modified nucleotides
at alternating positions may run the full length of the strand, but
preferably includes at least 8, 12, 16, 20, 24, 28 nucleotides
containing at least 4, 6, 8, 10, 12 or 14 modified nucleotides,
respectively.
[0113] As used herein, "base analog" refers to a heterocyclic
moiety which is located at the 1' position of a nucleotide sugar
moiety in a modified nucleotide that can be incorporated into a
nucleic acid duplex (or the equivalent position in a nucleotide
sugar moiety substitution that can be incorporated into a nucleic
acid duplex). In the double stranded nucleic acids of the
invention, a base analog is generally either a purine or pyrimidine
base excluding the common bases guanine (G), cytosine (C), adenine
(A), thymine (T), and uracil (U). Base analogs can duplex with
other bases or base analogs in dsRNAs. Base analogs include those
useful in the compounds and methods of the invention., e.g., those
disclosed in U.S. Pat. Nos. 5,432,272 and 6,001,983 to Benner and
US Patent Publication No. 20080213891 to Manoharan, which are
herein incorporated by reference. Non-limiting examples of bases
include hypoxanthine (I), xanthine (X),
3.beta.-D-ribofuranosyl-(2,6-diaminopyrimidine) (K),
3-.beta.-D-ribofuranosyl-(1-methyl-pyrazolo[4,3-d]pyrimidine-5,7(4H,6H)-d-
ione) (P), iso-cytosine (iso-C), iso-guanine (iso-G),
1-.beta.-D-ribofuranosyl-(5-nitroindole),
1-.beta.-D-ribofuranosyl-(3-nitropyrrole), 5-bromouracil,
2-aminopurine, 4-thio-dT, 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds)
and pyrrole-2-carbaldehyde (Pa), 2-amino-6-(2-thienyl)purine
(S),2-oxopyridine (Y), difluorotolyl,
4-fluoro-6-methylbenzimidazole, 4-methylbenzimidazole, 3-methyl
isocarbostyrilyl, 5-methyl isocarbostyrilyl, and
3-methyl-7-propynyl isocarbostyrilyl, 7-azaindolyl,
6-methyl-7-azaindolyl, imidizopyridinyl, 9-methyl-imidizopyridinyl,
pyrrolopyrizinyl, isocarbostyrilyl, 7-propynyl isocarbostyrilyl,
propynyl-7-azaindolyl, 2,4,5-trimethylphenyl, 4-methylindolyl,
4,6-dimethylindolyl, phenyl, napthalenyl, anthracenyl,
phenanthracenyl, pyrenyl, stilbenzyl, tetracenyl, pentacenyl, and
structural derivates thereof (Schweitzer et al., J. Org. Chem.,
59:7238-7242 (1994); Berger et al., Nucleic Acids Research,
28(15):2911-2914 (2000); Moran et al., J. Am. Chem. Soc.,
119:2056-2057 (1997); Morales et al., J. Am. Chem. Soc.,
121:2323-2324 (1999); Guckian et al., J. Am. Chem. Soc.,
118:8182-8183 (1996); Morales et al., J. Am. Chem. Soc.,
122(6):1001-1007 (2000); McMinn et al., J. Am. Chem. Soc.,
121:11585-11586 (1999); Guckian et al., J. Org. Chem., 63:9652-9656
(1998); Moran et al., Proc. Natl. Acad. Sci., 94:10506-10511
(1997); Das et al., J. Chem. Soc., Perkin Trans., 1:197-206 (2002);
Shibata et al., J. Chem. Soc., Perkin Trans., 1: 1605-1611 (2001);
Wu et al., J. Am. Chem. Soc., 122(32):7621-7632 (2000); O'Neill et
al., J. Org. Chem., 67:5869-5875 (2002); Chaudhuri et al., J. Am.
Chem. Soc., 117:10434-10442 (1995); and U.S. Pat. No. 6,218,108.).
Base analogs may also be a universal base.
[0114] As used herein, "universal base" refers to a heterocyclic
moiety located at the 1' position of a nucleotide sugar moiety in a
modified nucleotide, or the equivalent position in a nucleotide
sugar moiety substitution, that, when present in a nucleic acid
duplex, can be positioned opposite more than one type of base
without altering the double helical structure (e.g., the structure
of the phosphate backbone). Additionally, the universal base does
not destroy the ability of the single stranded nucleic acid in
which it resides to duplex to a target nucleic acid. The ability of
a single stranded nucleic acid containing a universal base to
duplex a target nucleic can be assayed by methods apparent to one
in the art (e.g., UV absorbance, circular dichroism, gel shift,
single stranded nuclease sensitivity, etc.). Additionally,
conditions under which duplex formation is observed may be varied
to determine duplex stability or formation, e.g., temperature, as
melting temperature (Tm) correlates with the stability of nucleic
acid duplexes. Compared to a reference single stranded nucleic acid
that is exactly complementary to a target nucleic acid, the single
stranded nucleic acid containing a universal base forms a duplex
with the target nucleic acid that has a lower Tm than a duplex
formed with the complementary nucleic acid. However, compared to a
reference single stranded nucleic acid in which the universal base
has been replaced with a base to generate a single mismatch, the
single stranded nucleic acid containing the universal base forms a
duplex with the target nucleic acid that has a higher Tm than a
duplex formed with the nucleic acid having the mismatched base.
[0115] Some universal bases are capable of base pairing by forming
hydrogen bonds between the universal base and all of the bases
guanine (G), cytosine (C), adenine (A), thymine (T), and uracil (U)
under base pair forming conditions. A universal base is not a base
that forms a base pair with only one single complementary base. In
a duplex, a universal base may form no hydrogen bonds, one hydrogen
bond, or more than one hydrogen bond with each of G, C, A, T, and U
opposite to it on the opposite strand of a duplex. Preferably, the
universal bases does not interact with the base opposite to it on
the opposite strand of a duplex. In a duplex, base pairing between
a universal base occurs without altering the double helical
structure of the phosphate backbone. A universal base may also
interact with bases in adjacent nucleotides on the same nucleic
acid strand by stacking interactions. Such stacking interactions
stabilize the duplex, especially in situations where the universal
base does not form any hydrogen bonds with the base positioned
opposite to it on the opposite strand of the duplex. Non-limiting
examples of universal-binding nucleotides include inosine,
1-.beta.-D-ribofuranosyl-5-nitroindole, and/or
1-.beta.-D-ribofuranosyl-3-nitropyrrole (US Pat. Appl. Publ. No.
20070254362 to Quay et al.; Van Aerschot et al., An acyclic
5-nitroindazole nucleoside analogue as ambiguous nucleoside.
Nucleic Acids Res. 1995 Nov. 11; 23(21):4363-70; Loakes et al.,
3-Nitropyrrole and 5-nitroindole as universal bases in primers for
DNA sequencing and PCR. Nucleic Acids Res. 1995 Jul. 11;
23(13):2361-6; Loakes and Brown, 5-Nitroindole as an universal base
analogue. Nucleic Acids Res. 1994 Oct. 11; 22(20):4039-43).
[0116] As used herein, "increase" or "enhance" is meant to alter
positively by at least 5% compared to a reference in an assay. An
alteration may be by 5%, 10%, 25%, 30%, 50%, 75%, or even by 100%
compared to a reference in an assay. By "enhance Dicer cleavage,"
it is meant that the processing of a quantity of a dsRNA molecule
by Dicer results in more Dicer cleaved dsRNA products or that Dicer
cleavage reaction occurs more quickly compared to the processing of
the same quantity of a reference dsRNA in an in vivo or in vitro
assay of this disclosure. In one embodiment, enhanced or increased
Dicer cleavage of a dsRNA molecule is above the level of that
observed with an appropriate reference dsRNA molecule. In another
embodiment, enhanced or increased Dicer cleavage of a dsRNA
molecule is above the level of that observed with an inactive or
attenuated molecule.
[0117] As used herein "reduce" is meant to alter negatively by at
least 5% compared to a reference in an assay. An alteration may be
by 5%, 10%, 25%, 30%, 50%, 75%, or even by 100% compared to a
reference in an assay. By "reduce expression," it is meant that the
expression of the gene, or level of RNA molecules or equivalent RNA
molecules encoding one or more proteins or protein subunits, or
level or activity of one or more proteins or protein subunits
encoded by a target gene, is reduced below that observed in the
absence of the nucleic acid molecules (e.g., dsRNA molecule) in an
in vivo or in vitro assay of this disclosure. In one embodiment,
inhibition, down-regulation or reduction with a dsRNA molecule is
below that level observed in the presence of an inactive or
attenuated molecule. In another embodiment, inhibition,
down-regulation, or reduction with dsRNA molecules is below that
level observed in the presence of, e.g., an dsRNA molecules with
scrambled sequence or with mismatches. In another embodiment,
inhibition, down-regulation, or reduction of gene expression with a
nucleic acid molecule of the instant disclosure is greater in the
presence of the nucleic acid molecule than in its absence.
[0118] As used herein, "cell" is meant to include both prokaryotic
(e.g., bacterial) and eukaryotic (e.g., mammalian or plant) cells.
Cells may be of somatic or germ line origin, may be totipotent or
pluripotent, and may be dividing or non-dividing. Cells can also be
derived from or can comprise a gamete or an embryo, a stem cell, or
a fully differentiated cell. Thus, the term "cell" is meant to
retain its usual biological meaning and can be present in any
organism such as, for example, a bird, a plant, and a mammal,
including, for example, a human, a cow, a sheep, an ape, a monkey,
a pig, a dog, and a cat. Within certain aspects, the term "cell"
refers specifically to mammalian cells, such as human cells, that
contain one or more isolated dsRNA molecules of the present
disclosure. In particular aspects, a cell processes dsRNAs
resulting in RNA interference of target nucleic acids, and contains
proteins and protein complexes required for RNAi, e.g., Dicer and
RISC.
[0119] As used herein, "animal" is meant a multicellular,
eukaryotic organism, including a mammal, particularly a human. The
methods of the invention in general comprise administration of an
effective amount of the agents herein, such as an agent of the
structures of formulae herein, to a subject (e.g., animal, human)
in need thereof, including a mammal, particularly a human. Such
treatment will be suitably administered to subjects, particularly
humans, suffering from, having, susceptible to, or at risk for a
disease, or a symptom thereof.
[0120] By "pharmaceutically acceptable carrier" is meant, a
composition or formulation that allows for the effective
distribution of the nucleic acid molecules of the instant
disclosure in the physical location most suitable for their desired
activity.
[0121] The present invention is directed to compositions that
comprise both one or more double stranded RNA ("dsRNA") duplex
region(s) and a RNA:DNA duplex within the same agent, and methods
for preparing them, that are capable of reducing the expression of
target genes in eukaryotic cells. One of the strands of the one or
more dsRNA region(s) contains a region of nucleotide sequence that
has a length that ranges from about 15 to about 22 nucleotides that
can direct the destruction of the RNA transcribed from a target
gene. In certain embodiments, the RNA:DNA duplex region of such an
agent is not complemenatary to the target RNA, and, therefore, does
not enhance target RNA hybridization of the region of nucleotide
sequence capable of directing destruction of a target RNA. In
certain embodiments, nucleic acid duplex agents of the invention
can possess strands that are chemically linked, or can also possess
an extended loop, optionally comprising a tetraloop, that links the
first and second strands. In some embodiments, the extended loop
containing the tetraloop is at the 3' terminus of the sense strand,
at the 5' terminus of the antisense strand, or both.
[0122] The nucleic acid duplex (DsiRNA/RNA:DNA duplex) agents of
the instant invention can enhance the following attributes of such
agents relative to DsiRNAs lacking such RNA:DNA duplex regions:
potency or efficacy of compound therapeutics (specifically,
co-delivery of two or more DsiRNA agents directed against the same
target RNA sequence, distinct sequences within the same target RNA
sequence, or two distinct target RNA sequences, in a single agent),
pharmacokinetics, pharmacodynamics, intracellular uptake, nuclease
stabilization, and reduced toxicity.
[0123] As used herein, the term "pharmacokinetics" refers to the
process by which a drug is absorbed, distributed, metabolized, and
eliminated by the body. In certain embodiments of the instant
invention, enhanced pharmacokinetics of a DsiRNA/dsDNA agent
relative to an appropriate control DsiRNA refers to increased
absorption and/or distribution of such an agent, and/or slowed
metabolism and/or elimination of such a DsiRNA/dsDNA agent from a
subject administered such an agent.
[0124] As used herein, the term "pharmacodynamics" refers to the
action or effect of a drug on a living organism. In certain
embodiments of the instant invention, enhanced pharmacodynamics of
a nucleic acid duplex agent of the invention relative to an
appropriate control DsiRNA refers to an increased (e.g., more
potent or more prolonged) action or effect of a nucleic acid duplex
agent of the invention upon a subject administered such agent,
relative to an appropriate control DsiRNA.
[0125] As used herein, the term "stabilization" refers to a state
of enhanced persistence of an agent in a selected environment
(e.g., in a cell or organism). In certain embodiments, the nucleic
acid duplex agents of the instant invention exhibit enhanced
stability relative to appropriate control DsiRNAs. Such enhanced
stability can be achieved via enhanced resistance of such agents to
degrading enzymes (e.g., nucleases) or other agents.
DsiRNA Design/Synthesis
[0126] It was previously shown that longer dsRNA species of from 25
to about 30 nucleotides (DsiRNAs) yield unexpectedly effective RNA
inhibitory results in terms of potency and duration of action, as
compared to 19-23mer siRNA agents. Without wishing to be bound by
the underlying theory of the dsRNA processing mechanism, it is
thought that the longer dsRNA species serve as a substrate for the
Dicer enzyme in the cytoplasm of a cell. In addition to cleaving
the double stranded nucleic acid of the invention into shorter
segments, Dicer is thought to facilitate the incorporation of a
single-stranded cleavage product derived from the cleaved double
stranded nucleic acid into the RISC complex that is responsible for
the destruction of the cytoplasmic RNA of or derived from the
target gene. Prior studies (Rossi et al., U.S. Patent Application
No. 2007/0265220) have shown that the cleavability of a dsRNA
species (specifically, a DsiRNA agent) by Dicer corresponds with
increased potency and duration of action of the dsRNA species. The
instant invention, at least in part, provides for design of
compound RNA inhibitory agents that are joined by RNase H-cleavable
double-stranded nucleic acid double stranded nucleic acid
sequences, such that active DsiRNA moieties and, optionally,
released functional groups or payloads, are produced following
exposure of such agents to an RNase H-containing environment (e.g.,
administration to a subject, target cell or RNase-containing
solution).
[0127] Exemplary bifunctional DsiRNA structures and RNase H- and
Dicer-mediated processing of such structures is shown in FIGS. 1
and 2. An exemplary structure and RNase H- and Dicer-mediated
processing of a DsiRNA joined via an RNase H-cleavable double
stranded nucleic acid to a functional group is shown in FIG. 3.
[0128] As depicted in FIG. 1, a double-stranded oligonucleotide is
synthesized that possesses the following structure: (1) a first
region having a RISC-activating domain (preferably dsRNA) of about
23 to 33 duplexed nucleotides in length (the agent shown in FIG. 1
specifically possesses a 23 nucleotide length of duplexed dsRNAs);
(2) a second region that includes an RNA:DNA hybrid domain of at
least four duplexed nucleotides in length, with such RNA:DNA hybrid
domain constituting an RNase H-cleavable site (the agent shown in
FIG. 1 specifically possesses an RNA:DNA hybrid region of 8
duplexed nucleotides in length, with only the middle four base
pairs of such eight duplexed nucleotides constituting RNA:DNA base
paired nucleotides wherein the ribonucleotides are unmodified
ribonucleotides (the deoxyribonucleotides of this region may be
either modified or unmodified deoxyribonucleotides)--indeed,
modification of the ribonucleotides flanking this core, four base
pair long tract of (unmodified RNA):DNA duplexed nucleotides is
predicted to direct RNase H cleavage away from such modified
ribonucleotide sites, instead directing such RNase H cleavage to
occur at a location(s) within the (core four base pair length)
(unmodified RNA):DNA duplexed nucleotides); and (3) a third region
having a RISC-activating domain (preferably dsRNA) of about 23 to
33 duplexed nucleotides in length (the agent shown in FIG. 1
specifically possesses a 23 nucleotide length of duplexed dsRNAs
and a two base pair length DNA:RNA duplex at the 3' terminus of the
first strand/5' terminus of the second strand).
[0129] Like previously described DsiRNA agents, the first region of
an RNase H-cleavable agent such as the one depicted in FIG. 1 can
optionally comprise an overhang (optionally a 3' overhang of 1-4
nucleotides in length). In certain embodiments, the nucleotides of
such an overhang are modified ribonucleotides, or may comprise
deoxyribonucleotides. In addition, the duplexed nucleotides of the
first region can also comprise modified nucleotides, e.g., modified
ribonucleotides, e.g., at alternating locations within the span of
the second strand that is complementary to a target RNA and that is
modeled to lie 3' of the Dicer cleavage site of the DsiRNA agent
that is predicted to be formed from the first and second regions
via RNase H cleavage of the compound (precursor) RNase H-cleavable
DsiRNA-containing starting agent. Indeed, the RNase H-processed
products of the bifunctional agent shown in FIG. 1 are, in turn,
processed by Dicer to yield two independent, active siRNA
agents.
[0130] In view of the third region of the above-described RNase
H-cleavable "bifunctional DsiRNA" also comprising a RISC-activating
domain that is liberated, optionally in concert with a portion of
the second region to form a DsiRNA agent, via RNase H cleavage, the
nucleotides of this third region may also comprise modified
nucleotides, e.g., modified ribonucleotides, e.g., at alternating
locations within the span of the second strand that is
complementary to a target RNA and that is modeled to lie 3' on the
second strand from the Dicer cleavage site of the DsiRNA agent that
is predicted to be formed from the second and third regions via
RNase H cleavage of the compound (precursor) RNase H-cleavable
DsiRNA-containing starting agent (bifunctional DsiRNA agent). It is
noted that the first strand of this compound bifunctional DsiRNA
agent depicted in FIG. 1 also possesses a discontinuity (also known
as a "nick", with the first strand of this molecule optionally
referred to as a "nicked oligonucleotide"), with the presence of
such a discontinuity predicted to direct RNase H cleavage to form
double-stranded cleavage products having a precise structure.
Specifically, the presence of a discontinuity within the first
strand of the bifunctional DsiRNA agent depicted in FIG. 1
effectively primes the bifunctional DsiRNA agent for cleavage by
RNase H, as the RNase H enzyme need only cleave the unmodified
ribonucleotide-containing strand ("the RNase H-substrate domain")
that does not possess such discontinuity in order to liberate two
independent RNase H cleavage products (in FIG. 1, the second strand
is the continuous, "non-nicked" strand, and is the only strand that
RNase H need cleave in order to liberate two independent Dicer
substrate molecules; it is noted in FIG. 1 that the second strand
of the second region's most 5' ribonucleotides are modified
ribonucleotides, thereby directing RNase H cleavage to occur 3' of
these modified ribonucleotides of the second strand, thereby
liberating a cleavage product of the second and third regions that
possesses a 3' overhang of two modified ribonucleotides on the
second strand (refer to right-hand RNase H cleavage product of FIG.
1)).
[0131] In an alternate embodiment of the bifunctional DsiRNA agent
shown in FIG. 1, labelled sections 2 and 6 of FIG. 1 might
effectively be swapped, resulting in an agent possessing a
discontinuity (nick) to the immediate 5' of the 5' terminal
deoxyribonucleotide of the second strand (with labelled section 6
comprising deoxyribonucleotides and constituting an "RNase
H-activating domain") while labelled section 2 comprises at least
four unmodified ribonucleotides that base pair with each of the
four deoxyribonucleotides now constituting labelled section 6 (with
such unmodified nucleotides of labelled section 2 now constituting
an "RNase H-substrate domain"). As the skilled artisan will
recognize, these RNase H-activating domains and RNase H-substrate
domains can optionally be extended or modified, so long as this
region retains its character as an RNase H-cleavable domain, with
RNase H cleavage resulting in liberation of two independent Dicer
substrate agents.
[0132] FIG. 2 depicts a double-stranded oligonucleotide synthesized
to possess the following structure: (1) a first region having a
RISC-activating domain (preferably dsRNA) of about 23 to 33
duplexed nucleotides in length (the agent shown in FIG. 2
specifically possesses a 23 nucleotide length of duplexed dsRNAs
and a 2 nucleotide length of duplexed deoxyribonucleotides at the
3' end of the first strand/5' end of the second strand of this
first region of the bifunctional DsiRNA agent); (2) a second region
that includes an RNA:DNA hybrid domain of at least four duplexed
nucleotides in length, with such RNA:DNA hybrid domain constituting
an RNase H-cleavable site (the agent shown in FIG. 2 specifically
possesses an RNA:DNA hybrid region of 4 duplexed nucleotides in
length, with the ribonucleotides of this 4 base pair RNA:DNA span
being unmodified ribonucleotides (the deoxyribonucleotides of this
region may be either modified or unmodified
deoxyribonucleotides)--presence of DNA:DNA base pairs in those
parts of the first and third regions of the bifunctional DsiRNA
agent immediately flanking this RNA:DNA span are predicted to
direct RNase H cleavage away from such DNA:DNA domains, instead
directing such RNase H cleavage to occur at a location(s) within
the (unmodified RNA):DNA duplexed nucleotides of this second
region; and (3) a third region having a RISC-activating domain
(preferably dsRNA) of about 23 to 33 duplexed nucleotides in length
(the agent shown in FIG. 2 specifically possesses a 23 nucleotide
length of duplexed dsRNAs and a two base pair length DNA:DNA duplex
at the 5' terminus of the first strand/3' terminus of the second
strand of this third region of the bifunctional DsiRNA agent).
[0133] As with the agent depicted in FIG. 1, the first region of an
RNase H-cleavable agent such as the one depicted in FIG. 2 can
optionally comprise an overhang (optionally a 3' overhang of 1-4
nucleotides in length). In certain embodiments, the nucleotides of
such an overhang are modified ribonucleotides, or they may comprise
deoxyribonucleotides. In addition, the duplexed nucleotides of the
first region can also comprise modified nucleotides, e.g., modified
ribonucleotides, e.g., at alternating locations within the span of
the second strand that is complementary to a target RNA and that is
modeled to lie 3' of the Dicer cleavage site of the DsiRNA agent
that is predicted to be formed from the first and second regions
via RNase H cleavage of the bifunctional (precursor) RNase
H-cleavable DsiRNA-containing starting agent (bifunctional DsiRNA
agent). Indeed, the RNase H-processed products of the bifunctional
agent shown in FIG. 2 are, in turn, processed by Dicer to yield two
independent, active siRNA agents.
[0134] In view of the third region of the above-described RNase
H-cleavable "bifunctional DsiRNA" also comprising a RISC-activating
domain that is liberated, optionally in concert with a portion of
the second region, to form a DsiRNA agent via RNase H cleavage, the
nucleotides of this third region may also comprise modified
nucleotides, e.g., modified ribonucleotides. In certain
embodiments, such modified nucleotides are positioned at
alternating locations within the span of the first strand that is
complementary to a target RNA and that is modeled to lie 3' on the
first strand from the Dicer cleavage site of the DsiRNA agent that
is predicted to be formed from the second and third regions via
RNase H cleavage of the bifunctional (precursor) RNase H-cleavable
DsiRNA-containing starting agent. It is noted that the first strand
of the bifunctional DsiRNA agent depicted in FIG. 2 also possesses
a discontinuity (nick), with the presence of such a discontinuity
predicted to direct RNase H cleavage to form double-stranded
cleavage products having a precise structure. Specifically, the
presence of a discontinuity within the first strand of the
bifunctional DsiRNA agent depicted in FIG. 2 effectively primes the
bifunctional DsiRNA agent for cleavage by RNase H, as the RNase H
enzyme need only cleave the unmodified ribonucleotide-containing
strand ("the RNase H-substrate domain") that does not possess such
discontinuity in order to liberate two independent RNase H cleavage
products (in FIG. 2, the second strand is the continuous,
"non-nicked" strand, and is the only strand that RNase H need
cleave in order to liberate two independent Dicer substrate
molecules; it is noted in FIG. 2 that the most 5' nucleotides of
the second strand of the first region are deoxyribonucleotides (as
are the cognate most 3' nucleotides of the first strand of the
first region), thereby directing RNase H cleavage to occur 5' of
these deoxyribonucleotides of the second strand, thereby liberating
a cleavage product of the first region that possesses two
deoxyribonucleotides at the 3' terminus of the first strand that
base pair with two cognate deoxyribonucleotides of the second
strand. Even if RNase H cleavage occurs upstream of these
deoxyribonucleotides of the second strand, any single stranded RNAs
should be degraded ("processive"), yielding a blunt ended DsiRNA
agent at the 3' terminus of the first strand/5' terminus of the
second strand. Meanwhile, liberation of a DsiRNA agent from the
second and third regions of the bifunctional agent shown in FIG. 2
is modeled to involve RNase H cleavage, followed by degradation of
ribonucleotides of the second region, resulting in an RNase
H-liberated agent that possesses a 5' overhang of
deoxyribonucleotides and is subsequently processed by Dicer. As
noted above in reference to the structure of the bifunctional
DsiRNA agent of FIG. 2, the DsiRNA agent formed from regions 2 and
3 that is liberated via RNase H cleavage optionally contains
modified nucleotides, e.g., modified ribonucleotides, e.g.,
positioned at the 3' overhang nucleotides of the first strand
and/or present at alternating residues within the span of
nucleotides of the first strand that are predicted to be 3' of the
eventual Dicer cleavage site, in an agent having a structure such
as that shown in FIG. 2.
[0135] In alternate embodiments of the bifunctional DsiRNA agent
shown in FIG. 2, the RNA:DNA region and location of discontinuity
of the bifunctional DsiRNA agent can be exchanged between the two
strands. In a vertical flipping (inversion) of RNA/DNA identity
within such an RNA:DNA region possessing discontinuity, a resultant
structure has RNA residues on the first strand within the second
region, with such first strand being continuous across the expanse
of the bifunctional DsiRNA agent, while the second strand of the
second region would comprise cognate DNA residues, with the second
strand (rather than the first strand) now possessing a
discontinuity that is located at the immediate edge of the RNA:DNA
span of duplexed nucleotides (with such nick located at the 3' end
of the second strand of the second region).
[0136] As will be clear to the skilled artisan, the position of the
strand discontinuity (nick) shown or described in many of the
agents recited herein may be altered so long as activity of such
agents is retained. It is noted for the agent shown in FIG. 1 that
the positioning of a nick in the first strand deoxyribonucleotide
span as indicated directs RNase H cleavage such that a two
ribonucleotide 3' overhang is created in the released DsiRNA agent
comprising labelled domains 3, 4 and 7 of the FIG. 1 agent.
However, in the agent shown in FIG. 1, a nick in the first strand
deoxyribonucleotide span could also be introduced at any of the
following positions, even were the activity of the released DsiRNAs
to be less effective than the optimized nicked version shown (nick
is indicated in the following sequences by a vertical line, "|"):
5'- . . . AA|ttcaccggGGA . . . -3'; 5'- . . . AAt|tcaccggGGA . . .
-3'; 5'- . . . AAtt|caccggGGA . . . -3'; 5'- . . . AAttc|accggGGA .
. . -3'; 5'- . . . AAttca|ccggGGA . . . -3'; 5'- . . .
AAttcac|cggGGA . . . -3'; 5'- . . . AAttcacc|ggGGA . . . -3'; 5'- .
. . AAttcaccg|gGGA . . . -3'; 5'- . . . AAttcaccgg|GGA . . . -3'.
Similarly, for an agent of FIG. 1 that is altered to swap the
location of DNA and RNA residues within the RNA:DNA duplex domain,
a nick in the resultant second strand's deoxyribonucleotide span
can be introduced at any of the following positions (nick is
indicated in the following sequences by a vertical line, "|"): 5'-
. . . UCC|ccggugaaUUU . . . -3'; 5'- . . . UCCc|cggugaaUUU . . .
-3'; 5'- . . . UCCcc|ggugaaUUU . . . -3'; 5'- . . . UCCccg|gugaaUUU
. . . -3'; 5'- . . . UCCccgg|ugaaUUU . . . -3'; 5'- . . .
UCCccggu|gaaUUU . . . -3'; 5'- . . . UCCccggug|aaUUU . . . -3'; ;
5'- . . . UCCccgguga|aUUU . . . -3'; ; 5'- . . . UCCccggugaa|UUU .
. . -3'. It is also possible to introduce two or more nicks within
the deoxyribonucleotide stretches of any such domain, e.g., more
precise definition of DsiRNA structures generated via RNase H
cleavage of the agent shown in FIG. 1 might be obtained via
inclusion of nicks at the following locations of the first strand:
5'- . . . AAtt|caccgg|GGA . . . -3'.
[0137] As for bifunctional agents of the invention that possess
structures as shown in or akin to those of FIG. 1, bifunctional
agents such as those shown in FIG. 2 can also harbor a
discontinuity at any of a number of positions within the strand
that possesses the deoxyribonucleotides of the RNA:DNA duplexed
nucleotides which attract RNase H cleavage. Specifically, within
the agent shown in FIG. 2, such a discontinuity in the first strand
can be introduced at any of the following positions (nick is
indicated in the following sequences by a vertical line, "|"): 5'-
. . . AAA|ttcaccggUCG . . . -3'; 5'- . . . AAAt|tcaccggUCG . . .
-3'; 5'- . . . AAAtt|caccggUCG . . . -3'; 5'- . . . AAAttc|accggUCG
. . . -3'; 5'- . . . AAAttca|ccggUCG . . . -3'; 5'- . . .
AAAttcac|cggUCG . . . -3'; 5'- . . . AAAttcacc|ggUCG . . . -3'; 5'-
. . . AAAttcaccg|gUCG . . . -3'; 5'- . . . AAAttcaccgg|UCG . . .
-3'. In an agent such as that shown in FIG. 2, yet in which RNA and
DNA positions of the RNA:DNA duplex domain have been swapped, a
discontinuity can correspondingly be introduced into the second
strand at any of the following positions (nick is indicated in the
following sequences by a vertical line, "|"): 5'- . . .
CGA|ccggugaaUUU . . . -3'; 5'- . . . CGAc|cggugaaUUU . . . -3'; 5'-
. . . CGAcc|ggugaaUUU . . . -3'; 5'- . . . CGAccg|gugaaUUU . . .
-3'; 5'- . . . CGAccgg|ugaaUUU . . . -3'; 5'- . . . CGAccggu|gaaUUU
. . . -3'; 5'- . . . CGAccggug|aaUUU . . . -3'; 5'- . . .
CGAccgguga|aUUU . . . -3'; 5'- . . . CGAccggugaa|UUU . . . -3'
[0138] Bifunctional agents of the invention can also be generated
without nicks, with RNase H cleavage releasing DsiRNA agents that
retain activity.
[0139] RNase H-cleavable RNA:DNA duplex domains can also be used to
tether releasable functional groups/payloads to double-stranded
nucleotides harboring a DsiRNA agent which is released upon RNase H
cleavage. Specifically, FIG. 3 shows a composition having: (1) a
first region comprising dsRNA; (2) a second region comprising an
RNA:DNA duplex domain, within which at least 4 ribonucleotides of
such region are unmodified ribonucleotides and (3) a functional
group/payload that is attached to the RNA-containing strand of the
RNA:DNA duplex domain of the second region. Such a functional
group/payload may be attached via an art-recognized covalent or
non-covalent linkage. The DNA-containing strand of the agent shown
in FIG. 3 may optionally contain a discontinuity, e.g., at 5'- . .
. GAAAtt|caccgg-3'.
[0140] Many of the nucleotide modifications (e.g., 2'-O-methyl
groups, LNA, etc.) described herein can impact upon properties such
as biodistribution, formulation, adsorption, metabolism,
pharmacodynamic, cellular uptake, etc. of the double stranded
nucleic acid agents of the invention. In one aspect, the invention
features double stranded nucleic acid molecules having improved
qualities (e.g., bioavailability, cellular uptake, etc.) imparted
via tethering of a functional group to the structure of a
(DsiRNA-containing) double stranded nucleic acid (see, e.g., FIG.
3). Altered bioavailability or other properties attributable to
presence of such a functional group within a double stranded
nucleic acid of the invention can be assessed under conditions
suitable for isolating double stranded nucleic acid molecules
having improved bioavailability or other such properties. Such
functional groups can include ligands for cellular receptors, such
as peptides derived from naturally occurring protein ligands;
protein localization sequences, including cellular ZIP code
sequences; antibodies; nucleic acid aptamers; vitamins and other
co-factors, such as folate and N-acetylgalactosamine; polymers,
such as polyethyleneglycol (PEG); phospholipids; cholesterol;
polyamines, such as spermine or spermidine; and others.
[0141] Functional groups of the invention can include
intercalators, reporter molecules, polyamines, polyamides,
polyethylene glycols, polyethers, groups that enhance the
pharmaco-dynamic properties of nucleic acid agents, and groups that
enhance the pharmacokinetic properties of nucleic acid agents.
Typical functional groups include cholesterols, lipids, phospho
lipids, biotin, phenazine, folate, phenanthridine, anthraquinone,
acridine, fluoresceins, rhodamines, coumarins, and dyes. Groups
that enhance the pharmacodynamic properties, in the context of this
invention, include groups that improve uptake, enhance resistance
to degradation, enhance RISC residency and/or strengthen
sequence-specific hybridization with the target nucleic acid.
Groups that enhance the pharmacokinetic properties, in the context
of this invention, include groups that improve uptake,
distribution, metabolism or excretion of the compounds of the
present invention. Representative functional groups are disclosed
in International Patent Application PCT/US92/09196, filed Oct. 23,
1992, and U.S. Pat. No. 6,287,860. Functional group moieties
include but are not limited to lipid moieties such as a cholesterol
moiety, cholic acid, a thioether, e.g., hexyl-5-tritylthiol, a
thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecyl
residues, a phospholipid, e.g., di-hexadecyl-rac-glycerol or
triethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a
polyamine or a polyethylene glycol chain, or adamantane acetic
acid, a palmityl moiety, or an octadecylamine or
hexylamino-carbonyl-oxycholesterol moiety. Nucleic acid agents of
the invention may also be attached to active drug substances, for
example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen,
fenbufen, ketoprofen, (S)-(+)-pranoprofen, carprofen,
dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid,
folinic acid, a benzothiadiazide, chlorothiazide, a diazepine,
indomethicin, a barbiturate, a cephalosporin, a sulfa drug, an
antidiabetic, an antibacterial or an antibiotic.
Oligonucleotide-drug conjugates and their preparation are described
in U.S. patent application Ser. No. 09/334,130 (filed Jun. 15,
1999). Representative United States patents that teach the
preparation of oligonucleotide conjugates include, but are not
limited to, U.S. Pat. Nos. 4,828,979; 4,948,882; 5,218,105;
5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717, 5,580,731;
5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045; 5,414,077;
5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735;
4,667,025; 4,762,779; 4,789,737; 4,824,941; 4,835,263; 4,876,335;
4,904,582; 4,958,013; 5,082,830; 5,112,963; 5,214,136; 5,082,830;
5,112,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536;
5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723; 5,416,203,
5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810;
5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696; 5,599,923;
5,599,928 and 5,688,941.
[0142] Non-limiting further examples of functional groups
contemplated by the invention include conjugates and ligands
described in Vargeese et al., U.S. Application No. 2004/0110296. In
one embodiment, a functional group of the invention comprises a
molecule that facilitates delivery of a chemically-modified siNA
molecule into a biological system, such as a cell. In another
embodiment, the functional group attached to the double stranded
nucleic acid molecule is a polyethylene glycol, human serum
albumin, or a ligand for a cellular receptor that can mediate
cellular uptake. Examples of specific functional groups
contemplated by the instant invention that can be attached to
double stranded nucleic acids within the agents of the invention
are described, e.g., in Vargeese et al., U.S. Application No.
2003/0130186. The type and number of functional groups/conjugates
used in a double stranded nucleic acid of the invention can be
evaluated for improved pharmacokinetic profiles, bioavailability,
and/or stability of double stranded nucleic acid constructs while
at the same time maintaining the ability of the double stranded
nucleic acid to mediate RNAi activity. As such, one skilled in the
art can screen double stranded nucleic acid constructs that are
modified with various functional groups/conjugates to determine
whether the double stranded nucleic acid-functional group agent
possesses improved properties while maintaining the ability to
mediate RNAi, for example in animal models as are generally known
in the art.
[0143] The second region of any of the above-recited agents can be
extended in length, e.g., such that the RNA:DNA duplex domain has a
length of 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24 or 25 nucleotides in length. Optionally, the
length of such RNA:DNA duplex domain is of at least 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30,
35, 40, 45 or 50 nucleotides in length.
[0144] In one embodiment, the RNA:DNA duplex domain of the double
stranded nucleic acid agent of the instant invention can comprise
an antisense agent. In such embodiments, it is particularly
advantageous that the RNA:DNA duplex domain length be of at least
about 12 nucleotides in length. Where such a region includes an
antisense agent that is releasable upon RNase H cleavage of the
RNase H-cleavable starting agent of the instant invention,
modifications of the antisense deoxyribonucleotide domain can be
performed, including any such art-recognized modification of
antisense agents that has been described. Exemplary modifications
of such an antisense agent harbored within the RNA:DNA duplex
domain of a double stranded nucleic acid of the invention include
phosphorothioate modification of such a deoxynucleotide region,
with, e.g., inclusion of other (additional) modifications also
allowed. For example, a 12mer antisense agent may be included
within the RNA:DNA duplex domain of a double stranded nucleic acid
of the invention, with such DNAs of said RNA:DNA duplex domain
comprising phosphorothioate modifications (such modifications are
notably still capable of activating RNase H cleavage), with such
deoxyribonucleotide sequence optionally possessing LNA moieties at
each end of the deoxyribonucleotide domain, e.g., such that an 8mer
of unmodified DNA and/or only phosphorothioate-modified
deoxyribonucleotide residues are located at the center of such
12mer domain that activates RNase H. Exemplary modification
patterns that can be used within antisense agents contained within
double stranded nucleic acid agents of the instant invention can be
found, e.g., within U.S. Pat. No. 7,432,250. It is noted that in
the context of a bifunctional RNase H-cleavable double stranded
nucleic acid of the instant invention, such antisense
agent-containing double stranded nucleic acid of the invention can
also be referred to as "trifunctional" (specifically, RNase H
cleavage not only releases two, optionally independent, DsiRNA
agents, but also releases an antisense agent from the RNase
H-cleavable RNA:DNA region).
[0145] Following RNase H cleavage of the bifunctional and
functional group-tethered DsiRNA agents of the instant invention,
Dicer enzyme is predicted to bind to liberated DsiRNA agents,
resulting in cleavage of such DsiRNAs at a position 19-23
nucleotides removed from a Dicer PAZ domain-associated 3' overhang
sequence of the antisense strand of the DsiRNA agent. This Dicer
cleavage event results in excision of those duplexed nucleic acids
previously located at the 3' end of the passenger (sense) strand
and 5' end of the guide (antisense) strand. (Cleavage of the DsiRNA
typically yields a 19mer duplex with 2-base overhangs at each end.)
As presently modeled in FIGS. 1-3, this Dicer cleavage event
generates a 21-23 nucleotide guide (antisense) strand capable of
directing sequence-specific inhibition of target mRNA as a RISC
component.
[0146] The first and second oligonucleotide strands of the
bifunctional and functional group-tethered DsiRNA agents of the
instant invention are not required to be completely complementary.
In fact, in one embodiment, the 3'-terminus of the sense strand of
a constituent DsiRNA agent contains one or more mismatches. In one
aspect, about two mismatches are incorporated at the 3' terminus of
the sense (passenger) strand. In another embodiment, the
constituent DsiRNA(s) of the invention are a double stranded RNA
molecule containing two RNA oligonucleotides each of which is an
identical number of nucleotides in the range of 27-35 nucleotides
in length and, when annealed to each other, have blunt ends and a
two nucleotide mismatch on the 3'-terminus of the sense strand (the
5'-terminus of the antisense strand). The use of mismatches or
decreased thermodynamic stability (specifically at the
3'-sense/5'-antisense position) has been proposed to facilitate or
favor entry of the antisense strand into RISC (Schwarz et al.,
2003; Khvorova et al., 2003), presumably by affecting some
rate-limiting unwinding steps that occur with entry of the siRNA
into RISC. Thus, terminal base composition has been included in
design algorithms for selecting active 21mer siRNA duplexes (Ui-Tei
et al., 2004; Reynolds et al., 2004). With Dicer cleavage of the
dsRNA region of this embodiment, the small end-terminal sequence
which contains the mismatches will either be left unpaired with the
antisense strand (become part of a 3'-overhang) or be cleaved
entirely off the final 21-mer siRNA. These "mismatches", therefore,
do not persist as mismatches in the final RNA component of RISC.
The finding that base mismatches or destabilization of segments at
the 3'-end of the sense strand of Dicer substrate improved the
potency of synthetic duplexes in RNAi, presumably by facilitating
processing by Dicer, was a surprising finding of past works
describing the design and use of 25-30mer dsRNAs (also termed
"DsiRNAs" herein; Rossi et al., U.S. Patent Application Nos.
2005/0277610, 2005/0244858 and 2007/0265220). DsiRNAs having
base-paired deoxyribonucleotides at passenger (sense) strand
positions modeled to be 3' of the Dicer cleavage site have also
been identified as at least equally effective as RNA-RNA
duplex-extended DsiRNA agents (U.S. Patent Application No.
61/138,946, filed Dec. 18, 2008). Thus, dsDNA-extended DsiRNA
agents such as those described in U.S. Patent Application No.
61/138,946 may also be incorporated as constituent DsiRNA agents
within the RNase H-cleavable constructs of the instant
invention.
[0147] As shown in FIG. 4, bifunctional DsiRNA agents can be
synthesized that do not require a RNA:DNA RNase H cleavable joining
sequence to function as a bifunctional agent. Rather, a double
stranded DNA:DNA extended region of the DsiRNAs comprising such an
agent provides the joining sequence for the bifunctional agent. The
second region of such an agent can be extended in length, e.g.,
such that the DNA:DNA duplex domain has a length of 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 or 30 nucleotides in length. Optionally, the length
of such DNA:DNA duplex domain is of at least 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40,
45 or 50 nucleotides in length. Such a dsDNA extended joining
sequence may also be modified as described above, or may provide an
antisense agent within the dsDNA extended region, imparting
"trifunctionality" to such a dsDNA extended/joined agent.
[0148] In certain embodiments, a bifunctional inhibitory agent of
the invention is cleaved by Dicer following administration to a
cell, tissue and/or subject. In such aspects, the bifunctional
agents of the instant invention possess enhanced efficacy and/or
potency as compared to tandem siRNA agents that have previously
been described. Indeed, such bifunctional agents of the instant
invention can be capable of inhibiting expression of both targeted
genes (or, where the bifunctional agent targets two or more sites
within the same gene, of the single targeted gene) by at least 20%
at a concentration of 100 picomolar in the environment of a cell.
In certain embodiments, levels of both targeted genes are reduced
by at least 25%, at least 30%, at least 35%, at least 40%, at least
45%, at least 50%, at least 55%, at least 60%, at least 65%, at
least 70%, at least 75%, at least 80%, at least 85%, or at least
90% or more at a selected sub-nanomolar concentration in the
environment of a cell (e.g., 500 pM or less, 200 pM or less, 100 pM
or less, 50 pM or less, 25 pM or less, 20 pM or less, 10 pM or
less, 5 pM or less, 2 pM or less, or 1 pM or less). Such surprising
in vitro efficacies and/or potencies can also correspond to
enhanced in vivo efficacies and/or potencies for such bifunctional
agents of the instant invention, with respect to an appropriate
control molecule (e.g., tandem siRNAs) and/or pair of control
molecules (e.g., siRNAs that are not attached to one another).
Exemplary Structures of Constituent DsiRNAs of RNase H-Cleavable
DsiRNA Agent Compositions and dsDNA Extended Bifunctional
Agents
[0149] In one aspect, the present invention provides compositions
for RNA interference (RNAi) that comprise DsiRNA agent(s) that are
liberated from functional group(s) or additional DsiRNA agents via
RNase H cleavage of a RNA:DNA duplex-containing RNase H cleavable
region. (Alternatively, DsiRNA moieties are joined by a double
stranded DNA joining sequence in a bifunctional dsDNA extended
agent.) Certain compositions of the invention comprise a double
stranded nucleic acid which is a precursor molecule, i.e., the
double stranded nucleic acid of the present invention is initially
processed in vitro or in vivo by RNase H to yield one or more
DsiRNA agents. Such liberated DsiRNA agents are, in turn, processed
in vivo or in cells (or in an in vitro Dicer cleavage assay) to
produce an active small interfering nucleic acid (siRNA). The
double stranded nucleic acid is processed by Dicer to an active
siRNA which is incorporated into RISC.
[0150] In certain embodiments, the constituent DsiRNA component
agents of the bifunctional or functional group-tethered DsiRNA
agents of the invention can have any of the following exemplary
structures:
[0151] In one embodiment, the constituent DsiRNA agent(s)
comprises:
TABLE-US-00002 5'-pXXXXXXXXXXXXXXXXXXXXXXXDD-3'
3'-YXXXXXXXXXXXXXXXXXXXXXXXXXp-5'
wherein "X"=RNA, "p"=a phosphate group, "Y" is an overhang domain
comprised of 1-4 RNA monomers that are optionally 2'-O-methyl RNA
monomers, and "D"=DNA. The top strand is the sense strand, and the
bottom strand is the antisense strand.
[0152] In another such embodiment, the constituent DsiRNA agent(s)
comprises:
TABLE-US-00003 5'-pXXXXXXXXXXXXXXXXXXXXXXXDD-3'
3'-YXXXXXXXXXXXXXXXXXXXXXXXXXp-5'
wherein "X"=RNA, "p"=a phosphate group, "X"=2'-O-methyl RNA, "Y" is
an overhang domain comprised of 1-4 RNA monomers that are
optionally 2'-O-methyl RNA monomers, underlined residues are
2'-O-methyl RNA monomers, and "D"=DNA. The top strand is the sense
strand, and the bottom strand is the antisense strand.
[0153] In another such embodiment, the constituent DsiRNA agent(s)
comprises:
TABLE-US-00004 5'-pXXXXXXXXXXXXXXXXXXXXXXXDD-3'
3'-YXXXXXXXXXXXXXXXXXXXXXXXXXp-5'
wherein "X"=RNA, "p"=a phosphate group, "X"=2'-O-methyl RNA, "Y" is
an overhang domain comprised of 1-4 RNA monomers that are
optionally 2'-O-methyl RNA monomers, underlined residues are
2'-O-methyl RNA monomers, and "D"=DNA. The top strand is the sense
strand, and the bottom strand is the antisense strand.
[0154] In another embodiment, the constituent DsiRNA agent(s)
comprises strands having equal lengths possessing 1-3 mismatched
residues that serve to orient Dicer cleavage (specifically, one or
more of positions 1, 2 or 3 on the first strand of the constituent
DsiRNA, when numbering from the 3'-terminal residue, are mismatched
with corresponding residues of the 5'-terminal region on the second
strand when first and second strands are annealed to one another).
An exemplary 27mer constituent DsiRNA agent with two terminal
mismatched residues is shown:
TABLE-US-00005 5'-pXXXXXXXXXXXXXXXXXXXXXXXXX.sup.M.sup.M-3'
3'-XXXXXXXXXXXXXXXXXXXXXXXXX.sub.M.sub.Mp-5'
wherein "X"=RNA, "p"=a phosphate group, "M"=Nucleic acid residues
(RNA, DNA or non-natural or modified nucleic acids) that do not
base pair (hydrogen bond) with corresponding "M" residues of
otherwise complementary strand when strands are annealed. Any of
the residues of such agents can optionally be 2'-O-methyl RNA
monomers--alternating positioning of 2'-O-methyl RNA monomers that
commences from the 3'-terminal residue of the bottom (second)
strand, as shown for above asymmetric agents, can also be used in
the above "blunt/fray" DsiRNA agent. The top strand (first strand)
is the sense strand, and the bottom strand (second strand) is the
antisense strand.
[0155] In one embodiment, the constituent DsiRNA agent has an
asymmetric structure, with the sense strand having a 25-base pair
length, and the antisense strand having a 27-base pair length with
a 1-4 base 3'-overhang (e.g., a one base 3'-overhang, a two base
3'-overhang, a three base 3'-overhang or a four base 3'-overhang).
In another embodiment, this DsiRNA agent has an asymmetric
structure further containing 2 deoxynucleotides at the 3' end of
the sense strand.
[0156] In another embodiment, the constituent DsiRNA agent has an
asymmetric structure, with the antisense strand having a 25-base
pair length, and the sense strand having a 27-base pair length with
a 1-4 base 3'-overhang (e.g., a one base 3'-overhang, a two base
3'-overhang, a three base 3'-overhang or a four base 3'-overhang).
In another embodiment, this DsiRNA agent has an asymmetric
structure further containing 2 deoxynucleotides at the 3' end of
the antisense strand.
[0157] In additional embodiments, one or more constituent DsiRNA(s)
can comprise dsDNA-extended ("DNA handle") structures, such as:
TABLE-US-00006 5'-XXXXXXXXXXXXXXXXXXXXXXXD.sub.NDD-3'
3'-YXXXXXXXXXXXXXXXXXXXXXXXD.sub.NXX-5'
wherein "X"=RNA, "Y" is an optional overhang domain comprised of
0-10 RNA monomers that are optionally 2'-O-methyl RNA monomers--in
certain embodiments, "Y" is an overhang domain comprised of 1-4 RNA
monomers that are optionally 2'-O-methyl RNA monomers, "D"=DNA, and
"N"=1 to 50 or more, but is optionally 1-8. In one embodiment, the
top strand is the sense strand, and the bottom strand is the
antisense strand. Alternatively, the bottom strand is the sense
strand and the top strand is the antisense strand.
[0158] In a related embodiment, the constituent DsiRNA
comprises:
TABLE-US-00007 5'-XXXXXXXXXXXXXXXXXXXXXXXD.sub.NDD-3'
3'-YXXXXXXXXXXXXXXXXXXXXXXXD.sub.NDD-5'
wherein "X"=RNA, "Y" is an optional overhang domain comprised of
0-10 RNA monomers that are optionally 2'-O-methyl RNA monomers--in
certain embodiments, "Y" is an overhang domain comprised of 1-4 RNA
monomers that are optionally 2'-O-methyl RNA monomers, "D"=DNA, and
"N"=1 to 50 or more, but is optionally 1-8. In one embodiment, the
top strand is the sense strand, and the bottom strand is the
antisense strand. Alternatively, the bottom strand is the sense
strand and the top strand is the antisense strand.
[0159] In another such embodiment, the constituent DsiRNA
comprises:
TABLE-US-00008 5'-XXXXXXXXXXXXXXXXXXXXXXXD.sub.NDD-3'
3'-YXXXXXXXXXXXXXXXXXXXXXXXD.sub.NZZ-5'
wherein "X"=RNA, "X"=2'-O-methyl RNA, "Y" is an optional overhang
domain comprised of 0-10 RNA monomers that are optionally
2'-O-methyl RNA monomers--in certain embodiments, "Y" is an
overhang domain comprised of 1-4 RNA monomers that are optionally
2'-O-methyl RNA monomers, "D"=DNA, "Z"=DNA or RNA, and "N"=1 to 50
or more, but is optionally 1-8. In one embodiment, the top strand
is the sense strand, and the bottom strand is the antisense strand.
Alternatively, the bottom strand is the sense strand and the top
strand is the antisense strand, with 2'-O-methyl RNA monomers
located at alternating residues along the top strand, rather than
the bottom strand presently depicted in the above schematic.
[0160] In another such embodiment, the constituent DsiRNA
comprises:
TABLE-US-00009 5'-XXXXXXXXXXXXXXXXXXXXXXXD.sub.NDD-3'
3'-YXXXXXXXXXXXXXXXXXXXXXXXD.sub.NZZ-5'
wherein "X"=RNA, "X"=2'-O-methyl RNA, "Y" is an optional overhang
domain comprised of 0-10 RNA monomers that are optionally
2'-O-methyl RNA monomers--in certain embodiments, "Y" is an
overhang domain comprised of 1-4 RNA monomers that are optionally
2'-O-methyl RNA monomers, "D"=DNA, "Z"=DNA or RNA, and "N"=1 to 50
or more, but is optionally 1-8. In one embodiment, the top strand
is the sense strand, and the bottom strand is the antisense strand.
Alternatively, the bottom strand is the sense strand and the top
strand is the antisense strand, with 2'-O-methyl RNA monomers
located at alternating residues along the top strand, rather than
the bottom strand presently depicted in the above schematic.
[0161] In another embodiment, the constituent DsiRNA comprises:
TABLE-US-00010 5'-XXXXXXXXXXXXXXXXXXXXXXX[X1/D1].sub.NDD-3'
3'-YXXXXXXXXXXXXXXXXXXXXXXX[X2/D2].sub.NZZ-5'
wherein "X"=RNA, "Y" is an optional overhang domain comprised of
0-10 RNA monomers that are optionally 2'-O-methyl RNA monomers--in
certain embodiments, "Y" is an overhang domain comprised of 1-4 RNA
monomers that are optionally 2'-O-methyl RNA monomers, "D"=DNA,
"Z"=DNA or RNA, and "N"=1 to 50 or more, but is optionally 1-8,
where at least one D1.sub.N is present in the top strand and is
base paired with a corresponding D2.sub.N in the bottom strand.
Optionally, D1.sub.N and D1.sub.N+1 are base paired with
corresponding D2.sub.N and D2.sub.N+1; D1.sub.N; D1.sub.N+1 and
D1.sub.N+2 are base paired with corresponding D2.sub.N, D1.sub.N+1
and D1.sub.N+2, etc. In one embodiment, the top strand is the sense
strand, and the bottom strand is the antisense strand.
Alternatively, the bottom strand is the sense strand and the top
strand is the antisense strand, with 2'-O-methyl RNA monomers
located at alternating residues along the top strand, rather than
the bottom strand presently depicted in the above schematic.
[0162] In any of the above-depicted structures, the 5' end of
either the sense strand or antisense strand optionally comprises a
phosphate group.
[0163] In another embodiment, the constituent DNA:DNA-extended
DsiRNA comprises strands having equal lengths possessing 1-3
mismatched residues that serve to orient Dicer cleavage
(specifically, one or more of positions 1, 2 or 3 on the first
strand of the constituent DsiRNA, when numbering from the
3'-terminal residue, are mismatched with corresponding residues of
the 5'-terminal region on the second strand when first and second
strands are annealed to one another). An exemplary constituent
DNA:DNA-extended DsiRNA agent with two terminal mismatched residues
is shown:
TABLE-US-00011 5'-XXXXXXXXXXXXXXXXXXXXXXXXXD.sub.N.sup.M.sup.M-3'
3'-XXXXXXXXXXXXXXXXXXXXXXXXXD.sub.NM.sub.M-5'
wherein "X"=RNA, "M"=Nucleic acid residues (RNA, DNA or non-natural
or modified nucleic acids) that do not base pair (hydrogen bond)
with corresponding "M" residues of otherwise complementary strand
when strands are annealed, "D"=DNA and "N"=1 to 50 or more, but is
optionally 1-8. Any of the residues of such agents can optionally
be 2'-O-methyl RNA monomers--alternating positioning of 2'-O-methyl
RNA monomers that commences from the 3'-terminal residue of the
bottom (second) strand, as shown for above asymmetric agents, can
also be used in the above "blunt/fray" DsiRNA agent. In one
embodiment, the top strand (first strand) is the sense strand, and
the bottom strand (second strand) is the antisense strand.
Alternatively, the bottom strand is the sense strand and the top
strand is the antisense strand. Modification and DNA:DNA extension
patterns paralleling those shown above for asymmetric/overhang
agents can also be incorporated into such "blunt/frayed"
agents.
[0164] In one embodiment, a length-extended constituent DsiRNA
agent is provided that comprises deoxyribonucleotides positioned at
sites modeled to function via specific direction of Dicer cleavage,
yet which does not require the presence of a base-paired
deoxyribonucleotide in the double stranded nucleic acid structure.
An exemplary structure for such a molecule is shown:
TABLE-US-00012 5'-XXXXXXXXXXXXXXXXXXXDDXX-3'
3'-YXXXXXXXXXXXXXXXXXDDXXXX-5'
wherein "X"=RNA, "Y" is an optional overhang domain comprised of
0-10 RNA monomers that are optionally 2'-O-methyl RNA monomers--in
certain embodiments, "Y" is an overhang domain comprised of 1-4 RNA
monomers that are optionally 2'-O-methyl RNA monomers, and "D"=DNA.
In one embodiment, the top strand is the sense strand, and the
bottom strand is the antisense strand. Alternatively, the bottom
strand is the sense strand and the top strand is the antisense
strand. The above structure is modeled to force Dicer to cleave a
minimum of a 21mer duplex as its primary post-processing form. In
embodiments where the bottom strand of the above structure is the
antisense strand, the positioning of two deoxyribonucleotide
residues at the ultimate and penultimate residues of the 5' end of
the antisense strand is likely to reduce off-target effects (as
prior studies have shown a 2'-O-methyl modification of at least the
penultimate position from the 5' terminus of the antisense strand
to reduce off-target effects; see, e.g., US 2007/0223427).
[0165] In certain embodiments, the "D" residues of any of the above
structures include at least one PS-DNA or PS-RNA. Optionally, the
"D" residues of any of the above structures include at least one
modified nucleotide that inhibits Dicer cleavage.
[0166] In some embodiments, the constituent DsiRNA agent of the
instant invention further comprises a linking moiety or domain that
joins the sense and antisense strands of a constituent
DNA:DNA-extended DsiRNA agent. Optionally, such a linking moiety
domain joins the 3' end of the sense strand and the 5' end of the
antisense strand. The linking moiety may be a chemical
(non-nucleotide) linker, such as an oligomethylenediol linker,
oligoethylene glycol linker, or other art-recognized linker moiety.
Alternatively, the linker can be a nucleotide linker, optionally
including an extended loop and/or tetraloop.
[0167] In one embodiment, the constituent DsiRNA agent has an
asymmetric structure, with the sense strand having a 27-base pair
length, the antisense strand having a 29-base pair length with a
1-4 base 3'-overhang (e.g., a one base 3'-overhang, a two base
3'-overhang, a three base 3'-overhang or a four base 3'-overhang),
and with deoxyribonucleotides located at positions 24 and 25 of the
sense strand (numbering from position 1 at the 5' of the sense
strand) and each base paired with a cognate deoxyribonucleotide of
the antisense strand. In another embodiment, this constituent
DsiRNA agent has an asymmetric structure further containing 2
deoxyribonucleotides at the 3' end of the sense strand.
Modification of Constituent DsiRNA(s) of Bifunctional or Functional
Group-Tethered DsiRNA Agents
[0168] One major factor that inhibits the effect of double stranded
RNAs ("dsRNAs") is the degradation of dsRNAs (e.g., siRNAs and
DsiRNAs) by nucleases. A 3'-exonuclease is the primary nuclease
activity present in serum and modification of the 3'-ends of
antisense DNA oligonucleotides is crucial to prevent degradation
(Eder et al., 1991). An RNase-T family nuclease has been identified
called ERI-1 which has 3' to 5' exonuclease activity that is
involved in regulation and degradation of siRNAs (Kennedy et al.,
2004; Hong et al., 2005). This gene is also known as Thex1
(NM.sub.--02067) in mice or THEX1 (NM.sub.--153332) in humans and
is involved in degradation of histone mRNA; it also mediates
degradation of 3'-overhangs in siRNAs, but does not degrade duplex
RNA (Yang et al., 2006). It is therefore reasonable to expect that
3'-end-stabilization of dsRNAs, including the DsiRNAs of the
instant invention, will improve stability.
[0169] XRN1 (NM.sub.--019001) is a 5' to 3' exonuclease that
resides in P-bodies and has been implicated in degradation of mRNA
targeted by miRNA (Rehwinkel et al., 2005) and may also be
responsible for completing degradation initiated by internal
cleavage as directed by a siRNA. XRN2 (NM.sub.--012255) is a
distinct 5' to 3' exonuclease that is involved in nuclear RNA
processing. Although not currently implicated in degradation or
processing of siRNAs and miRNAs, these both are known nucleases
that can degrade RNAs and may also be important to consider.
[0170] RNase A is a major endonuclease activity in mammals that
degrades RNAs. It is specific for ssRNA and cleaves at the 3'-end
of pyrimidine bases. SiRNA degradation products consistent with
RNase A cleavage can be detected by mass spectrometry after
incubation in serum (Turner et al., 2007). The 3'-overhangs enhance
the susceptibility of siRNAs to RNase degradation. Depletion of
RNase A from serum reduces degradation of siRNAs; this degradation
does show some sequence preference and is worse for sequences
having poly A/U sequence on the ends (Haupenthal et al., 2006).
This suggests the possibility that lower stability regions of the
duplex may "breathe" and offer transient single-stranded species
available for degradation by RNase A. RNase A inhibitors can be
added to serum and improve siRNA longevity and potency (Haupenthal
et al., 2007).
[0171] In 21mers, phosphorothioate or boranophosphate modifications
directly stabilize the internucleoside phosphate linkage.
Boranophosphate modified RNAs are highly nuclease resistant, potent
as silencing agents, and are relatively non-toxic. Boranophosphate
modified RNAs cannot be manufactured using standard chemical
synthesis methods and instead are made by in vitro transcription
(IVT) (Hall et al., 2004 and Hall et al., 2006). Phosphorothioate
(PS) modifications can be readily placed in an RNA duplex at any
desired position and can be made using standard chemical synthesis
methods, though the ability to use such modifications within an RNA
duplex that retains RNA silencing activity can be limited. Because
PS moieties are likely to require greater spacing when included
within an RNA duplex-containing agent in order to retain RNA
inhibitory activity, dsDNA extension of constituent DsiRNAs such as
those described herein can provide a means of including more PS
modifications (either PS-DNA or PS-RNA) within a single constituent
DsiRNA agent than would otherwise be available were no such
extension used. It is noted, however, that the PS modification
shows dose-dependent toxicity, so most investigators have
recommended limited incorporation in siRNAs, historically favoring
the 3'-ends where protection from nucleases is most important
(Harborth et al., 2003; Chiu and Rana, 2003; Braasch et al., 2003;
Amarzguioui et al., 2003). More extensive PS modification can be
compatible with potent RNAi activity; however, use of sugar
modifications (such as 2'-O-methyl RNA) may be superior (Choung et
al., 2006).
[0172] A variety of substitutions can be placed at the 2'-position
of the ribose which generally increases duplex stability (T.sub.m)
and can greatly improve nuclease resistance. 2'-O-methyl RNA is a
naturally occurring modification found in mammalian ribosomal RNAs
and transfer RNAs. 2'-O-methyl modification in siRNAs is known, but
the precise position of modified bases within the duplex is
important to retain potency and complete substitution of
2'-O-methyl RNA for RNA will inactivate the siRNA. For example, a
pattern that employs alternating 2'-O-methyl bases can have potency
equivalent to unmodified RNA and is quite stable in serum (Choung
et al., 2006; Czauderna et al., 2003).
[0173] The 2'-fluoro (2'-F) modification is also compatible with
dsRNA (e.g., siRNA and DsiRNA) function; it is most commonly placed
at pyrimidine sites (due to reagent cost and availability) and can
be combined with 2'-O-methyl modification at purine positions; 2'-F
purines are available and can also be used. Heavily modified
duplexes of this kind can be potent triggers of RNAi in vitro
(Allerson et al., 2005; Prakash et al., 2005; Kraynack and Baker,
2006) and can improve performance and extend duration of action
when used in vivo (Morrissey et al., 2005a; Morrissey et al.,
2005b). A highly potent, nuclease stable, blunt 19mer duplex
containing alternative 2'-F and 2'-O-Me bases is taught by
Allerson. In this design, alternating 2'-O-Me residues are
positioned in an identical pattern to that employed by Czauderna,
however the remaining RNA residues are converted to 2'-F modified
bases. A highly potent, nuclease resistant siRNA employed by
Morrissey employed a highly potent, nuclease resistant siRNA in
vivo. In addition to 2'-O-Me RNA and 2'-F RNA, this duplex includes
DNA, RNA, inverted abasic residues, and a 3'-terminal PS
internucleoside linkage. While extensive modification has certain
benefits, more limited modification of the duplex can also improve
in vivo performance and is both simpler and less costly to
manufacture. Soutschek et al. (2004) employed a duplex in vivo and
was mostly RNA with two 2'-O-Me RNA bases and limited 3'-terminal
PS internucleoside linkages.
[0174] Locked nucleic acids (LNAs) are a different class of
2'-modification that can be used to stabilize dsRNA (e.g., siRNA
and DsiRNA). Patterns of LNA incorporation that retain potency are
more restricted than 2'-O-methyl or 2'-F bases, so limited
modification is preferred (Braasch et al., 2003; Grunweller et al.,
2003; Elmen et al., 2005). Even with limited incorporation, the use
of LNA modifications can improve dsRNA performance in vivo and may
also alter or improve off target effect profiles (Mook et al.,
2007).
[0175] Synthetic nucleic acids introduced into cells or live
animals can be recognized as "foreign" and trigger an immune
response. Immune stimulation constitutes a major class of
off-target effects which can dramatically change experimental
results and even lead to cell death. The innate immune system
includes a collection of receptor molecules that specifically
interact with DNA and RNA that mediate these responses, some of
which are located in the cytoplasm and some of which reside in
endosomes (Marques and Williams, 2005; Schlee et al., 2006).
Delivery of siRNAs by cationic lipids or liposomes exposes the
siRNA to both cytoplasmic and endosomal compartments, maximizing
the risk for triggering a type 1 interferon (IFN) response both in
vitro and in vivo (Morrissey et al., 2005b; Sioud and Sorensen,
2003; Sioud, 2005; Ma et al., 2005). RNAs transcribed within the
cell are less immunogenic (Robbins et al., 2006) and synthetic RNAs
that are immunogenic when delivered using lipid-based methods can
evade immune stimulation when introduced unto cells by mechanical
means, even in vivo (Heidel et al., 2004). However, lipid based
delivery methods are convenient, effective, and widely used. Some
general strategy to prevent immune responses is needed, especially
for in vivo application where all cell types are present and the
risk of generating an immune response is highest. Use of chemically
modified RNAs may solve most or even all of these problems.
[0176] Although certain sequence motifs are clearly more
immunogenic than others, it appears that the receptors of the
innate immune system in general distinguish the presence or absence
of certain base modifications which are more commonly found in
mammalian RNAs than in prokaryotic RNAs. For example,
pseudouridine, N6-methyl-A, and 2'-O-methyl modified bases are
recognized as "self" and inclusion of these residues in a synthetic
RNA can help evade immune detection (Kariko et al., 2005).
Extensive 2'-modification of a sequence that is strongly
immunostimulatory as unmodified RNA can block an immune response
when administered to mice intravenously (Morrissey et al., 2005b).
However, extensive modification is not needed to escape immune
detection and substitution of as few as two 2'-O-methyl bases in a
single strand of a siRNA duplex can be sufficient to block a type 1
IFN response both in vitro and in vivo; modified U and G bases are
most effective (Judge et al., 2006). As an added benefit, selective
incorporation of 2'-O-methyl bases can reduce the magnitude of
off-target effects (Jackson et al., 2006). Use of 2'-O-methyl bases
should therefore be considered for all dsRNAs intended for in vivo
applications as a means of blocking immune responses and has the
added benefit of improving nuclease stability and reducing the
likelihood of off-target effects.
[0177] Although cell death can result from immune stimulation,
assessing cell viability is not an adequate method to monitor
induction of IFN responses. IFN responses can be present without
cell death, and cell death can result from target knockdown in the
absence of IFN triggering (for example, if the targeted gene is
essential for cell viability). Relevant cytokines can be directly
measured in culture medium and a variety of commercial kits exist
which make performing such assays routine. While a large number of
different immune effector molecules can be measured, testing levels
of IFN-.alpha., TNF-.alpha., and IL-6 at 4 and 24 hours post
transfection is usually sufficient for screening purposes. It is
important to include a "transfection reagent only control" as
cationic lipids can trigger immune responses in certain cells in
the absence of any nucleic acid cargo. Including controls for IFN
pathway induction should be considered for cell culture work. It is
essential to test for immune stimulation whenever administering
nucleic acids in vivo, where the risk of triggering IFN responses
is highest.
[0178] Modifications can be included in the bifunctional or
functional group-tethered DsiRNA agents of the present invention so
long as the modification does not prevent the bifunctional or
functional group-tethered DsiRNA agent from serving as a substrate
for RNase H, and so long as such modification also does not prevent
constituent DsiRNA agent(s) that are liberated post-RNase H
cleavage from serving as a substrate for Dicer. As recently
described in U.S. Patent Application 61/138,946, base paired
deoxyribonucleotides can be attached to DsiRNA molecules, resulting
in enhanced RNAi efficacy and duration, provided that such
extension is performed in a region of the extended molecule that
does not interfere with Dicer processing (e.g., 3' of the Dicer
cleavage site of the sense strand/5' of the Dicer cleavage site of
the antisense strand). In one embodiment, one or more modifications
are made that enhance Dicer processing of the constituent DsiRNA
agent(s) of a bifunctional or functional group-tethered DsiRNA
agent of the invention. In a second embodiment, one or more
modifications are made that result in more effective RNAi
generation. In a third embodiment, one or more modifications are
made that support a greater RNAi effect. In a fourth embodiment,
one or more modifications are made that result in greater potency
per each constituent DsiRNA agent molecule to be delivered to the
cell. Modifications can be incorporated in the 3'-terminal region,
the 5'-terminal region, in both the 3'-terminal and 5'-terminal
region of a constituent DsiRNA agent or in some instances in
various positions within the sequence. With the restrictions noted
above in mind, any number and combination of modifications can be
incorporated into the constituent DsiRNA agent(s). Where multiple
modifications are present, they may be the same or different.
Modifications to bases, sugar moieties, the phosphate backbone, and
their combinations are contemplated. Either 5'-terminus of a
constituent DsiRNA agent can be phosphorylated.
[0179] Examples of modifications contemplated for the phosphate
backbone of the bifunctional or functional group-tethered DsiRNA
agents of the instant invention include phosphonates, including
methylphosphonate, phosphorothioate, and phosphotriester
modifications such as alkylphosphotriesters, and the like. Examples
of modifications contemplated for the sugar moiety include 2'-alkyl
pyrimidine, such as 2'-O-methyl, 2'-fluoro, amino, and deoxy
modifications and the like (see, e.g., Amarzguioui et al., 2003).
Examples of modifications contemplated for the base groups include
abasic sugars, 2-O-alkyl modified pyrimidines, 4-thiouracil,
5-bromouracil, 5-iodouracil, and 5-(3-aminoallyl)-uracil and the
like. Locked nucleic acids, or LNA's, could also be incorporated.
Many other modifications are known and can be used so long as the
above criteria are satisfied. Examples of modifications are also
disclosed in U.S. Pat. Nos. 5,684,143, 5,858,988 and 6,291,438 and
in U.S. published patent application No. 2004/0203145 A1. Other
modifications are disclosed in Herdewijn (2000), Eckstein (2000),
Rusckowski et al. (2000), Stein et al. (2001); Vorobjev et al.
(2001).
[0180] One or more modifications contemplated can be incorporated
into either strand. The placement of the modifications in the
constituent DsiRNA agent(s) of the bifunctional or functional
group-tethered DsiRNA agents of the invention can greatly affect
the characteristics of the constituent DsiRNA agent(s), including
conferring greater potency and stability, reducing toxicity,
enhancing Dicer processing, and minimizing an immune response. In
one embodiment, the antisense strand or the sense strand or both
strands have one or more 2'-O-methyl modified nucleotides. In
another embodiment, the antisense strand contains 2'-O-methyl
modified nucleotides. In another embodiment, the antisense stand
contains a 3' overhang that is comprised of 2'-O-methyl modified
nucleotides. The antisense strand could also include additional
2'-O-methyl modified nucleotides.
[0181] In certain embodiments of the present invention, the
constituent DsiRNA(s) of the bifunctional or functional
group-tethered DsiRNA agents of the invention possess one or more
properties which enhance constituent DsiRNA processing by Dicer.
According to these embodiments, the constituent DsiRNA agent has a
length sufficient such that it is processed by Dicer to produce an
active siRNA and at least one of the following properties: (i) the
constituent DsiRNA agent is asymmetric, e.g., has a 3' overhang on
the antisense strand and (ii) the constituent DsiRNA agent has a
modified 3' end on the sense strand to direct orientation of Dicer
binding and processing of the dsRNA region to an active siRNA. In
certain such embodiments, the presence of one or more base paired
deoxyribonucleotides in a region of the sense strand that is 3' to
the projected site of Dicer enzyme cleavage and corresponding
region of the antisense strand that is 5' of the projected site of
Dicer enzyme cleavage can also serve to orient such a constituent
DsiRNA molecule for appropriate directionality of Dicer enzyme
cleavage.
[0182] In certain embodiments, the length of such a dsDNA region
(or length of the region comprising DNA:DNA base pairs) is 1-50
base pairs, optionally 2-30 base pairs, preferably 2-20 base pairs,
and more preferably 2-10 base pairs. Thus, a DNA:DNA-extended
constituent DsiRNA of the instant invention may possess a dsDNA
region that is 1, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
50 or more base pairs in length.
[0183] In some embodiments, the longest strand in a constituent
DsiRNA of the bifunctional or functional group-tethered DsiRNA
agent of the invention comprises 29-43 nucleotides. In one
embodiment, the constituent DsiRNA agent is asymmetric such that
the 3' end of the sense strand and 5' end of the antisense strand
form a blunt end, and the 3' end of the antisense strand overhangs
the 5' end of the sense strand. In certain embodiments, the 3'
overhang of the antisense strand is 1-10 nucleotides, and
optionally is 1-4 nucleotides, for example 2 nucleotides. Both the
sense and the antisense strand may also have a 5' phosphate.
[0184] In certain embodiments, the sense strand of a constituent
DsiRNA of the bifunctional or functional group-tethered DsiRNA
agent of the invention that comprises base paired
deoxyribonucleotide residues has a total length of between 26
nucleotides and 39 nucleotides. In certain embodiments, the length
of the sense strand is between 27 and 35 nucleotides, or,
optionally, is between 27 and 33 nucleotides in length. Optionally,
the sense strand has a length of 26, 27, 28, 29, 30, 31, 32, 33,
34, 35, 36, 37, 38 or 39 nucleotides. In related embodiments, the
antisense strand has a length of between 27 and 43 nucleotides in
length. In certain such embodiments, the antisense strand has a
length of between 27 and 39 nucleotides in length, of between 27
and 35 nucleotides in length, of between 28 and 37 nucleotides in
length, or, optionally, of between 29 and 35 nucleotides in length.
Optionally, the antisense strand has a length of 27, 28, 29, 30,
31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42 or 43
nucleotides.
[0185] In certain embodiments, the presence of one or more base
paired deoxyribonucleotides in a region of the sense strand that is
3' of the projected site of Dicer enzyme cleavage and corresponding
region of the antisense strand that is 5' of the projected site of
Dicer enzyme cleavage within a constituent DsiRNA can serve to
direct Dicer enzyme cleavage of such a molecule. While certain
constituent DsiRNA agents can possess a sense strand
deoxyribonucleotide that is located at position 24 or more 3' when
counting from position 1 at the 5' end of the sense strand, and
having this position 24 or more 3' deoxyribonucleotide of the sense
strand base pairing with a cognate deoxyribonucleotide of the
antisense strand, in some embodiments, it is also possible to
direct Dicer to cleave a shorter product, e.g., a 19mer or a 20mer
via inclusion of deoxyribonucleotide residues at, e.g., position 20
of the sense strand. Such a position 20 deoxyribonucleotide base
pairs with a corresponding deoxyribonucleotide of the antisense
strand, thereby directing Dicer-mediated excision of a 19mer as the
most prevalent Dicer product (it is noted that the antisense strand
can also comprise one or two deoxyribonucleotide residues
immediately 3' of the antisense residue that base pairs with the
position 20 deoxyribonucleotide residue of the sense strand in such
embodiments, to further direct Dicer cleavage of the antisense
strand). In such embodiments, the double-stranded DNA region (which
is inclusive of modified nucleic acids that block Dicer cleavage)
will generally possess a length of greater than 1 or 2 base pairs
(e.g., 3 to 5 base pairs or more), in order to direct Dicer
cleavage to generate what is normally a non-preferred length of
Dicer cleavage product. A parallel approach can also be taken to
direct Dicer excision of 20mer siRNAs from constituent DsiRNA(s) of
the bifunctional or functional group-tethered DsiRNA agents of the
invention, with the positioning of the first deoxyribonucleotide
residue of the sense strand (when surveying the sense strand from
position 1 at the 5' terminus of the sense strand of a constituent
DsiRNA) occurring at position 21.
[0186] In certain embodiments, the sense strand of the constituent
DsiRNA of the bifunctional or functional group-tethered DsiRNA
agent of the invention is modified for Dicer processing by suitable
modifiers located at the 3' end of the sense strand, i.e., the
constituent DsiRNA agent is designed to direct orientation of Dicer
binding and processing via sense strand modification. Suitable
modifiers include nucleotides such as deoxyribonucleotides,
dideoxyribonucleotides, acyclonucleotides and the like and
sterically hindered molecules, such as fluorescent molecules and
the like. Acyclonucleotides substitute a 2-hydroxyethoxymethyl
group for the 2'-deoxyribofuranosyl sugar normally present in
dNMPs. Other nucleotide modifiers could include 3'-deoxyadenosine
(cordycepin), 3'-azido-3'-deoxythymidine (AZT),
2',3'-dideoxyinosine (ddI), 2',3'-dideoxy-3'-thiacytidine (3TC),
2',3'-didehydro-2',3'-dideoxythymidine (d4T) and the monophosphate
nucleotides of 3'-azido-3'-deoxythymidine (AZT),
2',3'-dideoxy-3'-thiacytidine (3TC) and
2',3'-didehydro-2',3'-dideoxythymidine (d4T). In one embodiment,
deoxynucleotides are used as the modifiers. When nucleotide
modifiers are utilized, 1-3 nucleotide modifiers, or 2 nucleotide
modifiers are substituted for the ribonucleotides on the 3' end of
the sense strand. When sterically hindered molecules are utilized,
they are attached to the ribonucleotide at the 3' end of the
antisense strand. Thus, the length of the strand does not change
with the incorporation of the modifiers. In another embodiment, the
invention contemplates substituting two DNA bases in the DsiRNA
agent to direct the orientation of Dicer processing of the
antisense strand. In a further embodiment of the present invention,
two terminal DNA bases are substituted for two ribonucleotides on
the 3'-end of the sense strand forming a blunt end of the duplex on
the 3' end of the sense strand and the 5' end of the antisense
strand, and a two-nucleotide RNA overhang is located on the 3'-end
of the antisense strand. This is an asymmetric composition with DNA
on the blunt end and RNA bases on the overhanging end. In certain
embodiments of the instant invention, the modified nucleotides
(e.g., deoxyribonucleotides) of the penultimate and ultimate
positions of the 3' terminus of the sense strand base pair with
corresponding modified nucleotides (e.g., deoxyribonucleotides) of
the antisense strand (optionally, the penultimate and ultimate
residues of the 5' end of the antisense strand in those constituent
DsiRNA agents of the instant invention possessing a blunt end at
the 3' terminus of the sense strand/5' terminus of the antisense
strand).
[0187] The sense and antisense strands of a constituent(s) DsiRNA
of the bifunctional or functional group-tethered DsiRNA agent of
the instant invention anneal under biological conditions, such as
the conditions found in the cytoplasm of a cell. In addition, a
region of one of the sequences, particularly of the antisense
strand, of the constituent DsiRNA agent has a sequence length of at
least 19 nucleotides, wherein these nucleotides are in the
21-nucleotide region adjacent to the 3' end of the antisense strand
and are sufficiently complementary to a nucleotide sequence of the
RNA produced from the target gene to anneal with and/or decrease
levels of such a target RNA.
[0188] The constituent DsiRNA(s) of the bifunctional or functional
group-tethered DsiRNA agent of the instant invention may possess
one or more deoxyribonucleotide base pairs located at any positions
of sense and antisense strands that are located 3' of the projected
Dicer cleavage site of the sense strand and 5' of the projected
Dicer cleavage site of the antisense strand. In certain
embodiments, one, two, three or all four of positions 24-27 of the
sense strand (starting from position 1 at the 5' terminus of the
sense strand) are deoxyribonucleotides, each deoxyribonucleotide of
which base pairs with a corresponding deoxyribonucleotide of the
antisense strand. In certain embodiments, the deoxyribonucleotides
of the 5' region of the antisense strand (e.g., the region of the
antisense strand located 5' of the projected Dicer cleavage site
for a given constituent DsiRNA molecule) are not complementary to
the target RNA to which the constituent DsiRNA agent is directed.
In related embodiments, the entire region of the antisense strand
located 5' of the projected Dicer cleavage site of a constituent
DsiRNA agent is not complementary to the target RNA to which the
constituent DsiRNA agent is directed. In certain embodiments, the
deoxyribonucleotides of the antisense strand or the entire region
of the antisense strand that is located 5' of the projected Dicer
cleavage site of the constituent DsiRNA agent is not sufficiently
complementary to the target RNA to enhance annealing of the
antisense strand of the constituent DsiRNA to the target RNA when
the antisense strand is annealed to the target RNA under conditions
sufficient to allow for annealing between the antisense strand and
the target RNA (e.g., a "core" antisense strand sequence lacking
the DNA-extended region anneals equally well to the target RNA as
the same "core" antisense strand sequence also extended with
sequence of the DNA-extended region, optionally also comprising
residual sequence from the RNase H-cleaved domain post-RNase H
processing).
[0189] A constituent DsiRNA of a bifunctional or functional
group-tethered DsiRNA agent may also have one or more of the
following additional properties: (a) the antisense strand has a
right shift from the typical 21mer, (b) the strands may not be
completely complementary, i.e., the strands may contain simple
mismatch pairings and (c) base modifications such as locked nucleic
acid(s) may be included in the 5' end of the sense strand. A
"typical" 21mer siRNA is designed using conventional techniques. In
one technique, a variety of sites are commonly tested in parallel
or pools containing several distinct siRNA duplexes specific to the
same target with the hope that one of the reagents will be
effective (Ji et al., 2003). Other techniques use design rules and
algorithms to increase the likelihood of obtaining active RNAi
effector molecules (Schwarz et al., 2003; Khvorova et al., 2003;
Ui-Tei et al., 2004; Reynolds et al., 2004; Krol et al., 2004; Yuan
et al., 2004; Boese et al., 2005). High throughput selection of
siRNA has also been developed (U.S. published patent application
No. 2005/0042641 A1). Potential target sites can also be analyzed
by secondary structure predictions (Heale et al., 2005). This 21mer
is then used to design a right shift to include 3-9 additional
nucleotides on the 5' end of the 21mer. The sequence of these
additional nucleotides may have any sequence. In one embodiment,
the added ribonucleotides are based on the sequence of the target
gene. Even in this embodiment, full complementarity between the
target sequence and the antisense siRNA is not required.
[0190] The first and second oligonucleotides of a bifunctional or
functional group-tethered DsiRNA agent of the instant invention are
not required to be completely complementary. They only need to be
substantially complementary to anneal under biological conditions
and to provide a substrate for RNase H and, in turn, for Dicer that
produces siRNA(s) sufficiently complementary to target sequence(s).
Locked nucleic acids, or LNA's, are well known to a skilled artisan
(Elman et al., 2005; Kurreck et al., 2002; Crinelli et al., 2002;
Braasch and Corey, 2001; Bondensgaard et al., 2000; Wahlestedt et
al., 2000). In one embodiment, an LNA is incorporated at the 5'
terminus of the sense strand of a constituent DsiRNA agent. In
another embodiment, an LNA is incorporated at the 5' terminus of
the sense strand in duplexes designed to include a 3' overhang on
the antisense strand (within a constituent DsiRNA agent of the
bifunctional or functional group-tethered DsiRNA agent of the
instant invention).
[0191] In certain embodiments, the constituent DsiRNA of a
bifunctional or functional group-tethered DsiRNA agent of the
instant invention has an asymmetric structure, with the sense
strand having a 27-base pair length, and the antisense strand
having a 29-base pair length with a 2 base 3'-overhang. Such
constituent agents optionally may possess between one and four
deoxyribonucleotides of the 3' terminal region (specifically, the
region 3' of the projected Dicer cleavage site) of the sense
strand, at least one of which base pairs with a cognate
deoxyribonucleotide of the 5' terminal region (specifically, the
region 5' of the projected Dicer cleavage site) of the antisense
strand. In other embodiments, the sense strand has a 28-base pair
length, and the antisense strand has a 30-base pair length with a 2
base 3'-overhang. Such agents optionally may possess between one
and five deoxyribonucleotides of the 3' terminal region
(specifically, the region 3' of the projected Dicer cleavage site)
of the sense strand, at least one of which base pairs with a
cognate deoxyribonucleotide of the 5' terminal region
(specifically, the region 5' of the projected Dicer cleavage site)
of the antisense strand. In additional embodiments, the sense
strand has a 29-base pair length, and the antisense strand has a
31-base pair length with a 2 base 3'-overhang. Such agents
optionally possess between one and six deoxyribonucleotides of the
3' terminal region (specifically, the region 3' of the projected
Dicer cleavage site) of the sense strand, at least one of which
base pairs with a cognate deoxyribonucleotide of the 5' terminal
region (specifically, the region 5' of the projected Dicer cleavage
site) of the antisense strand. In further embodiments, the sense
strand has a 30-base pair length, and the antisense strand has a
32-base pair length with a 2 base 3'-overhang. Such agents
optionally possess between one and seven deoxyribonucleotides of
the 3' terminal region (specifically, the region 3' of the
projected Dicer cleavage site) of the sense strand, at least one of
which base pairs with a cognate deoxyribonucleotide of the 5'
terminal region (specifically, the region 5' of the projected Dicer
cleavage site) of the antisense strand. In other embodiments, the
sense strand has a 31-base pair length, and the antisense strand
has a 33-base pair length with a 2 base 3'-overhang. Such agents
optionally possess between one and eight deoxyribonucleotides of
the 3' terminal region (specifically, the region 3' of the
projected Dicer cleavage site) of the sense strand, at least one of
which base pairs with a cognate deoxyribonucleotide of the 5'
terminal region (specifically, the region 5' of the projected Dicer
cleavage site) of the antisense strand. In additional embodiments,
the sense strand has a 32-base pair length, and the antisense
strand has a 34-base pair length with a 2 base 3'-overhang. Such
agents optionally possess between one and nine deoxyribonucleotides
of the 3' terminal region (specifically, the region 3' of the
projected Dicer cleavage site) of the sense strand, at least one of
which base pairs with a cognate deoxyribonucleotide of the 5'
terminal region (specifically, the region 5' of the projected Dicer
cleavage site) of the antisense strand. In certain further
embodiments, the sense strand has a 33-base pair length, and the
antisense strand has a 35-base pair length with a 2 base
3'-overhang. Such agents optionally possess between one and ten
deoxyribonucleotides of the 3' terminal region (specifically, the
region 3' of the projected Dicer cleavage site) of the sense
strand, at least one of which base pairs with a cognate
deoxyribonucleotide of the 5' terminal region (specifically, the
region 5' of the projected Dicer cleavage site) of the antisense
strand. In still other embodiments, any of these constituent DsiRNA
agents have an asymmetric structure that further contains 2
deoxyribonucleotides at the 3' end of the sense strand in place of
two of the ribonucleotides; optionally, these 2
deoxyribonucleotides base pair with cognate deoxyribonucleotides of
the antisense strand.
[0192] Certain bifunctional or functional group-tethered DsiRNA
agents containing two separate oligonucleotides can be linked by a
third structure. The third structure will not block Dicer activity
on the constituent DsiRNA agent and will not interfere with the
directed destruction of the RNA transcribed from the target gene.
In one embodiment, the third structure may be a chemical linking
group. Many suitable chemical linking groups are known in the art
and can be used. Alternatively, the third structure may be an
oligonucleotide that links the two oligonucleotides of the
bifunctional or functional group-tethered DsiRNA agent in a manner
such that a hairpin structure is produced upon annealing of the two
oligonucleotides making up the double stranded nucleic acid
composition. The hairpin structure will not block Dicer activity on
a constituent DsiRNA agent and will not interfere with the directed
destruction of target RNA(s) by such constituent DsiRNA
agent(s).
[0193] In certain embodiments, the constituent DsiRNA agent(s) of
the constituent of the invention has several properties which
enhance processing of constituent DsiRNA agents by Dicer. According
to such embodiments, the constituent DsiRNA agent has a length
sufficient such that it is processed by Dicer to produce an siRNA
and at least one of the following properties: (i) the constituent
DsiRNA agent is asymmetric, e.g., has a 3' overhang on the sense
strand and (ii) the constituent DsiRNA agent has a modified 3' end
on the antisense strand to direct orientation of Dicer binding and
processing of the dsRNA region to an active siRNA. According to
these embodiments, the longest strand in the constituent DsiRNA
agent comprises 25-43 nucleotides. In one embodiment, the sense
strand comprises 25-39 nucleotides and the antisense strand
comprises 26-43 nucleotides. The resulting double stranded nucleic
acid can have an overhang on the 3' end of the sense strand. The
overhang is 1-4 nucleotides, such as 2 nucleotides. The antisense
or sense strand may also have a 5' phosphate.
[0194] In certain embodiments, the sense strand of a constituent
DsiRNA agent is modified for Dicer processing by suitable modifiers
located at the 3' end of the sense strand, i.e., the constituent
DsiRNA agent is designed to direct orientation of Dicer binding and
processing. Suitable modifiers include nucleotides such as
deoxyribonucleotides, dideoxyribonucleotides, acyclonucleotides and
the like and sterically hindered molecules, such as fluorescent
molecules and the like. Acyclonucleotides substitute a
2-hydroxyethoxymethyl group for the 2'-deoxyribofuranosyl sugar
normally present in dNMPs. Other nucleotide modifiers could include
3'-deoxyadenosine (cordycepin), 3'-azido-3'-deoxythymidine (AZT),
2',3'-dideoxyinosine (ddI), 2',3'-dideoxy-3'-thiacytidine (3TC),
2',3'-didehydro-2',3'-dideoxythymidine (d4T) and the monophosphate
nucleotides of 3'-azido-3'-deoxythymidine (AZT),
2',3'-dideoxy-3'-thiacytidine (3TC) and
2',3'-didehydro-2',3'-dideoxythymidine (d4T). In one embodiment,
deoxynucleotides are used as the modifiers. When nucleotide
modifiers are utilized, 1-3 nucleotide modifiers, or 2 nucleotide
modifiers are substituted for the ribonucleotides on the 3' end of
the sense strand. When sterically hindered molecules are utilized,
they are attached to the ribonucleotide at the 3' end of the
antisense strand. Thus, the length of the strand does not change
with the incorporation of the modifiers. In another embodiment, the
invention contemplates substituting two DNA bases in the double
stranded nucleic acid to direct the orientation of Dicer
processing. In a further embodiment, two terminal DNA bases are
located on the 3' end of the sense strand in place of two
ribonucleotides forming a blunt end of the duplex on the 5' end of
the antisense strand and the 3' end of the sense strand, and a
two-nucleotide RNA overhang is located on the 3'-end of the
antisense strand. This is an asymmetric composition with DNA on the
blunt end and RNA bases on the overhanging end.
[0195] In certain other embodiments, the antisense strand of a
constituent DsiRNA agent is modified for Dicer processing by
suitable modifiers located at the 3' end of the antisense strand,
i.e., the constituent DsiRNA agent is designed to direct
orientation of Dicer binding and processing. Suitable modifiers
include nucleotides such as deoxyribonucleotides,
dideoxyribonucleotides, acyclonucleotides and the like and
sterically hindered molecules, such as fluorescent molecules and
the like. Acyclonucleotides substitute a 2-hydroxyethoxymethyl
group for the 2'-deoxyribofuranosyl sugar normally present in
dNMPs. Other nucleotide modifiers could include 3'-deoxyadenosine
(cordycepin), 3'-azido-3'-deoxythymidine (AZT),
2',3'-dideoxyinosine (ddI), 2',3'-dideoxy-3'-thiacytidine (3TC),
2',3'-didehydro-2',3'-dideoxythymidine (d4T) and the monophosphate
nucleotides of 3'-azido-3'-deoxythymidine (AZT),
2',3'-dideoxy-3'-thiacytidine (3TC) and
2',3'-didehydro-2',3'-dideoxythymidine (d4T). In one embodiment,
deoxynucleotides are used as the modifiers. When nucleotide
modifiers are utilized, 1-3 nucleotide modifiers, or 2 nucleotide
modifiers are substituted for the ribonucleotides on the 3' end of
the antisense strand. When sterically hindered molecules are
utilized, they are attached to the ribonucleotide at the 3' end of
the antisense strand. Thus, the length of the strand does not
change with the incorporation of the modifiers. In another
embodiment, the invention contemplates substituting two DNA bases
in the double stranded nucleic acid to direct the orientation of
Dicer processing. In a further invention, two terminal DNA bases
are located on the 3' end of the antisense strand in place of two
ribonucleotides forming a blunt end of the duplex on the 5' end of
the sense strand and the 3' end of the antisense strand, and a
two-nucleotide RNA overhang is located on the 3'-end of the sense
strand. This is also an asymmetric composition with DNA on the
blunt end and RNA bases on the overhanging end.
[0196] The sense and antisense strands anneal under biological
conditions, such as the conditions found in the cytoplasm of a
cell. In addition, a region of one of the sequences, particularly
of the antisense strand, of the double stranded nucleic acid has a
sequence length of at least 19 nucleotides, wherein these
nucleotides are adjacent to the 3' end of antisense strand and are
sufficiently complementary to a nucleotide sequence of the target
RNA to direct RNA interference.
[0197] Additionally, a constituent DsiRNA agent structure can be
optimized to ensure that the oligonucleotide segment generated from
Dicer's cleavage will be the portion of the oligonucleotide that is
most effective in inhibiting gene expression. For example, in one
embodiment, a 27-35-bp oligonucleotide of the constituent DsiRNA
agent structure is synthesized wherein the anticipated 21 to 22-bp
segment that will inhibit gene expression is located on the 3'-end
of the antisense strand. The remaining bases located on the 5'-end
of the antisense strand will be cleaved by Dicer and will be
discarded. This cleaved portion can be homologous (i.e., based on
the sequence of the target sequence) or non-homologous and added to
extend the nucleic acid strand. Such extension can be performed
with base paired DNA residues (double stranded DNA:DNA extensions),
resulting in extended constituent DsiRNA agents having improved
efficacy or duration of effect than corresponding double stranded
RNA:RNA-extended constituent DsiRNA agents. Indeed, in certain
embodiments, such regions of DNA:DNA extension can be used as
sequences that join two otherwise independent DsiRNA moieties into
a single bifunctional agent (such as the agent shown in FIG.
4).
[0198] US 2007/0265220 discloses that 27mer DsiRNAs show improved
stability in serum over comparable 21mer siRNA compositions, even
absent chemical modification. Modifications of constituent DsiRNA
agents, such as inclusion of 2'-O-methyl RNA in the antisense
strand, in patterns such as detailed in US 2007/0265220 and
otherwise herein, when coupled with addition of a 5' Phosphate, can
improve stability of constituent DsiRNA agents. Addition of
5'-phosphate to all strands in synthetic RNA duplexes may be an
inexpensive and physiological method to confer some limited degree
of nuclease stability.
[0199] The chemical modification patterns of the constituent DsiRNA
agents of the instant invention are designed to enhance the
efficacy of such agents. Accordingly, such modifications are
designed to avoid reducing potency of constituent DsiRNA agents; to
avoid interfering with Dicer processing of constituent DsiRNA
agents; to improve stability in biological fluids (reduce nuclease
sensitivity) of constituent DsiRNA agents; or to block or evade
detection by the innate immune system. Such modifications are also
designed to avoid being toxic and to avoid increasing the cost or
impact the ease of manufacturing the instant bifunctional and
functional group-tethered DsiRNA agents of the invention.
Joining of Constituent DsiRNA Agents to Form Bifunctional or
Functional Group-Tethered DsiRNA Agents
[0200] Certain bifunctional and functional group-tethered DsiRNA
agents of the instant invention comprise an RNase H cleavable
domain, with such an RNase H cleavable domain constituting a
double-stranded span of nucleotides that joins a constituent DsiRNA
either to another constituent DsiRNA or to a functional group. The
exemplary RNase H cleavable domain of the invention is a double
stranded sequence comprising a sufficient length of RNA:DNA
duplexed nucleotides to provoke RNase H cleavage. In certain
embodiments, the length of such a double-stranded RNA:DNA RNase
H-cleavable region is 4-50 base pairs, optionally 4-30 base pairs,
4-20 base pairs, 4-16 base pairs, 4-10 base pairs, 6-10 base pairs
and in certain embodiments 7-9 base pairs. Thus, an RNase
H-cleavable agent of the instant invention may possess a
double-stranded RNA:DNA RNase H-cleavable region that is 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, 34, 35, 36, 37, 38, 39, 40,
41, 42, 43, 44, 45, 46, 47, 48, 49, 50 or more base pairs in
length.
Conjugation and Delivery of Bifunctional and Functional
Group-Tethered DsiRNA Agents
[0201] In certain embodiments, the present invention relates to a
method for treating a subject having or at risk of developing a
disease or disorder. In such embodiments, the DsiRNA can act as a
novel therapeutic agent for controlling the disease or disorder.
The method comprises administering a pharmaceutical composition of
the invention to the patient (e.g., human), such that the
expression, level and/or activity a target RNA is reduced. The
expression, level and/or activity of a polypeptide endoded by the
target RNA might also be reduced by a DsiRNA of the instant
invention.
[0202] In the treatment of a disease or disorder, the DsiRNA can be
brought into contact with the cells or tissue exhibiting or
associated with a disease or disorder. For example, DsiRNA
substantially identical to all or part of a target RNA sequence,
may be brought into contact with or introduced into a diseased,
disease-associated or infected cell, either in vivo or in vitro.
Similarly, DsiRNA substantially identical to all or part of a
target RNA sequence may administered directly to a subject having
or at risk of developing a disease or disorder.
[0203] Therapeutic use of the DsiRNA agents of the instant
invention can involve use of formulations of DsiRNA agents
comprising multiple different DsiRNA agent sequences. For example,
two or more, three or more, four or more, five or more, etc. of the
presently described agents can be combined to produce a formulation
that, e.g., targets multiple different regions of one or more
target RNA(s). A DsiRNA agent of the instant invention may also be
constructed such that either strand of the DsiRNA agent
independently targets two or more regions of a target RNA. Use of
multifunctional DsiRNA molecules that target more then one region
of a target nucleic acid molecule is expected to provide potent
inhibition of RNA levels and expression. For example, a single
multifunctional DsiRNA construct of the invention can target both
conserved and variable regions of a target nucleic acid molecule,
thereby allowing down regulation or inhibition of, e.g., different
strain variants of a virus, or splice variants encoded by a single
target gene.
[0204] A DsiRNA agent of the invention can be conjugated (e.g., at
its 5' or 3' terminus of its sense or antisense strand) or
unconjugated to another moiety (e.g. a non-nucleic acid moiety such
as a peptide), an organic compound (e.g., a dye, cholesterol, or
the like). Modifying DsiRNA agents in this way may improve cellular
uptake or enhance cellular targeting activities of the resulting
DsiRNA agent derivative as compared to the corresponding
unconjugated DsiRNA agent, are useful for tracing the DsiRNA agent
derivative in the cell, or improve the stability of the DsiRNA
agent derivative compared to the corresponding unconjugated DsiRNA
agent.
Enhanced In Vivo Efficacy and Duration of Effect of Bifunctional
DsiRNA Agents
[0205] In certain embodiments, the bifunctional agents of the
invention (both RNase H-cleavable bifunctional agents and dsDNA
extension sequence-joined bifunctional agents) can exhibit enhanced
in vivo efficacy, enhanced in vivo duration of effect, or both, as
compared to a tandem siRNA agent directed against the same target
RNA sequence(s) (e.g., tandem siRNA agents in which 19-21mer siRNA
moieties are joined by an RNase H-cleavable sequence). In vivo
assessment of the extent of inhibition of target RNA(s) by such
bifunctional agents can be assessed either phenotypically (e.g.,
via assessment of therapeutic effect following administration of
such an agent to a subject) or via direct assessment of expression
levels of target RNAs and/or encoded target protein(s), e.g., via
art-recognized methods of expression level assessment, including
Northern blot or other hybridization-based detection (e.g.,
array-based expression profiling), RT-PCR (qRT-PCR), ELISA, Western
blot, etc. The extent to which a bifunctional agent of the
invention inhibits expression of a target RNA can be assessed
relative to an untreated control, e.g., a bifunctional agent of the
invention can be shown to reduce a target RNA (or multiple target
RNAs) by at least 10%, at least 20%, at least 30%, at least 40%, at
least 50%, at least 60%, at least 70%, at least 75%, at least 80%,
at least 85%, at least 90%, at least 95%, at least 96%, at least
97%, at least 98%, or at least 99% or more than in an untreated
subject (and/or cell). Additionally or alternatively, the extent to
which a bifunctional agent of the invention inhibits the level of a
target RNA(s) can be assessed relative to a corresponding 19-21mer
tandem siRNA agent (e.g., an agent in which 19-21mer siRNA moieties
are joined by an RNase H-cleavable sequence). In such embodiments,
the bifunctional DsiRNA agents of the invention are identified to
exhibit at least 10% greater levels of inhibition of a target
RNA(s) than a corresponding tandem siRNA. In related embodiments,
the bifunctional DsiRNA agents of the invention are identified to
exhibit at least 20% greater levels of inhibition of a target
RNA(s), at least 30% greater levels of inhibition of a target
RNA(s), at least 40% greater levels of inhibition of a target
RNA(s), at least 50% greater levels of inhibition of a target
RNA(s), at least 60% greater levels of inhibition of a target
RNA(s), at least 70% greater levels of inhibition of a target
RNA(s), at least 80% greater levels of inhibition of a target
RNA(s), at least 90% greater levels of inhibition of a target
RNA(s) or at least 95% greater levels of inhibition of a target
RNA(s) than a corresponding tandem siRNA. In certain other
embodiments, the bifunctional DsiRNA agents of the invention are
identified to exhibit at least 1.5-fold greater inhibition of
target RNA level(s) than a corresponding tandem siRNA. In a related
embodiment, the bifunctional DsiRNA agents of the invention are
identified to exhibit at least two-fold greater, at least 3-fold
greater, at least 4-fold greater, at least 5-fold greater, at least
10-fold greater, or at least 20-fold greater inhibition of target
RNA level(s) than a corresponding tandem siRNA (e.g., administered
at the same concentration as the bifunctional DsiRNA of the
invention).
[0206] In vivo assessment of the duration of inhibition of target
RNA(s) by bifunctional agents of the invention can also be assessed
either via phenotypic evaluation (e.g., via assessment of
therapeutic effect at a specified time/over a time course following
administration of such an agent to a subject) or via direct
assessment of expression levels of target RNAs and/or encoded
target protein(s) at a specified time/over a time course following
administration of a bifunctional DsiRNA agent of the invention,
e.g., via art-recognized methods of expression level assessment,
including Northern blot or other hybridization-based detection
(e.g., array-based expression profiling), RT-PCR (qRT-PCR), ELISA,
Western blot, etc. The duration of time for which a bifunctional
agent of the invention inhibits expression of a target RNA, (e.g.,
the duration of time over which target RNA levels are reduced by
greater than a specified amount, e.g., greater than 10% reduction,
greater than 20% reduction, greater than 30% reduction, greater
than 40% reduction, greater than 50% reduction, greater than 60%
reduction, greater than 70% reduction, greater than 80% reduction,
greater than 90% reduction, or more) can be assessed relative to an
untreated control level, e.g., a bifunctional agent of the
invention can be shown to reduce a target RNA (or multiple target
RNAs) by a stated percentage for a duration of at least 24 hours,
at least 48 hours, at least 3 days, at least 4 days, at least 5
days, at least 6 days, at least 7 days, at least 8 days, at least 9
days, at least 10 days, at least 12 days, at least 14 days, at
least 16 days, at least 18 days, or at least 20 days or more in a
subject (and/or cell). Additionally or alternatively, the duration
of time for which a bifunctional agent of the invention inhibits
the level of a target RNA(s) can be assessed relative to a
corresponding 19-21mer tandem siRNA agent (e.g., an agent in which
19-21mer siRNA moieties are joined by an RNase H-cleavable
sequence). In such embodiments, the bifunctional DsiRNA agents of
the invention are identified to reduce a target RNA (or multiple
target RNAs) by a stated percentage for a duration of at least 24
hours more, at least 48 hours more, at least 3 days more, at least
4 days more, at least 5 days more, at least 6 days more, at least 7
days more, at least 8 days more, at least 9 days more, at least 10
days more, at least 12 days more, at least 14 days more, at least
16 days more, at least 18 days more, or at least 20 days more in a
subject (and/or cell) than a corresponding tandem siRNA. In related
embodiments, the bifunctional DsiRNA agents of the invention are
identified to exhibit at least 20% longer duration of inhibition of
a target RNA(s) to a given percent or fold reduction, at least 30%
longer duration of inhibition of a target RNA(s) to a given percent
or fold reduction, at least 40% longer duration of inhibition of a
target RNA(s) to a given percent or fold reduction, at least 50%
longer duration of inhibition of a target RNA(s) to a given percent
or fold reduction, at least 60% longer duration of inhibition of a
target RNA(s) to a given percent or fold reduction, at least 70%
longer duration of inhibition of a target RNA(s) to a given percent
or fold reduction, at least 80% longer duration of inhibition of a
target RNA(s) to a given percent or fold reduction, at least 90%
longer duration of inhibition of a target RNA(s) to a given percent
or fold reduction or at least 95% longer duration of inhibition of
a target RNA(s) to a given percent or fold reduction than a
corresponding tandem siRNA. In certain other embodiments, the
bifunctional DsiRNA agents of the invention are identified to
exhibit at least 1.5-fold longer duration of inhibition of target
RNA level(s) than a corresponding tandem siRNA. In a related
embodiment, the bifunctional DsiRNA agents of the invention are
identified to exhibit at least two-fold longer duration of
inhibition, at least 3-fold longer duration of inhibition, at least
4-fold longer duration of inhibition, at least 5-fold longer
duration of inhibition, at least 10-fold longer duration of
inhibition, or at least 20-fold longer duration of inhibition of
target RNA level(s) than a corresponding tandem siRNA (e.g.,
administered at the same concentration as the bifunctional DsiRNA
of the invention).
[0207] The therapeutic impact of a bifunctional agent of the
invention can also be assessed in evaluating the efficacy of such
an agent. In such embodiments, a bifunctional DsiRNA agent of the
invention can be shown to exhibit, e.g., at least a 10% reduction
in symptoms and/or indicator of disease status relative to an
untreated control subject, relative to a subject treated with a
tandem siRNA agent (e.g., an agent in which 19-21mer siRNA moieties
are joined by an RNase H-cleavable sequence), or relative to
appropriate control. In related embodiments, a bifunctional DsiRNA
agent of the invention can be shown to exhibit, e.g., at least a
20% reduction in symptoms and/or indicator of disease status, at
least a 30% reduction in symptoms and/or indicator of disease
status, at least a 40% reduction in symptoms and/or indicator of
disease status, at least a 50% reduction in symptoms and/or
indicator of disease status, at least a 60% reduction in symptoms
and/or indicator of disease status, at least a 70% reduction in
symptoms and/or indicator of disease status, at least a 80%
reduction in symptoms and/or indicator of disease status, at least
a 90% reduction in symptoms and/or indicator of disease status, at
least a 95% reduction in symptoms and/or indicator of disease
status, or a complete reduction in symptoms and/or indicator of
disease status, relative to an untreated control subject, relative
to a subject treated with a tandem siRNA agent, or relative to
other appropriate control.
[0208] One advantage of DsiRNA agents, including the bifunctional
DsiRNA agents of the invention, is their ability to act as
effective inhibitor agents at concentrations in the environment of
a cell of 1 nanomolar or less (e.g., efficacy at approximately 500
pM or less, efficacy at approximately 200 pM or less, efficacy at
approximately 100 pM or less, efficacy at approximately 50 pM or
less, efficacy at about 20 pM or less, or efficacy at about 10 pM
or less). Given the observed potency of DsiRNA agents, as well as
the duration of effects identified for such agents, the
bifunctional DsiRNA agents of the invention can be administered at
therapeutically effective doses to a subject that are lower than
those which would correspondingly be necessary for a tandem
19-21mer siRNA agent to be therapeutically effective. With the
caveat that dosage ranges for a bifunctional DsiRNA agent of the
invention will vary depending upon variables such as mode of
delivery, nature of delivery vehicle, etc., exemplary dosage ranges
for the bifunctional DsiRNA agents of the invention include 0.005
to 5.0 mg of bifunctional DsiRNA agent per kilogram of body weight
of a subject, including, e.g., dosage ranges of 0.05 to 2.0 mg/kg
per dose administered as a therapeutically effective dose to a
subject.
[0209] In certain embodiments, the bifunctional DsiRNA agents of
the invention exhibit enhanced therapeutic efficacy because the
delivery of conjoined DsiRNA moieties in a single molecule achieves
equivalent dosage and distribution of such DsiRNA moieties,
relative to the dosing and distribution that could be achieved via
administration of independent DsiRNA moieties to a subject. As
such, the bifunctional DsiRNA agents of the invention can also be
assessed for enhanced therapeutic efficacy when structured as a
bifunctional DsiRNA, as compared to independent DsiRNA moieties
(e.g., administered separately). The synergistic impact of
packaging DsiRNA agents within such bifunctional structures can be
assessed in a subject via evaluation of phenotype and/or
therapeutic outcome, e.g., bifunctional DsiRNA agents are 20% more
effective (or 30% more effective, 40% more effective, 50% more
effective, 60% more effective, 70% more effective, 80% more
effective, 90% more effective or 95% more effective) and/or exhibit
1.5-fold or greater duration of effect (or two-fold or greater
duration of effect, 3-fold or greater duration of effect, 4-fold or
greater duration of effect, 5-fold or greater duration of effect,
10-fold or greater duration of effect or 20-fold or greater
duration of effect) upon phenotype, therapeutic outcome and/or RNA
levels than corresponding, independent DsiRNA agents directed
against the same target RNA(s).
RNAi In Vitro Assay to Assess DsiRNA Agent Activity
[0210] An in vitro assay that recapitulates RNAi in a cell-free
system can optionally be used to evaluate DsiRNA-containing
constructs. For example, such an assay comprises a system described
by Tuschl et al., 1999, Genes and Development, 13, 3191-3197 and
Zamore et al., 2000, Cell, 101, 25-33, adapted for use with DsiRNA
agents directed against target RNA. A Drosophila extract derived
from syncytial blastoderm is used to reconstitute RNAi activity in
vitro. Target RNA is generated via in vitro transcription from an
appropriate plasmid using T7 RNA polymerase or via chemical
synthesis. Sense and antisense DsiRNA strands (for example 20 uM
each) are annealed by incubation in buffer (such as 100 mM
potassium acetate, 30 mM HEPES-KOH, pH 7.4, 2 mM magnesium acetate)
for 1 minute at 90.degree. C. followed by 1 hour at 37.degree. C.,
then diluted in lysis buffer (for example 100 mM potassium acetate,
30 mM HEPES-KOH at pH 7.4, 2 mM magnesium acetate) Annealing can be
monitored by gel electrophoresis on an agarose gel in TBE buffer
and stained with ethidium bromide. The Drosophila lysate is
prepared using zero to two-hour-old embryos from Oregon R flies
collected on yeasted molasses agar that are dechorionated and
lysed. The lysate is centrifuged and the supernatant isolated. The
assay comprises a reaction mixture containing 50% lysate [vol/vol],
RNA (10-50 .mu.M final concentration), and 10% [vol/vol] lysis
buffer containing DsiRNA (10 nM final concentration). The reaction
mixture also contains 10 mM creatine phosphate, 10 ug/ml creatine
phosphokinase, 100 um GTP, 100 uM UTP, 100 uM CTP, 500 uM ATP, 5 mM
DTT, 0.1 U/uL RNasin (Promega), and 100 uM of each amino acid. The
final concentration of potassium acetate is adjusted to 100 mM. The
reactions are pre-assembled on ice and preincubated at 25.degree.
C. for 10 minutes before adding RNA, then incubated at 25.degree.
C. for an additional 60 minutes. Reactions are quenched with 4
volumes of 1.25.times. Passive Lysis Buffer (Promega). Target RNA
cleavage is assayed by RT-PCR analysis or other methods known in
the art and are compared to control reactions in which DsiRNA is
omitted from the reaction.
[0211] Alternately, internally-labeled target RNA for the assay is
prepared by in vitro transcription in the presence of [alpha-32P]
CTP, passed over a G50 Sephadex column by spin chromatography and
used as target RNA without further purification. Optionally, target
RNA is 5'-32P-end labeled using T4 polynucleotide kinase enzyme.
Assays are performed as described above and target RNA and the
specific RNA cleavage products generated by RNAi are visualized on
an autoradiograph of a gel. The percentage of cleavage is
determined by PHOSPHOR IMAGER.RTM. (autoradiography) quantitation
of bands representing intact control RNA or RNA from control
reactions without DsiRNA and the cleavage products generated by the
assay.
Bifunctional Agent Targets
[0212] The bifunctional agents of the invention can target two
regions of the same target RNA, or can target two independent sites
within two or more target RNAs. As will be appreciated by the
skilled artisan, it will be desirable in certain experimental,
clinical or therapeutic settings to ensure equivalent levels of
delivery of two active agents via use of a single bifunctional
molecule such as the ones disclosed herein. Specific pairs of,
e.g., oncogenes, growth regulation genes, ligand/receptor pairs
(e.g., VEGF/VEGFR, EGF/EGFR, etc.), genes of autocrine loops,
angiogenesis factors, etc. can advantageously be simultaneously
targeted with the bifunctional agents of the instant invention.
Methods of Introducing Nucleic Acids, Vectors, and Host Cells
[0213] Bifunctional and functional group-tethered DsiRNA agents of
the invention may be directly introduced into a cell (i.e.,
intracellularly); or introduced extracellularly into a cavity,
interstitial space, into the circulation of an organism, introduced
orally, or may be introduced by bathing a cell or organism in a
solution containing the nucleic acid. Vascular or extravascular
circulation, the blood or lymph system, and the cerebrospinal fluid
are sites where the nucleic acid may be introduced.
[0214] The bifunctional and functional group-tethered DsiRNA agents
of the invention can be introduced using nucleic acid delivery
methods known in art including injection of a solution containing
the nucleic acid, bombardment by particles covered by the nucleic
acid, soaking the cell or organism in a solution of the nucleic
acid, or electroporation of cell membranes in the presence of the
nucleic acid. Other methods known in the art for introducing
nucleic acids to cells may be used, such as lipid-mediated carrier
transport, chemical-mediated transport, and cationic liposome
transfection such as calcium phosphate, and the like. The nucleic
acid may be introduced along with other components that perform one
or more of the following activities: enhance nucleic acid uptake by
the cell or other-wise increase inhibition of the target RNA.
[0215] A cell having a target RNA may be from the germ line or
somatic, totipotent or pluripotent, dividing or non-dividing,
parenchyma or epithelium, immortalized or transformed, or the like.
The cell may be a stem cell or a differentiated cell. Cell types
that are differentiated include adipocytes, fibroblasts, myocytes,
cardiomyocytes, endothelium, neurons, glia, blood cells,
megakaryocytes, lymphocytes, macrophages, neutrophils, eosinophils,
basophils, mast cells, leukocytes, granulocytes, keratinocytes,
chondrocytes, osteoblasts, osteoclasts, hepatocytes, and cells of
the endocrine or exocrine glands.
[0216] Depending on the particular target RNA sequence and the dose
of DsiRNA agent material delivered, this process may provide
partial or complete loss of function for the target RNA. A
reduction or loss of RNA levels or expression (either RNA
expression or encoded polypeptide expression) in at least 50%, 60%,
70%, 80%, 90%, 95% or 99% or more of targeted cells is exemplary.
Inhibition of target RNA levels or expression refers to the absence
(or observable decrease) in the level of RNA or RNA-encoded
protein. Specificity refers to the ability to inhibit the target
RNA without manifest effects on other genes of the cell. The
consequences of inhibition can be confirmed by examination of the
outward properties of the cell or organism (as presented below in
the examples) or by biochemical techniques such as RNA solution
hybridization, nuclease protection, Northern hybridization, reverse
transcription, gene expression monitoring with a microarray,
antibody binding, enzyme linked immunosorbent assay (ELISA),
Western blotting, radioimmunoassay (RIA), other immunoassays, and
fluorescence activated cell analysis (FACS). Inhibition of target
RNA sequence(s) by the bifunctional and functional group-tethered
DsiRNA agents of the invention also can be measured based upon the
effect of administration of such bifunctional and functional
group-tethered DsiRNA agents upon measurable phenotypes such as
tumor size for cancer treatment, viral load/titer for viral
infectious diseases, etc. either in vivo or in vitro. For viral
infectious diseases, reductions in viral load or titer can include
reductions of, e.g., 50%, 60%, 70%, 80%, 90%, 95% or 99% or more,
and are often measured in logarithmic terms, e.g., 10-fold,
100-fold, 1000-fold, 10.sup.5-fold, 10.sup.6-fold, 10.sup.7-fold
reduction in viral load or titer can be achieved via administration
of the bifunctional and functional group-tethered DsiRNA agents of
the invention to cells, a tissue, or a subject.
[0217] For RNAi-mediated inhibition in a cell line or whole
organism, expression of a reporter or drug resistance gene whose
protein product is easily assayed can be measured. Such reporter
genes include acetohydroxyacid synthase (AHAS), alkaline
phosphatase (AP), beta galactosidase (LacZ), beta glucoronidase
(GUS), chloramphenicol acetyltransferase (CAT), green fluorescent
protein (GFP), horseradish peroxidase (HRP), luciferase (Luc),
nopaline synthase (NOS), octopine synthase (OCS), and derivatives
thereof. Multiple selectable markers are available that confer
resistance to ampicillin, bleomycin, chloramphenicol, gentarnycin,
hygromycin, kanamycin, lincomycin, methotrexate, phosphinothricin,
puromycin, and tetracyclin. Depending on the assay, quantitation of
the amount of gene expression allows one to determine a degree of
inhibition which is greater than 10%, 33%, 50%, 90%, 95% or 99% as
compared to a cell not treated according to the present
invention.
[0218] Lower doses of injected material and longer times after
administration of RNA silencing agent may result in inhibition in a
smaller fraction of cells (e.g., at least 10%, 20%, 50%, 75%, 90%,
or 95% of targeted cells). Quantitation of gene expression in a
cell may show similar amounts of inhibition at the level of
accumulation of target RNA or translation of target protein. As an
example, the efficiency of inhibition may be determined by
assessing the amount of gene product in the cell; RNA may be
detected with a hybridization probe having a nucleotide sequence
outside the region used for the inhibitory DsiRNA, or translated
polypeptide may be detected with an antibody raised against the
polypeptide sequence of that region.
[0219] The bifunctional or functional group-tethered DsiRNA agent
of the invention may be introduced in an amount which allows
delivery of at least one copy per cell. Higher doses (e.g., at
least 5, 10, 100, 500 or 1000 copies per cell) of material may
yield more effective inhibition; lower doses may also be useful for
specific applications.
RNA Interference Based Therapy
[0220] As is known, RNAi methods are applicable to a wide variety
of genes in a wide variety of organisms and the disclosed
compositions and methods can be utilized in each of these contexts.
Examples of genes which can be targeted by the disclosed
compositions and methods include endogenous genes which are genes
that are native to the cell or to genes that are not normally
native to the cell. Without limitation, these genes include
oncogenes, cytokine genes, idiotype (Id) protein genes, prion
genes, genes that expresses molecules that induce angiogenesis,
genes for adhesion molecules, cell surface receptors, proteins
involved in metastasis, proteases, apoptosis genes, cell cycle
control genes, genes that express EGF and the EGF receptor,
multi-drug resistance genes, such as the MDR1 gene.
[0221] More specifically, a target mRNA of the invention can
specify the amino acid sequence of a cellular protein (e.g., a
nuclear, cytoplasmic, transmembrane, or membrane-associated
protein). In another embodiment, the target mRNA of the invention
can specify the amino acid sequence of an extracellular protein
(e.g., an extracellular matrix protein or secreted protein). As
used herein, the phrase "specifies the amino acid sequence" of a
protein means that the mRNA sequence is translated into the amino
acid sequence according to the rules of the genetic code. The
following classes of proteins are listed for illustrative purposes:
developmental proteins (e.g., adhesion molecules, cyclin kinase
inhibitors, Wnt family members, Pax family members, Winged helix
family members, Hox family members, cytokines/lymphokines and their
receptors, growth/differentiation factors and their receptors,
neurotransmitters and their receptors); oncogene-encoded proteins
(e.g., ABLI, BCLI, BCL2, BCL6, CBFA2, CBL, CSFIR, ERBA, ERBB,
EBRB2, ETSI, ETSI, ETV6, FGR, FOS, FYN, HCR, HRAS, JUN, K-RAS, LCK,
LYN, MDM2, MLL, MYB, MYC, MYCLI, MYCN, NRAS, PIM I, PML, RET, SRC,
TALI, TCL3, and YES); tumor suppressor proteins (e.g., APC, BRCA1,
BRCA2, MADH4, MCC, NF I, NF2, RB I, TP53, and WTI); and enzymes
(e.g., ACC synthases and oxidases, ACP desaturases and
hydroxylases, ADP-glucose pyrophorylases, ATPases, alcohol
dehydrogenases, amylases, amyloglucosidases, catalases, cellulases,
chalcone synthases, chitinases, cyclooxygenases, decarboxylases,
dextriinases, DNA and RNA polymerases, galactosidases, glucanases,
glucose oxidases, granule-bound starch synthases, GTPases,
helicases, hernicellulases, integrases, inulinases, invertases,
isomerases, kinases, lactases, lipases, lipoxygenases, lysozymes,
nopaline synthases, octopine synthases, pectinesterases,
peroxidases, phosphatases, phospholipases, phosphorylases,
phytases, plant growth regulator synthases, polygalacturonases,
proteinases and peptidases, pullanases, recombinases, reverse
transcriptases, RUBISCOs, topoisomerases, and xylanases).
[0222] In one aspect, the target mRNA molecule(s) of the invention
specifies the amino acid sequence of a protein associated with a
pathological condition. For example, the protein may be a
pathogen-associated protein (e.g., a viral protein involved in
immunosuppression of the host, replication of the pathogen,
transmission of the pathogen, or maintenance of the infection), or
a host protein which facilitates entry of the pathogen into the
host, drug metabolism by the pathogen or host, replication or
integration of the pathogen's genome, establishment or spread of
infection in the host, or assembly of the next generation of
pathogen. Pathogens include RNA viruses such as flaviviruses,
picornaviruses, rhabdoviruses, filoviruses, retroviruses, including
lentiviruses, or DNA viruses such as adenoviruses, poxviruses,
herpes viruses, cytomegaloviruses, hepadnaviruses or others.
Additional pathogens include bacteria, fungi, helminths,
schistosomes and trypanosomes. Other kinds of pathogens can include
mammalian transposable elements. Alternatively, the protein may be
a tumor-associated protein or an autoimmune disease-associated
protein.
[0223] The target gene(s) may be derived from or contained in any
organism. The organism may be a plant, animal, protozoa, bacterium,
virus or fungus. See, e.g., U.S. Pat. No. 6,506,559, incorporated
herein by reference.
Pharmaceutical Compositions
[0224] In certain embodiments, the present invention provides for a
pharmaceutical composition comprising the DsiRNA agent of the
present invention. The DsiRNA agent sample can be suitably
formulated and introduced into the environment of the cell by any
means that allows for a sufficient portion of the sample to enter
the cell to induce gene silencing, if it is to occur. Many
formulations for double stranded nucleic acid are known in the art
and can be used so long as the double stranded nucleic acid gains
entry to the target cells so that it can act. See, e.g., U.S.
published patent application Nos. 2004/0203145 A1 and 2005/0054598
A1. For example, the DsiRNA agent of the instant invention can be
formulated in buffer solutions such as phosphate buffered saline
solutions, liposomes, micellar structures, and capsids.
Formulations of DsiRNA agent with cationic lipids can be used to
facilitate transfection of the DsiRNA agent into cells. For
example, cationic lipids, such as lipofectin (U.S. Pat. No.
5,705,188), cationic glycerol derivatives, and polycationic
molecules, such as polylysine (published PCT International
Application WO 97/30731), can be used. Suitable lipids include
Oligofectamine, Lipofectamine (Life Technologies), NC388 (Ribozyme
Pharmaceuticals, Inc., Boulder, Colo.), or FuGene 6 (Roche) all of
which can be used according to the manufacturer's instructions.
[0225] Such compositions typically include the nucleic acid
molecule and a pharmaceutically acceptable carrier. As used herein
the language "pharmaceutically acceptable carrier" includes saline,
solvents, dispersion media, coatings, antibacterial and antifungal
agents, isotonic and absorption delaying agents, and the like,
compatible with pharmaceutical administration. Supplementary active
compounds can also be incorporated into the compositions.
[0226] A pharmaceutical composition is formulated to be compatible
with its intended route of administration. Examples of routes of
administration include parenteral, e.g., intravenous, intradermal,
subcutaneous, oral (e.g., inhalation), transdermal (topical),
transmucosal, and rectal administration. Solutions or suspensions
used for parenteral, intradermal, or subcutaneous application can
include the following components: a sterile diluent such as water
for injection, saline solution, fixed oils, polyethylene glycols,
glycerine, propylene glycol or other synthetic solvents;
antibacterial agents such as benzyl alcohol or methyl parabens;
antioxidants such as ascorbic acid or sodium bisulfite; chelating
agents such as ethylenediaminetetraacetic acid; buffers such as
acetates, citrates or phosphates and agents for the adjustment of
tonicity such as sodium chloride or dextrose. pH can be adjusted
with acids or bases, such as hydrochloric acid or sodium hydroxide.
The parenteral preparation can be enclosed in ampoules, disposable
syringes or multiple dose vials made of glass or plastic.
[0227] Pharmaceutical compositions suitable for injectable use
include sterile aqueous solutions (where water soluble) or
dispersions and sterile powders for the extemporaneous preparation
of sterile injectable solutions or dispersion. For intravenous
administration, suitable carriers include physiological saline,
bacteriostatic water, Cremophor EL.TM. (BASF, Parsippany, N.J.) or
phosphate buffered saline (PBS). In all cases, the composition must
be sterile and should be fluid to the extent that easy
syringability exists. It should be stable under the conditions of
manufacture and storage and must be preserved against the
contaminating action of microorganisms such as bacteria and fungi.
The carrier can be a solvent or dispersion medium containing, for
example, water, ethanol, polyol (for example, glycerol, propylene
glycol, and liquid polyetheylene glycol, and the like), and
suitable mixtures thereof. The proper fluidity can be maintained,
for example, by the use of a coating such as lecithin, by the
maintenance of the required particle size in the case of dispersion
and by the use of surfactants. Prevention of the action of
microorganisms can be achieved by various antibacterial and
antifungal agents, for example, parabens, chlorobutanol, phenol,
ascorbic acid, thimerosal, and the like. In many cases, it will be
preferable to include isotonic agents, for example, sugars,
polyalcohols such as manitol, sorbitol, sodium chloride in the
composition. Prolonged absorption of the injectable compositions
can be brought about by including in the composition an agent which
delays absorption, for example, aluminum monostearate and
gelatin.
[0228] Sterile injectable solutions can be prepared by
incorporating the active compound in the required amount in an
appropriate solvent with one or a combination of ingredients
enumerated above, as required, followed by filtered sterilization.
Generally, dispersions are prepared by incorporating the active
compound into a sterile vehicle, which contains a basic dispersion
medium and the required other ingredients from those enumerated
above. In the case of sterile powders for the preparation of
sterile injectable solutions, the preferred methods of preparation
are vacuum drying and freeze-drying which yields a powder of the
active ingredient plus any additional desired ingredient from a
previously sterile-filtered solution thereof.
[0229] Oral compositions generally include an inert diluent or an
edible carrier. For the purpose of oral therapeutic administration,
the active compound can be incorporated with excipients and used in
the form of tablets, troches, or capsules, e.g., gelatin capsules.
Oral compositions can also be prepared using a fluid carrier for
use as a mouthwash. Pharmaceutically compatible binding agents,
and/or adjuvant materials can be included as part of the
composition. The tablets, pills, capsules, troches and the like can
contain any of the following ingredients, or compounds of a similar
nature: a binder such as microcrystalline cellulose, gum tragacanth
or gelatin; an excipient such as starch or lactose, a
disintegrating agent such as alginic acid, Primogel, or corn
starch; a lubricant such as magnesium stearate or Sterotes; a
glidant such as colloidal silicon dioxide; a sweetening agent such
as sucrose or saccharin; or a flavoring agent such as peppermint,
methyl salicylate, or orange flavoring.
[0230] For administration by inhalation, the compounds are
delivered in the form of an aerosol spray from pressured container
or dispenser which contains a suitable propellant, e.g., a gas such
as carbon dioxide, or a nebulizer. Such methods include those
described in U.S. Pat. No. 6,468,798.
[0231] Systemic administration can also be by transmucosal or
transdermal means. For transmucosal or transdermal administration,
penetrants appropriate to the barrier to be permeated are used in
the formulation. Such penetrants are generally known in the art,
and include, for example, for transmucosal administration,
detergents, bile salts, and fusidic acid derivatives. Transmucosal
administration can be accomplished through the use of nasal sprays
or suppositories. For transdermal administration, the active
compounds are formulated into ointments, salves, gels, or creams as
generally known in the art.
[0232] The compounds can also be prepared in the form of
suppositories (e.g., with conventional suppository bases such as
cocoa butter and other glycerides) or retention enemas for rectal
delivery.
[0233] The compounds can also be administered by transfection or
infection using methods known in the art, including but not limited
to the methods described in McCaffrey et al. (2002), Nature,
418(6893), 38-9 (hydrodynamic transfection); Xia et al. (2002),
Nature Biotechnol., 20(10), 1006-10 (viral-mediated delivery); or
Putnam (1996), Am. J. Health Syst. Pharm. 53(2), 151-160, erratum
at Am. J. Health Syst. Pharm. 53(3), 325 (1996).
[0234] The compounds can also be administered by any method
suitable for administration of nucleic acid agents, such as a DNA
vaccine. These methods include gene guns, bio injectors, and skin
patches as well as needle-free methods such as the micro-particle
DNA vaccine technology disclosed in U.S. Pat. No. 6,194,389, and
the mammalian transdermal needle-free vaccination with powder-form
vaccine as disclosed in U.S. Pat. No. 6,168,587. Additionally,
intranasal delivery is possible, as described in, inter alia,
Hamajima et al. (1998), Clin. Immunol. Immunopathol., 88(2),
205-10. Liposomes (e.g., as described in U.S. Pat. No. 6,472,375)
and microencapsulation can also be used. Biodegradable targetable
microparticle delivery systems can also be used (e.g., as described
in U.S. Pat. No. 6,471,996).
[0235] In one embodiment, the active compounds are prepared with
carriers that will protect the compound against rapid elimination
from the body, such as a controlled release formulation, including
implants and microencapsulated delivery systems. Biodegradable,
biocompatible polymers can be used, such as ethylene vinyl acetate,
polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and
polylactic acid. Such formulations can be prepared using standard
techniques. The materials can also be obtained commercially from
Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal
suspensions (including liposomes targeted to infected cells with
monoclonal antibodies to viral antigens) can also be used as
pharmaceutically acceptable carriers. These can be prepared
according to methods known to those skilled in the art, for
example, as described in U.S. Pat. No. 4,522,811.
[0236] Toxicity and therapeutic efficacy of such compounds can be
determined by standard pharmaceutical procedures in cell cultures
or experimental animals, e.g., for determining the LD.sub.50 (the
dose lethal to 50% of the population) and the ED.sub.50 (the dose
therapeutically effective in 50% of the population). The dose ratio
between toxic and therapeutic effects is the therapeutic index and
it can be expressed as the ratio LD.sub.50/ED.sub.50. Compounds
which exhibit high therapeutic indices are preferred. While
compounds that exhibit toxic side effects may be used, care should
be taken to design a delivery system that targets such compounds to
the site of affected tissue in order to minimize potential damage
to uninfected cells and, thereby, reduce side effects.
[0237] The data obtained from the cell culture assays and animal
studies can be used in formulating a range of dosage for use in
humans. The dosage of such compounds lies preferably within a range
of circulating concentrations that include the ED.sub.50 with
little or no toxicity. The dosage may vary within this range
depending upon the dosage form employed and the route of
administration utilized. For any compound used in the method of the
invention, the therapeutically effective dose can be estimated
initially from cell culture assays. A dose may be formulated in
animal models to achieve a circulating plasma concentration range
that includes the IC.sub.50 (i.e., the concentration of the test
compound which achieves a half-maximal inhibition of symptoms) as
determined in cell culture. Such information can be used to more
accurately determine useful doses in humans. Levels in plasma may
be measured, for example, by high performance liquid
chromatography.
[0238] As defined herein, a therapeutically effective amount of a
nucleic acid molecule (i.e., an effective dosage) depends on the
nucleic acid selected. For instance, if a plasmid encoding a DsiRNA
agent is selected, single dose amounts in the range of
approximately 1 pg to 1000 mg may be administered; in some
embodiments, 10, 30, 100, or 1000 pg, or 10, 30, 100, or 1000 ng,
or 10, 30, 100, or 1000 .mu.g, or 10, 30, 100, or 1000 mg may be
administered. In some embodiments, 1-5 g of the compositions can be
administered. The compositions can be administered from one or more
times per day to one or more times per week; including once every
other day. The skilled artisan will appreciate that certain factors
may influence the dosage and timing required to effectively treat a
subject, including but not limited to the severity of the disease
or disorder, previous treatments, the general health and/or age of
the subject, and other diseases present. Moreover, treatment of a
subject with a therapeutically effective amount of a protein,
polypeptide, or antibody can include a single treatment or,
preferably, can include a series of treatments.
[0239] It can be appreciated that the method of introducing DsiRNA
agents into the environment of the cell will depend on the type of
cell and the make up of its environment. For example, when the
cells are found within a liquid, one preferable formulation is with
a lipid formulation such as in lipofectamine and the DsiRNA agents
can be added directly to the liquid environment of the cells. Lipid
formulations can also be administered to animals such as by
intravenous, intramuscular, or intraperitoneal injection, or orally
or by inhalation or other methods as are known in the art. When the
formulation is suitable for administration into animals such as
mammals and more specifically humans, the formulation is also
pharmaceutically acceptable. Pharmaceutically acceptable
formulations for administering oligonucleotides are known and can
be used. In some instances, it may be preferable to formulate
DsiRNA agents in a buffer or saline solution and directly inject
the formulated DsiRNA agents into cells, as in studies with
oocytes. The direct injection of DsiRNA agents duplexes may also be
done. For suitable methods of introducing double stranded nucleic
acid (e.g., DsiRNA agents), see U.S. published patent application
No. 2004/0203145 A1.
[0240] Suitable amounts of a DsiRNA agent must be introduced and
these amounts can be empirically determined using standard methods.
Typically, effective concentrations of individual DsiRNA agent
species in the environment of a cell will be about 50 nanomolar or
less, 10 nanomolar or less, or compositions in which concentrations
of about 1 nanomolar or less can be used. In another embodiment,
methods utilizing a concentration of about 200 picomolar or less,
and even a concentration of about 50 picomolar or less, can be used
in many circumstances.
[0241] The method can be carried out by addition of the DsiRNA
agent compositions to any extracellular matrix in which cells can
live provided that the DsiRNA agent composition is formulated so
that a sufficient amount of the DsiRNA agent can enter the cell to
exert its effect. For example, the method is amenable for use with
cells present in a liquid such as a liquid culture or cell growth
media, in tissue explants, or in whole organisms, including
animals, such as mammals and especially humans.
[0242] The level or activity of a target RNA can be determined by
any suitable method now known in the art or that is later
developed. It can be appreciated that the method used to measure a
target RNA and/or the expression of a target RNA can depend upon
the nature of the target RNA. For example, if the target RNA
encodes a protein, the term "expression" can refer to a protein or
the RNA/transcript derived from the target RNA. In such instances,
the expression of a target RNA can be determined by measuring the
amount of RNA corresponding to the target RNA or by measuring the
amount of that protein. Protein can be measured in protein assays
such as by staining or immunoblotting or, if the protein catalyzes
a reaction that can be measured, by measuring reaction rates. All
such methods are known in the art and can be used. Where target RNA
levels are to be measured, any art-recognized methods for detecting
RNA levels can be used (e.g., RT-PCR, Northern Blotting, etc.). In
targeting viral RNAs with the DsiRNA agents of the instant
invention, it is also anticipated that measurement of the efficacy
of a DsiRNA agent in reducing levels of a target virus in a
subject, tissue, in cells, either in vitro or in vivo, or in cell
extracts can also be used to determine the extent of reduction of
target viral RNA level(s). Any of the above measurements can be
made on cells, cell extracts, tissues, tissue extracts or any other
suitable source material.
[0243] The determination of whether the expression of a target RNA
has been reduced can be by any suitable method that can reliably
detect changes in RNA levels. Typically, the determination is made
by introducing into the environment of a cell undigested DsiRNA
such that at least a portion of that DsiRNA agent enters the
cytoplasm, and then measuring the level of the target RNA. The same
measurement is made on identical untreated cells and the results
obtained from each measurement are compared.
[0244] The DsiRNA agent can be formulated as a pharmaceutical
composition which comprises a pharmacologically effective amount of
a DsiRNA agent and pharmaceutically acceptable carrier. A
pharmacologically or therapeutically effective amount refers to
that amount of a DsiRNA agent effective to produce the intended
pharmacological, therapeutic or preventive result. The phrases
"pharmacologically effective amount" and "therapeutically effective
amount" or simply "effective amount" refer to that amount of an RNA
effective to produce the intended pharmacological, therapeutic or
preventive result. For example, if a given clinical treatment is
considered effective when there is at least a 20% reduction in a
measurable parameter associated with a disease or disorder, a
therapeutically effective amount of a drug for the treatment of
that disease or disorder is the amount necessary to effect at least
a 20% reduction in that parameter.
[0245] Suitably formulated pharmaceutical compositions of this
invention can be administered by any means known in the art such as
by parenteral routes, including intravenous, intramuscular,
intraperitoneal, subcutaneous, transdermal, airway (aerosol),
rectal, vaginal and topical (including buccal and sublingual)
administration. In some embodiments, the pharmaceutical
compositions are administered by intravenous or intraparenteral
infusion or injection.
[0246] In general, a suitable dosage unit of double stranded
nucleic acid will be in the range of 0.001 to 0.25 milligrams per
kilogram body weight of the recipient per day, or in the range of
0.01 to 20 micrograms per kilogram body weight per day, or in the
range of 0.01 to 10 micrograms per kilogram body weight per day, or
in the range of 0.10 to 5 micrograms per kilogram body weight per
day, or in the range of 0.1 to 2.5 micrograms per kilogram body
weight per day. Pharmaceutical composition comprising the double
stranded nucleic acid can be administered once daily. However, the
therapeutic agent may also be dosed in dosage units containing two,
three, four, five, six or more sub-doses administered at
appropriate intervals throughout the day. In that case, the double
stranded nucleic acid contained in each sub-dose must be
correspondingly smaller in order to achieve the total daily dosage
unit. The dosage unit can also be compounded for a single dose over
several days, e.g., using a conventional sustained release
formulation which provides sustained and consistent release of the
double stranded nucleic acid over a several day period. Sustained
release formulations are well known in the art. In this embodiment,
the dosage unit contains a corresponding multiple of the daily
dose. Regardless of the formulation, the pharmaceutical composition
must contain double stranded nucleic acid in a quantity sufficient
to inhibit expression of the target gene in the animal or human
being treated. The composition can be compounded in such a way that
the sum of the multiple units of double stranded nucleic acid
together contain a sufficient dose.
[0247] Data can be obtained from cell culture assays and animal
studies to formulate a suitable dosage range for humans. The dosage
of compositions of the invention lies within a range of circulating
concentrations that include the ED.sub.50 (as determined by known
methods) with little or no toxicity. The dosage may vary within
this range depending upon the dosage form employed and the route of
administration utilized. For any compound used in the method of the
invention, the therapeutically effective dose can be estimated
initially from cell culture assays. A dose may be formulated in
animal models to achieve a circulating plasma concentration range
of the compound that includes the IC.sub.50 (i.e., the
concentration of the test compound which achieves a half-maximal
inhibition of symptoms) as determined in cell culture. Such
information can be used to more accurately determine useful doses
in humans. Levels of double stranded nucleic acid in plasma may be
measured by standard methods, for example, by high performance
liquid chromatography.
[0248] The pharmaceutical compositions can be included in a kit,
container, pack, or dispenser together with instructions for
administration.
Methods of Treatment
[0249] The present invention provides for both prophylactic and
therapeutic methods of treating a subject at risk of (or
susceptible to) a disease or disorder caused, in whole or in part,
by the expression of a target RNA and/or the presence of such
target RNA (e.g., in the context of a viral infection, the presence
of a target RNA of the viral genome, capsid, host cell component,
etc.).
[0250] "Treatment", or "treating" as used herein, is defined as the
application or administration of a therapeutic agent (e.g., a
DsiRNA agent or vector or transgene encoding same) to a patient, or
application or administration of a therapeutic agent to an isolated
tissue or cell line from a patient, who has the disease or
disorder, a symptom of disease or disorder or a predisposition
toward a disease or disorder, with the purpose to cure, heal,
alleviate, relieve, alter, remedy, ameliorate, improve or affect
the disease or disorder, the symptoms of the disease or disorder,
or the predisposition toward disease.
[0251] In one aspect, the invention provides a method for
preventing in a subject, a disease or disorder as described above,
by administering to the subject a therapeutic agent (e.g., a DsiRNA
agent or vector or transgene encoding same). Subjects at risk for
the disease can be identified by, for example, any or a combination
of diagnostic or prognostic assays as described herein.
Administration of a prophylactic agent can occur prior to the
detection of, e.g., viral particles in a subject, or the
manifestation of symptoms characteristic of the disease or
disorder, such that the disease or disorder is prevented or,
alternatively, delayed in its progression.
[0252] Another aspect of the invention pertains to methods of
treating subjects therapeutically, i.e., alter onset of symptoms of
the disease or disorder. These methods can be performed in vitro
(e.g., by culturing the cell with the DsiRNA agent) or,
alternatively, in vivo (e.g., by administering the DsiRNA agent to
a subject).
[0253] With regard to both prophylactic and therapeutic methods of
treatment, such treatments may be specifically tailored or
modified, based on knowledge obtained from the field of
pharmacogenomics. "Pharmacogenomics", as used herein, refers to the
application of genomics technologies such as gene sequencing,
statistical genetics, and gene expression analysis to drugs in
clinical development and on the market. More specifically, the term
refers the study of how a patient's genes determine his or her
response to a drug (e.g., a patient's "drug response phenotype", or
"drug response genotype"). Thus, another aspect of the invention
provides methods for tailoring an individual's prophylactic or
therapeutic treatment with either the target RNA molecules of the
present invention or target RNA modulators according to that
individual's drug response genotype. Pharmacogenomics allows a
clinician or physician to target prophylactic or therapeutic
treatments to patients who will most benefit from the treatment and
to avoid treatment of patients who will experience toxic
drug-related side effects.
[0254] Therapeutic agents can be tested in an appropriate animal
model. For example, a DsiRNA agent (or expression vector or
transgene encoding same) as described herein can be used in an
animal model to determine the efficacy, toxicity, or side effects
of treatment with said agent. Alternatively, a therapeutic agent
can be used in an animal model to determine the mechanism of action
of such an agent. For example, an agent can be used in an animal
model to determine the efficacy, toxicity, or side effects of
treatment with such an agent. Alternatively, an agent can be used
in an animal model to determine the mechanism of action of such an
agent.
[0255] The practice of the present invention employs, unless
otherwise indicated, conventional techniques of chemistry,
molecular biology, microbiology, recombinant DNA, genetics,
immunology, cell biology, cell culture and transgenic biology,
which are within the skill of the art. See, e.g., Maniatis et al.,
1982, Molecular Cloning (Cold Spring Harbor Laboratory Press, Cold
Spring Harbor, N.Y.); Sambrook et al., 1989, Molecular Cloning, 2nd
Ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor,
N.Y.); Sambrook and Russell, 2001, Molecular Cloning, 3rd Ed. (Cold
Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.); Ausubel
et al., 1992), Current Protocols in Molecular Biology (John Wiley
& Sons, including periodic updates); Glover, 1985, DNA Cloning
(IRL Press, Oxford); Anand, 1992; Guthrie and Fink, 1991; Harlow
and Lane, 1988, Antibodies, (Cold Spring Harbor Laboratory Press,
Cold Spring Harbor, N.Y.); Jakoby and Pastan, 1979; Nucleic Acid
Hybridization (B. D. Hames & S. J. Higgins eds. 1984);
Transcription And Translation (B. D. Hames & S. J. Higgins eds.
1984); Culture Of Animal Cells (R. I. Freshney, Alan R. Liss, Inc.,
1987); Immobilized Cells And Enzymes (IRL Press, 1986); B. Perbal,
A Practical Guide To Molecular Cloning (1984); the treatise,
Methods In Enzymology (Academic Press, Inc., N.Y.); Gene Transfer
Vectors For Mammalian Cells (J. H. Miller and M. P. Calos eds.,
1987, Cold Spring Harbor Laboratory); Methods In Enzymology, Vols.
154 and 155 (Wu et al. eds.), Immunochemical Methods In Cell And
Molecular Biology (Mayer and Walker, eds., Academic Press, London,
1987); Handbook Of Experimental Immunology, Volumes I-IV (D. M.
Weir and C. C. Blackwell, eds., 1986); Riott, Essential Immunology,
6th Edition, Blackwell Scientific Publications, Oxford, 1988; Hogan
et al., Manipulating the Mouse Embryo, (Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y., 1986); Westerfield, M.,
The zebrafish book. A guide for the laboratory use of zebrafish
(Danio rerio), (4th Ed., Univ. of Oregon Press, Eugene, 2000).
[0256] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention belongs. Although
methods and materials similar or equivalent to those described
herein can be used in the practice or testing of the present
invention, suitable methods and materials are described below. All
publications, patent applications, patents, and other references
mentioned herein are incorporated by reference in their entirety.
In case of conflict, the present specification, including
definitions, will control. In addition, the materials, methods, and
examples are illustrative only and not intended to be limiting.
EXAMPLES
[0257] The present invention is described by reference to the
following Examples, which are offered by way of illustration and
are not intended to limit the invention in any manner. Standard
techniques well known in the art or the techniques specifically
described below were utilized.
Example 1
Methods
Oligonucleotide Synthesis
[0258] Individual RNA strands are synthesized and HPLC purified
according to standard methods (Integrated DNA Technologies,
Coralville, Iowa). All oligonucleotides are quality control
released on the basis of chemical purity by HPLC analysis and full
length strand purity by mass spectrometry analysis. Duplex RNA
DsiRNAs are prepared before use by mixing equal quantities of each
strand, briefly heating to 100.degree. C. in RNA buffer (IDT) and
then allowing the mixtures to cool to room temperature.
Cell Culture and RNA Transfection
[0259] HeLa cells are obtained from ATCC and maintained in
Dulbecco's modified Eagle medium (HyClone) supplemented with 10%
fetal bovine serum (HyClone) at 37.degree. C. under 5% CO.sub.2.
For RNA transfections, HeLa cells are seeded overnight in 6-well
plates at a density of 4.times.10.sup.5 cells/well in a final
volume of 2 mL. 24 hours later, cells are transfected with the
DsiRNA duplexes as specified at a final concentration of 10 pM, 100
pM, 1 nM, 10 nM or 20 nM using Oligofectamine.TM. (Invitrogen) and
following the manufacturer's instructions. For 20 nM transfections,
84, of a 5 .mu.M stock solution of each bifunctional or functional
group-tethered DsiRNA is mixed with 200 .mu.L of Opti-MEM I
(Invitrogen). In a separate tube, 12 .mu.L of Oligofectamine is
mixed with 484, of Opti-MEM I. After a 5 minute incubation at room
temperature (RT) the bifunctional or functional group-tethered
DsiRNA and Oligofectamine aliquots are combined, gently vortexed,
and further incubated for 20 minutes at RT to allow bifunctional or
functional group-tethered DsiRNA:Oligofectamine complexes
(transfection mixes) to form. Finally, culture medium is added to
bring each transfection mix to a final volume of 2 mL. After a 6
hour incubation, the transfection/culture medium in each well is
replaced with fresh culture medium and cells are incubated for an
additional 18 hours.
RNA Isolation and Analysis
[0260] Cells are washed once with 2 mL of PBS, and total RNA is
extracted using RNeasy Mini Kit.TM. (Qiagen) and eluted in a final
volume of 30 .mu.L. 1 .mu.g of total RNA is reverse-transcribed
using Transcriptor 1.sup.st Strand cDNA Kit.TM. (Roche) and random
hexamers following manufacturer's instructions. One-thirtieth (0.66
.mu.L) of the resulting cDNA is mixed with 54, of IQ Multiplex
Powermix (Bio-Rad) together with 3.33 .mu.L of H.sub.2O and 1 .mu.L
of a 3 .mu.M mix containing 2 sets of primers and probes specific
for human genes that are assayed (e.g., K-RAS, HPRT1, etc.).
Quantitative RT-PCR
[0261] A CFX96 Real-time System with a C1000 Thermal cycler
(Bio-Rad) is used for the amplification reactions. PCR conditions
are: 95.degree. C. for 3 min; and then cycling at 95.degree. C., 10
sec; 55.degree. C., 1 min for 40 cycles. Each sample is tested in
triplicate. Relative test mRNA levels are compared with mRNA levels
obtained in control samples treated with the transfection reagent
plus a control mismatch duplex, or untreated. Data is analyzed
using Bio-Rad CFX Manager version 1.0 software.
Example 2
Efficacy of RNase H-Cleavable Bifunctional DsiRNA Agents
[0262] Bifunctional DsiRNA agents possessing RNase H-cleavable
joining sequences are examined for efficacy of sequence-specific
target mRNA inhibition. Specifically, bifunctional DsiRNA agents
possessing RNase H-cleavable joining sequences and targeting HPRT1
and K-RAS targets with sequences as shown in FIG. 1 and FIG. 2 are
transfected into HeLa cells at a fixed concentration of 10 pM, 100
pM, 1 nM, 10 nM or 20 nM and HPRT1 and K-RAS expression levels are
measured 24 hours later. Transfections are performed in duplicate,
and each duplicate is assayed in triplicate for HPRT1 and K-RAS
expression by qPCR. Under these conditions (10 pM, 100 pM, 1 nM, 10
nM or 20 nM duplexes, Oligofectamine transfection), HPRT1 and K-RAS
gene expression is reduced.
Example 3
Efficacy of RNase H-Cleavable Functional Group-Tethered DsiRNA
Agents
[0263] Functional group-tethered DsiRNA agents possessing RNase
H-cleavable joining sequences are examined for efficacy of
sequence-specific target mRNA inhibition and for efficacy of
functional group activity. Specifically, functional group-tethered
DsiRNA agents possessing RNase H-cleavable joining sequences and as
shown in FIG. 3 are synthesized and transfected into HeLa cells at
a fixed concentration of 10 pM, 100 pM, 1 nM, 10 nM or 20 nM and
HPRT1 expression levels are measured 24 hours later. Transfections
are performed in duplicate, and each duplicate is assayed in
triplicate for HPRT1 expression by qPCR. Under these conditions (10
pM, 100 pM, 1 nM, 10 nM or 20 nM duplexes, Oligofectamine
transfection), HPRT1 gene expression is reduced. Release of the
functional group from such agents is also assessed.
Example 4
Efficacy of dsDNA Extended Bifunctional DsiRNA Agents
[0264] Bifunctional DsiRNA agents possessing dsDNA extension
joining sequences are examined for efficacy of sequence-specific
target mRNA inhibition. Specifically, bifunctional DsiRNA agents
possessing dsDNA extension joining sequences and targeting HPRT1
and K-RAS targets with sequences as shown in FIG. 4 are transfected
into HeLa cells at a fixed concentration of 10 pM, 100 pM, 1 nM, 10
nM or 20 nM and HPRT1 and K-RAS expression levels are measured 24
hours later. Transfections are performed in duplicate, and each
duplicate is assayed in triplicate for HPRT1 and K-RAS expression
by qPCR. Under these conditions (10 pM, 100 pM, 1 nM, 10 nM or 20
nM duplexes, Oligofectamine transfection), HPRT1 and K-RAS gene
expression is reduced.
Example 5
Enhanced Efficacy of RNase H-Cleavable Bifunctional DsiRNA Agents
as Compared to Tandem siRNA Agents
[0265] Bifunctional agents such as those described in Examples 2
and 4 above (and as detailed in FIGS. 1, 2 and 4) are synthesized
and transfected into HeLa cells at a fixed concentration of 10 pM,
100 pM, 1 nM or 10 nM. In parallel, tandem 19mer siRNA agents
having either RNase H cleavable joining sequences (such as the
agent shown at paragraph [0209] of U.S. Patent Application No.
2008/0293655, yet directed against identical target sequences as
tested bifunctional DsiRNA sequences (e.g., HPRT1 and K-RAS) or
having dsDNA extension joining sequences are synthesized and also
transfected into HeLa cells at a fixed concentration of 10 pM, 100
pM, 1 nM or 10 nM. Expression levels are measured at time points of
24 hours later, 2 days later, 4 days later, 6 days later and 10
days later. Transfections are performed in duplicate, and each
duplicate is assayed in triplicate for HPRT1 and K-RAS expression
by qPCR. Under these conditions (10 pM, 100 pM, 1 nM, 10 nM or 20
nM duplexes, Oligofectamine transfection), HPRT1 and K-RAS gene
expression is identified as reduced to a greater extent (showing
greater efficacy) and with enhanced duration of effect with
bifunctional DsiRNA agents than for corresponding tandem 19mer
siRNA agents directed against identical target RNA sequences.
[0266] All patents and publications mentioned in the specification
are indicative of the levels of skill of those skilled in the art
to which the invention pertains. All references cited in this
disclosure are incorporated by reference to the same extent as if
each reference had been incorporated by reference in its entirety
individually.
[0267] One skilled in the art would readily appreciate that the
present invention is well adapted to carry out the objects and
obtain the ends and advantages mentioned, as well as those inherent
therein. The methods and compositions described herein as presently
representative of preferred embodiments are exemplary and are not
intended as limitations on the scope of the invention. Changes
therein and other uses will occur to those skilled in the art,
which are encompassed within the spirit of the invention, are
defined by the scope of the claims.
[0268] It will be readily apparent to one skilled in the art that
varying substitutions and modifications can be made to the
invention disclosed herein without departing from the scope and
spirit of the invention. Thus, such additional embodiments are
within the scope of the present invention and the following claims.
The present invention teaches one skilled in the art to test
various combinations and/or substitutions of chemical modifications
described herein toward generating nucleic acid constructs with
improved activity for mediating RNAi activity. Such improved
activity can comprise improved stability, improved bioavailability,
and/or improved activation of cellular responses mediating RNAi.
Therefore, the specific embodiments described herein are not
limiting and one skilled in the art can readily appreciate that
specific combinations of the modifications described herein can be
tested without undue experimentation toward identifying DsiRNA
molecules with improved RNAi activity.
[0269] The invention illustratively described herein suitably can
be practiced in the absence of any element or elements, limitation
or limitations that are not specifically disclosed herein. Thus,
for example, in each instance herein any of the terms "comprising",
"consisting essentially of", and "consisting of" may be replaced
with either of the other two terms. The terms and expressions which
have been employed are used as terms of description and not of
limitation, and there is no intention that in the use of such terms
and expressions of excluding any equivalents of the features shown
and described or portions thereof, but it is recognized that
various modifications are possible within the scope of the
invention claimed. Thus, it should be understood that although the
present invention has been specifically disclosed by preferred
embodiments, optional features, modification and variation of the
concepts herein disclosed may be resorted to by those skilled in
the art, and that such modifications and variations are considered
to be within the scope of this invention as defined by the
description and the appended claims.
[0270] In addition, where features or aspects of the invention are
described in terms of Markush groups or other grouping of
alternatives, those skilled in the art will recognize that the
invention is also thereby described in terms of any individual
member or subgroup of members of the Markush group or other
group.
[0271] The use of the terms "a" and "an" and "the" and similar
referents in the context of describing the invention (especially in
the context of the following claims) are to be construed to cover
both the singular and the plural, unless otherwise indicated herein
or clearly contradicted by context. The terms "comprising,"
"having," "including," and "containing" are to be construed as
open-ended terms (i.e., meaning "including, but not limited to,")
unless otherwise noted. Recitation of ranges of values herein are
merely intended to serve as a shorthand method of referring
individually to each separate value falling within the range,
unless otherwise indicated herein, and each separate value is
incorporated into the specification as if it were individually
recited herein. All methods described herein can be performed in
any suitable order unless otherwise indicated herein or otherwise
clearly contradicted by context. The use of any and all examples,
or exemplary language (e.g., "such as") provided herein, is
intended merely to better illuminate the invention and does not
pose a limitation on the scope of the invention unless otherwise
claimed. No language in the specification should be construed as
indicating any non-claimed element as essential to the practice of
the invention.
Embodiments of this invention are described herein, including the
best mode known to the inventors for carrying out the invention.
Variations of those embodiments may become apparent to those of
ordinary skill in the art upon reading the foregoing description.
The inventors expect skilled artisans to employ such variations as
appropriate, and the inventors intend for the invention to be
practiced otherwise than as specifically described herein.
Accordingly, this invention includes all modifications and
equivalents of the subject matter recited in the claims appended
hereto as permitted by applicable law. Moreover, any combination of
the above-described elements in all possible variations thereof is
encompassed by the invention unless otherwise indicated herein or
otherwise clearly contradicted by context.
Sequence CWU 1
1
27113DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 1aattcaccgg gga 13214RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 2uccccgguga auuu 14314DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 3aaattcaccg gucg 14414RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 4cgaccgguga auuu 14512DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 5gaaattcacc gg 12656DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 6gccagacuuu guuggauuug aaattcaccg gggagggcuu
ucuuugugua uuugcc 56758RNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 7ggcaaauaca
caaagaaagc ccuccccggu gaauuucaaa uccaacaaag ucuggcgc
58831DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 8gccagacuuu guuggauuug aaattcaccg g
31925RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 9ggagggcuuu cuuuguguau uugcc
251031RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 10ggugaauuuc aaauccaaca aagucuggcg c
311127RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 11ggcaaauaca caaagaaagc ccucccc
271221RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 12gccagacuuu guuggauuug a
211321RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 13ggagggcuuu cuuuguguau u
211421RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 14aaauccaaca aagucuggcg c
211521RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 15uacacaaaga aagcccuccc c
211658DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 16gccagacuuu guuggauuug aaattcaccg
gucggagggc uuucuuugug uauuugcc 581758RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 17caaauacaca aagaaagccc uccgaccggu gaauuucaaa
uccaacaaag ucuggcgc 581825DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 18gccagacuuu
guuggauuug aaatt 251933RNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 19caccggucgg
agggcuuucu uuguguauuu gcc 332027RNAArtificial SequenceDescription
of Artificial Sequence Synthetic oligonucleotide 20aauuucaaau
ccaacaaagu cuggcgc 272127RNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 21caaauacaca
aagaaagccc uccgacc 272221RNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 22gccagacuuu
guuggauuug a 212321RNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 23ggcuuucuuu guguauuugc c
212421RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 24aaauccaaca aagucuggcg c
212521RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 25caaauacaca aagaaagccc u
212633RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 26ccggugaauu ucaaauccaa caaagucugg cgc
332727RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 27aauuucaaau ccaacaaagu cuggcgc 27
* * * * *