5' TARGETING OLIGONUCLEOTIDES FOR MODULATING RNA
Aspects of the invention relate to methods for increasing gene expression in a targeted manner. In some embodiments, methods and compositions are provided that are useful for posttranscriptionally altering protein and/or RNA levels in a targeted manner. Aspects of the invention disclosed herein provide methods and compositions that are useful for protecting RNAs from degradation (e.g., exonuclease mediated degradation).
1 - 63 . (canceled)
64 . An oligonucleotide comprising the general formula 5′-X—X 2 -3′, wherein
X 1 comprises 5 to 20 nucleotides that have a region of complementarity that is complementary with at least 5 contiguous nucleotides of an RNA transcript, wherein the nucleotide at the 3′-end of the region of complementary of X 1 is complementary with the nucleotide at the transcription start site of the RNA transcript; and X 2 comprises 1 to 20 nucleotides.
65 . The oligonucleotide of claim 64 , wherein the RNA transcript has a 7-methylguanosine cap at its 5′-end.
66 . The oligonucleotide of claim 64 , wherein the RNA transcript has a 7-methylguanosine cap, and wherein the nucleotide at the 3′-end of the region of complementary of X 1 is complementary with the nucleotide of the RNA transcript that is immediately internal to the 7-methylguanosine cap.
67 . The oligonucleotide of claim 64 , wherein at least the first nucleotide at the 5′-end of X 2 is a pyrimidine complementary with guanine.
68 . The oligonucleotide of claim 67 , wherein the second nucleotide at the 5′-end of X 2 is a pyrimidine complementary with guanine.
69 . The oligonucleotide of claim 64 , wherein X 2 comprises the formula 5′-Y 1 —Y 2 —Y 3 -3′, wherein X 2 forms a stem-loop structure having a loop region comprising the nucleotides of Y 2 and a stem region comprising at least two contiguous nucleotides of Y 1 hybridized with at least two contiguous nucleotides of Y 3 .
70 . The oligonucleotide of claim 69 , wherein Y 1 , Y 2 and Y 3 independently comprise 1 to 10 nucleotides.
71 . The oligonucleotide of claim 69 , wherein Y 3 comprises, at a position immediately following the 3′-end of the stem region, a pyrimidine complementary with guanine.
72 . The oligonucleotide of claim 67 , wherein the pyrimidine complementary with guanine is cytosine.
73 - 76 . (canceled)
77 . The oligonucleotide of claim 64 , wherein the RNA transcript is an mRNA, non-coding RNA, long non-coding RNA, miRNA, or snoRNA.
78 - 89 . (canceled)
90 . The oligonucleotide of claim 64 , wherein the oligonucleotide is 10 to 50 nucleotide in length.
91 - 93 . (canceled)
94 . The oligonucleotide of claim 64 , wherein the oligonucleotide comprises at least one modified internucleoside linkage.
95 . The oligonucleotide of claim 64 , wherein the oligonucleotide comprises at least one modified nucleotide.
96 . The oligonucleotide of claim 64 , wherein at least one nucleotide comprises a 2′ O-methyl.
97 . The oligonucleotide of claim 64 , wherein the oligonucleotide comprises at least one ribonucleotide, at least one deoxyribonucleotide, at least one 2′-fluoro-deoxyribonucleotides or at least one bridged nucleotide.
98 . The oligonucleotide of claim 97 , wherein the bridged nucleotide is a LNA nucleotide, a cEt nucleotide or a ENA modified nucleotide.
99 . The oligonucleotide of claim 64 , wherein each nucleotide of the oligonucleotide is a LNA nucleotide.
100 . The oligonucleotide of claim 64 , wherein the nucleotides of the oligonucleotide comprise alternating deoxyribonucleotides and 2′-fluoro-deoxyribonucleotides, 2′-O-methyl nucleotides, or bridged nucleotides.
101 . The oligonucleotide of claim 64 , wherein the oligonucleotide is mixmer.
102 - 108 . (canceled)
109 . A composition comprising a plurality of oligonucleotides,
wherein each of at least 75% of the oligonucleotides is an oligonucleotide of claim 64 .
110 - 114 . (canceled)
118 . A pharmaceutical composition comprising an oligonucleotide of claim 64 and a pharmaceutically acceptable carrier.
119 - 155 . (canceled)