Superior Silencing by 2′,4′-BNANC-Based Short Antisense Oligonucleotides Compared to 2′,4′-BNA/LNA-Based Apolipoprotein B Antisense Inhibitors
The duplex stability with target mRNA and the gene silencing potential of a novel bridged nucleic acid analogue are described. The analogue, 2′,4′-BNANC antisense oligonucleotides (AONs) ranging from 10- to 20-nt-long, targeted apolipoprotein B. 2′,4′-BNANC was directly compared to its conventional...
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| Format: | Article |
| Language: | English |
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Wiley
2012-01-01
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| Series: | Journal of Nucleic Acids |
| Online Access: | http://dx.doi.org/10.1155/2012/707323 |
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| author | Tsuyoshi Yamamoto Hidenori Yasuhara Fumito Wada Mariko Harada-Shiba Takeshi Imanishi Satoshi Obika |
| author_facet | Tsuyoshi Yamamoto Hidenori Yasuhara Fumito Wada Mariko Harada-Shiba Takeshi Imanishi Satoshi Obika |
| author_sort | Tsuyoshi Yamamoto |
| collection | DOAJ |
| description | The duplex stability with target mRNA and the gene silencing potential of a novel bridged nucleic acid analogue are described. The analogue, 2′,4′-BNANC antisense oligonucleotides (AONs) ranging from 10- to 20-nt-long, targeted apolipoprotein B. 2′,4′-BNANC was directly compared to its conventional bridged (or locked) nucleic acid (2′,4′-BNA/LNA)-based counterparts. Melting temperatures of duplexes formed between 2′,4′-BNANC-based antisense oligonucleotides and the target mRNA surpassed those of 2′,4′-BNA/LNA-based counterparts at all lengths. An in vitro transfection study revealed that when compared to the identical length 2′,4′-BNA/LNA-based counterpart, the corresponding 2′,4′-BNANC-based antisense oligonucleotide showed significantly stronger inhibitory activity. This inhibitory activity was more pronounced in shorter (13-, 14-, and 16-mer) oligonucleotides. On the other hand, the 2′,4′-BNANC-based 20-mer AON exhibited the highest affinity but the worst IC50 value, indicating that very high affinity may undermine antisense potency. These results suggest that the potency of AONs requires a balance between reward term and penalty term. Balance of these two parameters would depend on affinity, length, and the specific chemistry of the AON, and fine-tuning of this balance could lead to improved potency. We demonstrate that 2′,4′-BNANC may be a better alternative to conventional 2′,4′-BNA/LNA, even for “short” antisense oligonucleotides, which are attractive in terms of drug-likeness and cost-effective bulk production. |
| format | Article |
| id | doaj-art-847ece0d41d04df6a535804f9fbc3856 |
| institution | Kabale University |
| issn | 2090-0201 2090-021X |
| language | English |
| publishDate | 2012-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Journal of Nucleic Acids |
| spelling | doaj-art-847ece0d41d04df6a535804f9fbc38562025-08-20T03:37:42ZengWileyJournal of Nucleic Acids2090-02012090-021X2012-01-01201210.1155/2012/707323707323Superior Silencing by 2′,4′-BNANC-Based Short Antisense Oligonucleotides Compared to 2′,4′-BNA/LNA-Based Apolipoprotein B Antisense InhibitorsTsuyoshi Yamamoto0Hidenori Yasuhara1Fumito Wada2Mariko Harada-Shiba3Takeshi Imanishi4Satoshi Obika5Applied Biopharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, JapanApplied Biopharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, JapanApplied Biopharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, JapanDepartment of Molecular Innovation in Lipidology, National Cerebral and Cardiovascular Center Research Institute, 5-7-1 Fujishirodai, Suita, Osaka 565-8565, JapanBNA Inc, 7-7-20 Saito-Asagi, Ibaraki, Osaka 567-0085, JapanApplied Biopharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, JapanThe duplex stability with target mRNA and the gene silencing potential of a novel bridged nucleic acid analogue are described. The analogue, 2′,4′-BNANC antisense oligonucleotides (AONs) ranging from 10- to 20-nt-long, targeted apolipoprotein B. 2′,4′-BNANC was directly compared to its conventional bridged (or locked) nucleic acid (2′,4′-BNA/LNA)-based counterparts. Melting temperatures of duplexes formed between 2′,4′-BNANC-based antisense oligonucleotides and the target mRNA surpassed those of 2′,4′-BNA/LNA-based counterparts at all lengths. An in vitro transfection study revealed that when compared to the identical length 2′,4′-BNA/LNA-based counterpart, the corresponding 2′,4′-BNANC-based antisense oligonucleotide showed significantly stronger inhibitory activity. This inhibitory activity was more pronounced in shorter (13-, 14-, and 16-mer) oligonucleotides. On the other hand, the 2′,4′-BNANC-based 20-mer AON exhibited the highest affinity but the worst IC50 value, indicating that very high affinity may undermine antisense potency. These results suggest that the potency of AONs requires a balance between reward term and penalty term. Balance of these two parameters would depend on affinity, length, and the specific chemistry of the AON, and fine-tuning of this balance could lead to improved potency. We demonstrate that 2′,4′-BNANC may be a better alternative to conventional 2′,4′-BNA/LNA, even for “short” antisense oligonucleotides, which are attractive in terms of drug-likeness and cost-effective bulk production.http://dx.doi.org/10.1155/2012/707323 |
| spellingShingle | Tsuyoshi Yamamoto Hidenori Yasuhara Fumito Wada Mariko Harada-Shiba Takeshi Imanishi Satoshi Obika Superior Silencing by 2′,4′-BNANC-Based Short Antisense Oligonucleotides Compared to 2′,4′-BNA/LNA-Based Apolipoprotein B Antisense Inhibitors Journal of Nucleic Acids |
| title | Superior Silencing by 2′,4′-BNANC-Based Short Antisense Oligonucleotides Compared to 2′,4′-BNA/LNA-Based Apolipoprotein B Antisense Inhibitors |
| title_full | Superior Silencing by 2′,4′-BNANC-Based Short Antisense Oligonucleotides Compared to 2′,4′-BNA/LNA-Based Apolipoprotein B Antisense Inhibitors |
| title_fullStr | Superior Silencing by 2′,4′-BNANC-Based Short Antisense Oligonucleotides Compared to 2′,4′-BNA/LNA-Based Apolipoprotein B Antisense Inhibitors |
| title_full_unstemmed | Superior Silencing by 2′,4′-BNANC-Based Short Antisense Oligonucleotides Compared to 2′,4′-BNA/LNA-Based Apolipoprotein B Antisense Inhibitors |
| title_short | Superior Silencing by 2′,4′-BNANC-Based Short Antisense Oligonucleotides Compared to 2′,4′-BNA/LNA-Based Apolipoprotein B Antisense Inhibitors |
| title_sort | superior silencing by 2 4 bnanc based short antisense oligonucleotides compared to 2 4 bna lna based apolipoprotein b antisense inhibitors |
| url | http://dx.doi.org/10.1155/2012/707323 |
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