Antisense Gapmers with LNA-Wings and (<i>S</i>)-5′-<i>C</i>-Aminopropyl-2′-arabinofluoro-nucleosides Could Efficiently Suppress the Expression of <i>KNTC2</i>
Previously reported (<i>S</i>)-5′-<i>C</i>-aminopropyl-2′-arabinofluoro-thymidine (<b>5ara-T</b>) and newly synthesized (<i>S</i>)-5′-<i>C</i>-aminopropyl-2′-arabinofluoro-5-methyl-cytidine (<b>5ara-<sup>Me</sup>C</b>...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/27/21/7384 |
| _version_ | 1797467115554340864 |
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| author | Yujun Zhou Shuichi Sakamoto Yoshihito Ueno |
| author_facet | Yujun Zhou Shuichi Sakamoto Yoshihito Ueno |
| author_sort | Yujun Zhou |
| collection | DOAJ |
| description | Previously reported (<i>S</i>)-5′-<i>C</i>-aminopropyl-2′-arabinofluoro-thymidine (<b>5ara-T</b>) and newly synthesized (<i>S</i>)-5′-<i>C</i>-aminopropyl-2′-arabinofluoro-5-methyl-cytidine (<b>5ara-<sup>Me</sup>C</b>) analogs were incorporated into a series of antisense gapmers containing multiple phosphorothioate (PS) linkages and locked nucleic acids (LNAs) in their wing regions. The functional properties of the gapmers were further evaluated in vitro. Compared with the positive control, for the LNA-wing full PS gapmer without <b>5ara</b> modification, it was revealed that each gapmer could have a high affinity and be thermally stable under biological conditions. Although the cleavage pattern was obviously changed; gapmers with <b>5ara</b> modification could still efficiently activate <i>E. coli</i> RNase H1. In addition, incorporating one <b>5ara</b> modification into the two phosphodiester linkages could reverse the destabilization in enzymatic hydrolysis caused by fewer PS linkages. In vitro cellular experiments were also performed, and the Lipofectamine<sup>®</sup> 2000 (LFA)+ group showed relatively higher antisense activity than the LFA-free group. KN5ara-10, which contains fewer PS linkages, showed similar or slightly better antisense activity than the corresponding full PS-modified KN5ara-3. Hence, KN5ara-10 may be the most promising candidate for <i>KNTC2</i>-targeted cancer therapy. |
| first_indexed | 2024-03-09T18:48:06Z |
| format | Article |
| id | doaj.art-8f7e2ed41f114768b6b56f27c639dcc6 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-09T18:48:06Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-8f7e2ed41f114768b6b56f27c639dcc62023-11-24T06:03:20ZengMDPI AGMolecules1420-30492022-10-012721738410.3390/molecules27217384Antisense Gapmers with LNA-Wings and (<i>S</i>)-5′-<i>C</i>-Aminopropyl-2′-arabinofluoro-nucleosides Could Efficiently Suppress the Expression of <i>KNTC2</i>Yujun Zhou0Shuichi Sakamoto1Yoshihito Ueno2United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, JapanInstitute of Microbial Chemistry (BIKAKEN) Numazu Branch, Microbial Chemistry Research Foundation, 18-24 Miyamoto, Numazu 410-0301, JapanUnited Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, JapanPreviously reported (<i>S</i>)-5′-<i>C</i>-aminopropyl-2′-arabinofluoro-thymidine (<b>5ara-T</b>) and newly synthesized (<i>S</i>)-5′-<i>C</i>-aminopropyl-2′-arabinofluoro-5-methyl-cytidine (<b>5ara-<sup>Me</sup>C</b>) analogs were incorporated into a series of antisense gapmers containing multiple phosphorothioate (PS) linkages and locked nucleic acids (LNAs) in their wing regions. The functional properties of the gapmers were further evaluated in vitro. Compared with the positive control, for the LNA-wing full PS gapmer without <b>5ara</b> modification, it was revealed that each gapmer could have a high affinity and be thermally stable under biological conditions. Although the cleavage pattern was obviously changed; gapmers with <b>5ara</b> modification could still efficiently activate <i>E. coli</i> RNase H1. In addition, incorporating one <b>5ara</b> modification into the two phosphodiester linkages could reverse the destabilization in enzymatic hydrolysis caused by fewer PS linkages. In vitro cellular experiments were also performed, and the Lipofectamine<sup>®</sup> 2000 (LFA)+ group showed relatively higher antisense activity than the LFA-free group. KN5ara-10, which contains fewer PS linkages, showed similar or slightly better antisense activity than the corresponding full PS-modified KN5ara-3. Hence, KN5ara-10 may be the most promising candidate for <i>KNTC2</i>-targeted cancer therapy.https://www.mdpi.com/1420-3049/27/21/7384antisense oligonucleotides5′-aminopropyl group2′-arabinofluoro groupRNase Hphosphorothioatelocked nucleic acid |
| spellingShingle | Yujun Zhou Shuichi Sakamoto Yoshihito Ueno Antisense Gapmers with LNA-Wings and (<i>S</i>)-5′-<i>C</i>-Aminopropyl-2′-arabinofluoro-nucleosides Could Efficiently Suppress the Expression of <i>KNTC2</i> Molecules antisense oligonucleotides 5′-aminopropyl group 2′-arabinofluoro group RNase H phosphorothioate locked nucleic acid |
| title | Antisense Gapmers with LNA-Wings and (<i>S</i>)-5′-<i>C</i>-Aminopropyl-2′-arabinofluoro-nucleosides Could Efficiently Suppress the Expression of <i>KNTC2</i> |
| title_full | Antisense Gapmers with LNA-Wings and (<i>S</i>)-5′-<i>C</i>-Aminopropyl-2′-arabinofluoro-nucleosides Could Efficiently Suppress the Expression of <i>KNTC2</i> |
| title_fullStr | Antisense Gapmers with LNA-Wings and (<i>S</i>)-5′-<i>C</i>-Aminopropyl-2′-arabinofluoro-nucleosides Could Efficiently Suppress the Expression of <i>KNTC2</i> |
| title_full_unstemmed | Antisense Gapmers with LNA-Wings and (<i>S</i>)-5′-<i>C</i>-Aminopropyl-2′-arabinofluoro-nucleosides Could Efficiently Suppress the Expression of <i>KNTC2</i> |
| title_short | Antisense Gapmers with LNA-Wings and (<i>S</i>)-5′-<i>C</i>-Aminopropyl-2′-arabinofluoro-nucleosides Could Efficiently Suppress the Expression of <i>KNTC2</i> |
| title_sort | antisense gapmers with lna wings and i s i 5 i c i aminopropyl 2 arabinofluoro nucleosides could efficiently suppress the expression of i kntc2 i |
| topic | antisense oligonucleotides 5′-aminopropyl group 2′-arabinofluoro group RNase H phosphorothioate locked nucleic acid |
| url | https://www.mdpi.com/1420-3049/27/21/7384 |
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