Abstract
We developed a new in vitro selection strategy “design and selection” to isolate effectively artificial ribozymes (catalytic RNAs). An overall RNA structure (scaffold) is initially designed, and then a relatively short randomized sequence is installed at the reaction point of the scaffold, followed by the in vitro selection. This method can reduce the length of randomized sequence, providing large coverage of the sequence space in contrast with the conventional way, which makes the selection experiment effectively. Additionally, further analysis of ribozymes obtained by this approach is practically easy since the overall molecular structure is predesigned and well known. Here we show the procedure to isolate artificial RNA ligase ribozymes by this strategy. We have succeeded in isolation of the designed and selected ligase (DSL) ribozymes.
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Acknowledgement
The authors would like to thank Prof. Tan Inoue, Kentaro Tsuda, and Dr. Kazutake Fukada for developing this method and fruitful discussion. This work was supported in part by Grant-in-Aid for Scientific Research on Innovative Areas “Molecular Robotics” (No. 25104518 to Y.I.), “Synthetic Biology” (No. 23119005 to Y.I.) from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), and also by Grant-in-Aid for Research Activity Start-up (No. 26891009 to S.M.) from Japan Society for the Promotion of Science (JSPS), Japan.
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Matsumura, S., Ikawa, Y. (2015). Artificial Ligase Ribozymes Isolated by a “Design and Selection” Strategy. In: Ponchon, L. (eds) RNA Scaffolds. Methods in Molecular Biology, vol 1316. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2730-2_10
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DOI: https://doi.org/10.1007/978-1-4939-2730-2_10
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2729-6
Online ISBN: 978-1-4939-2730-2
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