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Rational optimization of the DSL ligase ribozyme with GNRA/receptor interacting modules |
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| Authors: | Junya Ishikawa Luc Jaeger Hiroyuki Furuta |
| Institution: | a Department of Chemistry and Biochemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan b Institut de Science et d’Ingenierie Supramoleculaires (ISIS), Université de Strasbourg (UdS), 8 Allée Gaspard Monge, B. P. 70028, 67083 Strasbourg Cedex, France c Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California at Santa Barbara, Santa Barbara, CA 93106-9510, USA d Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan e ICORP, Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan f PRESTO, Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan |
| Abstract: | The DSL ribozyme is a class of artificial ligase ribozymes with a highly modular architecture, which catalyzes template-directed RNA ligation on a helical substrate module that can be either covalently connected (cis-DSL) or physically separated (trans-DSL) from the catalytic module. Substrate recognition by the catalytic module is promoted by one or two sets of GNRA/receptor interactions acting as clamps in the cis or trans configurations, respectively. In this study, we have rationally designed and analyzed the catalytic and self-assembly properties of several trans-DSL ribozymes with different sets of natural and artificial GNRA-receptor clamps. Two variants newly designed in this study showed significantly enhanced catalytic properties with respect of the original trans-DSL construct. While this work allows dissection of the turnover and catalytic properties of the trans-DSL ribozyme, it also emphasizes the remarkable modularity of RNA tertiary structure for nano-construction of complex functions. |
| Keywords: | Ribozyme RNA motifs RNA self-assembly RNA tertiary structure Self-folding tectoRNA |
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