Rational optimization of the DSL ligase ribozyme with GNRA/receptor interacting modules

Junya Ishikawa; Shigeyoshi Matsumura; Luc Jaeger; Tan Inoue; Hiroyuki Furuta; Yoshiya Ikawa

doi:10.1016/j.abb.2009.08.020

Rational optimization of the DSL ligase ribozyme with GNRA/receptor interacting modules

Junya Ishikawa, Shigeyoshi Matsumura, Luc Jaeger, Tan Inoue, Hiroyuki Furuta, Yoshiya Ikawa^*

^*Corresponding author for this work

Department of Chemistry

Research output: Contribution to journal › Article › peer-review

16 Scopus citations

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.

Original language	English
Pages (from-to)	163-170
Number of pages	8
Journal	Archives of Biochemistry and Biophysics
Volume	490
Issue number	2
DOIs	https://doi.org/10.1016/j.abb.2009.08.020
State	Published - 2009/10/15

Keywords

RNA motifs
RNA self-assembly
RNA tertiary structure
Ribozyme
Self-folding
tectoRNA

ASJC Scopus subject areas

Biophysics
Biochemistry
Molecular Biology

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10.1016/j.abb.2009.08.020

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title = "Rational optimization of the DSL ligase ribozyme with GNRA/receptor interacting modules",

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 = "RNA motifs, RNA self-assembly, RNA tertiary structure, Ribozyme, Self-folding, tectoRNA",

author = "Junya Ishikawa and Shigeyoshi Matsumura and Luc Jaeger and Tan Inoue and Hiroyuki Furuta and Yoshiya Ikawa",

note = "Funding Information: This research was partly supported by Grant-in-Aids on Innovative Areas “ Emergence in Chemistry ” [No. 21111518 to Y.I.], for Exploratory Research [No. 19657071 to Y.I.], and the Global COE program, “ Science for Future Molecular Systems ” [to H.F.] from The Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT), and also by a grant from the National Institutes of Health [ R01-GM079604 to L.J.]. L.J., H.F., and Y.I. also thank to a joint program between Kyushu University Global COE (Science for Future Molecular Systems) and the California NanoSystems Institute (CNSI) for supporting this research. ",

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AU - Ishikawa, Junya

AU - Matsumura, Shigeyoshi

AU - Jaeger, Luc

AU - Inoue, Tan

AU - Furuta, Hiroyuki

AU - Ikawa, Yoshiya

N1 - Funding Information: This research was partly supported by Grant-in-Aids on Innovative Areas “ Emergence in Chemistry ” [No. 21111518 to Y.I.], for Exploratory Research [No. 19657071 to Y.I.], and the Global COE program, “ Science for Future Molecular Systems ” [to H.F.] from The Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT), and also by a grant from the National Institutes of Health [ R01-GM079604 to L.J.]. L.J., H.F., and Y.I. also thank to a joint program between Kyushu University Global COE (Science for Future Molecular Systems) and the California NanoSystems Institute (CNSI) for supporting this research.

PY - 2009/10/15

Y1 - 2009/10/15

N2 - 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.

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KW - RNA self-assembly

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KW - Self-folding

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Rational optimization of the DSL ligase ribozyme with GNRA/receptor interacting modules

Abstract

Keywords

ASJC Scopus subject areas

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