Catalytic RNA, ribozyme, and its applications in synthetic biology

Park, Soyeon V; Yang, Jun; Jo, Hyesung; Kang, Byunghwa; Oh, Seung Soo; Jung, Gyoo Yeol

doi:10.1016/j.biotechadv.2019.107452

Cited by 44 publications

(35 citation statements)

References 188 publications

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“…Small self-cleaving ribozymes are simple yet elegant devices for controlling RNA function that are attractive starting points for therapeutic and biotechnology applications (35)(36)(37). The folding pathways of cleavable RNAs have been difficult to study, because they frequently react before they can be observed.…”

Section: Discussionmentioning

confidence: 99%

Light-controlled twister ribozyme with single-molecule detection resolves RNA function in time and space

Korman

Sun

Hua

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Small ribozymes such asOryza sativatwister spontaneously cleave their own RNA when the ribozyme folds into its active conformation. The coupling between twister folding and self-cleavage has been difficult to study, however, because the active ribozyme rapidly converts to product. Here, we describe the synthesis of a photocaged nucleotide that releases guanosine within microseconds upon photosolvolysis with blue light. Application of this tool toO. sativatwister achieved the spatial (75 µm) and temporal (≤30 ms) control required to resolve folding and self-cleavage events when combined with single-molecule fluorescence detection of the ribozyme folding pathway. Real-time observation of single ribozymes after photo-deprotection showed that the precleaved folded state is unstable and quickly unfolds if the RNA does not react. Kinetic analysis showed that Mg2+and Mn2+ions increase ribozyme efficiency by making transitions to the high energy active conformation more probable, rather than by stabilizing the folded ground state or the cleaved product. This tool for light-controlled single RNA folding should offer precise and rapid control of other nucleic acid systems.

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Section: Discussionmentioning

confidence: 99%

Light-controlled twister ribozyme with single-molecule detection resolves RNA function in time and space

Korman

Sun

Hua

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…The design step relies on well-characterized biological parts and computer-aided approaches. These parts comprise means to specifically control gene expression or translation, including promoters, 14 terminators, 15 variation in codon usage, 16 ribosome binding sites (RBSs), 17 ribozymes, 18 and protein degradation tags. 19 We see an increasing number of synthetic promoters developed, allowing for orthogonal function and robust fine-tuning of gene expression.…”

Section: The Design-build-test-learn Cycle In Synthetic Biologymentioning

confidence: 99%

“…(D) Engineered enzyme cascade including tyrosine ammonia-lyase (TAL), 4-coumaryl-CoA ligase (4CL), feruloyl CoA 6′-hydroxylase (F6′H), and flavin-dependent halogenase (RadH). 244 (E) Fluorinase (Fl ase ) and improved variants replace Cl with 18 F in 5′-chloro-5′-deoxyadenosine (5′-ClDA), even when the C2 position of the adenine ring presents a long moiety (brown) attached to a bioactive molecule (e.g., peptide with affinity for cancer cells). 249,251 Crystal structures of P450, UPO, catechol-O-methyltransferase (COMT), WelO5, RebH, and Fl ase correspond to PDB IDs 1JPZ, 2YOR, 1VID, 5IQS, 2OAL, and 1RQP, respectively.…”

Section: Late-stage C-h Functionalization Of Drug Leads Using Engineered Enzymesmentioning

confidence: 99%

A Perspective on Synthetic Biology in Drug Discovery and Development—Current Impact and Future Opportunities

et al. 2021

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“…Ribozymes are RNAs with catalytic activities [46,47], and some ribozymes are activated by binding of specific ligands. Theophylline ribozyme is a hammerhead ribozyme that recognizes and site-specifically digests a specific RNA sequence [48], and is activated in the presence of theophylline.…”

Section: Ribozymesmentioning

confidence: 99%

Extremely Low Leakage Expression Systems Using Dual Transcriptional-Translational Control for Toxic Protein Production

Kato

2020

IJMS

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Expression systems for highly toxic protein genes must be conditional and suppress leakage expression to almost zero because even faint leakage expression may kill host cells, inhibit host growth, and cause loss of plasmids containing the toxic protein genes. The most widely used conditional expression systems are controlled only at the transcriptional level, and complete suppression of leakage expression is challenging. Recent progress on translational control has enabled construction of dual transcriptional-translational control systems in which leakage expression is strongly suppressed. This review summarizes the principles, features, and practical examples of dual transcriptional-translational control systems in bacteria, and provides future perspectives on these systems.

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Catalytic RNA, ribozyme, and its applications in synthetic biology

Cited by 44 publications

References 188 publications

Light-controlled twister ribozyme with single-molecule detection resolves RNA function in time and space

Light-controlled twister ribozyme with single-molecule detection resolves RNA function in time and space

A Perspective on Synthetic Biology in Drug Discovery and Development—Current Impact and Future Opportunities

Extremely Low Leakage Expression Systems Using Dual Transcriptional-Translational Control for Toxic Protein Production

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