New Deoxyribozymes for the Native Ligation of RNA

Scheitl, Carolin P M; Lange, Sandra; Höbartner, Claudia

doi:10.3390/molecules25163650

Cited by 10 publications

(5 citation statements)

References 51 publications

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“…These molecules are deeply incorporated into cellular metabolism and RNA and DNA modifications [132] where they may represent chemical 'fossils' that were concurrent with or pre-dated the RNA world. Finally, the existence of the RNA world might also be accompanied by DNA through chemical coproduction [133], where DNA could either have a catalytic function (e.g., RNA ligation [134]) or be harnessed for genetic information storage. , which represent the preferred sites of tRNA fragmentation to generate diverse tsRNAs.…”

Section: Trends In Biochemical Sciencesmentioning

confidence: 99%

Origins and evolving functionalities of tRNA-derived small RNAs

Chen

Zhang

Shi

et al. 2021

Trends in Biochemical Sciences

122

109

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Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are among the most ancient small RNAs in all domains of life and are generated by the cleavage of tRNAs. Emerging studies have begun to reveal the versatile roles of tsRNAs in fundamental biological processes, including gene silencing, ribosome biogenesis, retrotransposition, and epigenetic inheritance, which are rooted in tsRNA sequence conservation, RNA modifications, and protein-binding abilities. We summarize the mechanisms of tsRNA biogenesis and the impact of RNA modifications, and propose how thinking of tsRNA functionality from an evolutionary perspective urges the expansion of tsRNA research into a wider spectrum, including cross-tissue/cross-species regulation and harnessing of the 'tsRNA code' for precision medicine. On the ancientness of tsRNAs/tRNAsWith the wide application of high-throughput RNA sequencing (RNA-seq), tRNA-derived small RNAs (tsRNAs) (also called tDRs or tRNA-derived fragments, tRFs) are increasingly recognized as an emerging class of functional small noncoding RNAs (sncRNAs) in various fundamental biological and disease conditions [1,2]. tsRNAs have been identified in a wide range of species across all three domains of life, including Archaea, Bacteria, and some unicellular organisms (e.g., Protozoa), where other specialized small RNA pathways, such as miRNAs, siRNAs, and Piwi-interacting RNAs (piRNAs), are lacking [3][4][5][6][7]. These observations have positioned tsRNAs among the most ancient classes of sncRNAs for intra-and intercellular functionality and communication that may pre-date the emergence of more specialized sncRNAs. Highlights tRNA-derived small RNAs (tsRNAs) are present across all three domains of life: Archaea, Bacteria, and Eukarya.

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Section: Trends In Biochemical Sciencesmentioning

confidence: 99%

Origins and evolving functionalities of tRNA-derived small RNAs

Chen

Zhang

Shi

et al. 2021

Trends in Biochemical Sciences

122

109

View full text Add to dashboard Cite

show abstract

“…Alternative routes for ligation include T4 RNA ligase 1 and 2, which are known to be highly efficient, and differ with regard to their sequence and structure specificity [43][44][45]. Also, a number of ribozymes and DNAzymes have opened new possibilities to ligate RNA in different contexts [46,47].…”

Section: Discussionmentioning

confidence: 99%

Enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR

et al. 2022

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Solution NMR spectroscopy is a well-established tool with unique advantages for structural studies of RNA molecules. However, for large RNA sequences, the NMR resonances often overlap severely. A reliable way to perform resonance assignment and allow further analysis despite spectral crowding is the use of site-specific isotope labeling in sample preparation. While solid-phase oligonucleotide synthesis has several advantages, RNA length and availability of isotope-labeled building blocks are persistent issues. Purely enzymatic methods represent an alternative and have been presented in the literature. In this study, we report on a method in which we exploit the preference of T7 RNA polymerase for nucleotide monophosphates over triphosphates for the 5’ position, which allows 5’-labeling of RNA. Successive ligation to an unlabeled RNA strand generates a site-specifically labeled RNA. We show the successful production of such an RNA sample for NMR studies, report on experimental details and expected yields, and present the surprising finding of a previously hidden set of peaks which reveals conformational exchange in the RNA structure. This study highlights the feasibility of site-specific isotope-labeling of RNA with enzymatic methods.

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“…Alternative routes for ligation include T4 RNA ligase 1 and 2, which are known to be highly efficient, and differ with regard to their sequence and structure specificity. Also, a number of ribozymes and DNAzymes have opened new possibilities to ligate RNA in different contexts (32,33).…”

Section: Discussionmentioning

confidence: 99%

Purely enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR

Feyrer

Gurdap

Marušič

et al. 2022

Preprint

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Solution NMR spectroscopy is a well-established tool with unique advantages for structural studies of RNA molecules. However, for large RNA sequences, the NMR resonances often overlap severely. A reliable way to perform resonance assignment and allow further analysis despite spectral crowding is the use of site-specific isotope labeling in sample preparation. While solid-phase oligonucleotide synthesis has several advantages, RNA length and availability of isotope-labeled building blocks are persistent issues. Purely enzymatic methods pose as an alternative and have been presented in the literature. In this study, we report on a method in which we exploit the preference of T7 RNA polymerase for nucleotide monophosphates over triphosphates for the 5’ position, which allows 5’-labeling of RNA. Successive ligation to an unlabeled RNA strand generates a site-specifically labeled RNA. We show the successful production of such an RNA sample for NMR studies, report on experimental details and expected yields, and present the surprising finding of a previously hidden set of peaks which reveals conformational exchange in the RNA structure. This study highlights the feasibility of site-specific isotope-labeling of RNA with enzymatic methods.

show abstract

New Deoxyribozymes for the Native Ligation of RNA

Cited by 10 publications

References 51 publications

Origins and evolving functionalities of tRNA-derived small RNAs

Origins and evolving functionalities of tRNA-derived small RNAs

Enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR

Purely enzymatic incorporation of an isotope-labeled adenine into RNA for the study of conformational dynamics by NMR

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