In silico design of artificial riboswitches is a challenging and intriguing task. Since experimental approaches such as in vitro selection are time-consuming processes, computational tools that guide riboswitch design are desirable to accelerate the design process. In this chapter, we describe the usage of the MODENA web server to design ON riboswitches on the basis of a multi-objective genetic algorithm and RNA secondary structure prediction.
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http://dx.doi.org/10.1007/978-1-0716-4079-1_3 | DOI Listing |
ACS Synth Biol
December 2024
Proteo-Science Center, Ehime University, 2-5 Bunkyo, Matsuyama, Ehime 790-8577, Japan.
Cell-free systems, which can express an easily detectable output (protein) with a DNA or mRNA template, are promising as foundations of biosensors devoid of cellular constraints. Moreover, by encasing them in membranes such as natural cells to create artificial cells, these systems can avoid the adverse effects of environmental inhibitory molecules. However, the bacterial systems generally used for this purpose do not function well at ambient temperatures.
View Article and Find Full Text PDFNucleic Acids Res
December 2024
Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
X-ray crystallography is a fundamental technique that provides atomic-level insights into RNA structures. However, obtaining crystals of RNA structures diffracting to high resolution is challenging. We introduce a simple strategy to enhance the resolution limit of RNA crystals by the selective substitution of Watson-Crick pairs by GU pairs within RNA sequences.
View Article and Find Full Text PDFNat Methods
December 2024
GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China.
Nat Commun
December 2024
Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA.
Genes (Basel)
November 2024
Konan Laboratory for Oligonucleotide Therapeutics (KOLOT), 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Hyogo, Japan.
: Riboswitches are functional nucleic acids that regulate biological processes by interacting with small molecules, such as metabolites, influencing gene expression. Artificial functional nucleic acids, including deoxyribozymes, have been developed through in vitro selection for various catalytic functions. In a previous study, an l-histidine-dependent deoxyribozyme was identified, exhibiting RNA cleavage activity in the presence of l-histidine resembling ribonuclease catalytic mechanisms.
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