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Biomolecules
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Recent Advances in RNA Synthetic Biology
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Recent Advances in RNA Synthetic Biology

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Synthetic Biology and Bioengineering".

Deadline for manuscript submissions: closed (1 June 2023) | Viewed by 7898

Special Issue Editors

Dr. Alexandra Peregrina

E-Mail Website
Guest Editor
Faculty of Sciences, University of Granada, Av. de Fuente Nueva, s/n, 18071 Granada, Spain
Interests: microbiology; small non-coding RNAs; RNases; gene expression; Polyhydroxyalkanoates (PHAs); Pseudomonas putida; Sinorhizobium meliloti
Dr. Chenguang Fan

E-Mail Website
Guest Editor
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
Interests: genetic code expansion; RNA biology; protein acetylation; protein phosphorylation; bacterial microcompartment; metabolism
Dr. Simon Schäper

E-Mail Website
Guest Editor
Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
Interests: the dynamics of cell division proteins and cell cycle regulatory mechanisms in Staphylococcus aureus

Special Issue Information

Dear Colleagues,

Synthetic biology is a multidisciplinary field of science that designs and reconstructs biological systems with the aim of giving them new abilities. RNA molecules play fundamental and diverse roles in cells, which rely on their interaction with other nucleic acids, proteins, and cell molecules. Regulatory RNAs, such as non-coding RNAs (ncRNAs), are being extensively studied, and their use is emerging in synthetic biology to program cellular behavior through the use of genetic and metabolic engineering. Diverse sets of regulatory RNA molecules can be employed to confer a specific activity (e.g., RNA-RNA binding, ligand-RNA binding, ribozyme activity) to the engineered RNA-based systems. The rapid increase in computational design and biotechnology tools permits the application of these versatile engineered RNA systems to expand our understanding of biomolecular networks. Further, the expanding catalog of designer RNAs opens the opportunity for novel applications to a wide range of organisms in biomedicine, therapeutics, or the development of microbial fuel cells, among others.

This Special Issue on “Recent Advances in RNA Synthetic Biology” will highlight original research papers, reviews, and articles that integrate the expertise from different areas related to the control of gene expression, genome engineering, and transcriptional and post-transcriptional fine-tuning of metabolic cellular pathways. 

Dr. Alexandra Peregrina
Dr. Chenguang Fan
Dr. Simon Schäper
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • RNA molecules
  • synthetic biology
  • metabolic engineering
  • control of gene expression
  • cell control

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Published Papers (2 papers)

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Review

21 pages, 6577 KiB  
Review
gRNA Design: How Its Evolution Impacted on CRISPR/Cas9 Systems Refinement
by Cristofer Motoche-Monar, Julián E. Ordoñez, Oscar Chang and Fernando A. Gonzales-Zubiate
Biomolecules 2023, 13(12), 1698; https://doi.org/10.3390/biom13121698 - 24 Nov 2023
Cited by 3 | Viewed by 4259
Abstract
Over the past decade, genetic engineering has witnessed a revolution with the emergence of a relatively new genetic editing tool based on RNA-guided nucleases: the CRISPR/Cas9 system. Since the first report in 1987 and characterization in 2007 as a bacterial defense mechanism, this [...] Read more.
Over the past decade, genetic engineering has witnessed a revolution with the emergence of a relatively new genetic editing tool based on RNA-guided nucleases: the CRISPR/Cas9 system. Since the first report in 1987 and characterization in 2007 as a bacterial defense mechanism, this system has garnered immense interest and research attention. CRISPR systems provide immunity to bacteria against invading genetic material; however, with specific modifications in sequence and structure, it becomes a precise editing system capable of modifying the genomes of a wide range of organisms. The refinement of these modifications encompasses diverse approaches, including the development of more accurate nucleases, understanding of the cellular context and epigenetic conditions, and the re-designing guide RNAs (gRNAs). Considering the critical importance of the correct performance of CRISPR/Cas9 systems, our scope will emphasize the latter approach. Hence, we present an overview of the past and the most recent guide RNA web-based design tools, highlighting the evolution of their computational architecture and gRNA characteristics over the years. Our study explains computational approaches that use machine learning techniques, neural networks, and gRNA/target interactions data to enable predictions and classifications. This review could open the door to a dynamic community that uses up-to-date algorithms to optimize and create promising gRNAs, suitable for modern CRISPR/Cas9 engineering. Full article
(This article belongs to the Special Issue Recent Advances in RNA Synthetic Biology)
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15 pages, 971 KiB  
Review
Real-Time Assessment of Intracellular Metabolites in Single Cells through RNA-Based Sensors
by Alvaro Darío Ortega
Biomolecules 2023, 13(5), 765; https://doi.org/10.3390/biom13050765 - 28 Apr 2023
Viewed by 2690
Abstract
Quantification of the concentration of particular cellular metabolites reports on the actual utilization of metabolic pathways in physiological and pathological conditions. Metabolite concentration also constitutes the readout for screening cell factories in metabolic engineering. However, there are no direct approaches that allow for [...] Read more.
Quantification of the concentration of particular cellular metabolites reports on the actual utilization of metabolic pathways in physiological and pathological conditions. Metabolite concentration also constitutes the readout for screening cell factories in metabolic engineering. However, there are no direct approaches that allow for real-time assessment of the levels of intracellular metabolites in single cells. In recent years, the modular architecture of natural bacterial RNA riboswitches has inspired the design of genetically encoded synthetic RNA devices that convert the intracellular concentration of a metabolite into a quantitative fluorescent signal. These so-called RNA-based sensors are composed of a metabolite-binding RNA aptamer as the sensor domain, connected through an actuator segment to a signal-generating reporter domain. However, at present, the variety of available RNA-based sensors for intracellular metabolites is still very limited. Here, we go through natural mechanisms for metabolite sensing and regulation in cells across all kingdoms, focusing on those mediated by riboswitches. We review the design principles underlying currently developed RNA-based sensors and discuss the challenges that hindered the development of novel sensors and recent strategies to address them. We finish by introducing the current and potential applicability of synthetic RNA-based sensors for intracellular metabolites. Full article
(This article belongs to the Special Issue Recent Advances in RNA Synthetic Biology)
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