4.7 Review

Advances in riboswitch-based biosensor as food samples detection tool

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Review Biotechnology & Applied Microbiology

Strategies to manipulate the performance of aptamers in SELEX, post-SELEX and microenvironment

Shuo Qi et al.

Summary: This article reviews the application potential of aptamers in biology and biomedicine, points out the limitations of aptamers at present, and proposes strategies to improve their performance.

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An upconversion nanosensor for rapid and sensitive detection of tetracycline in food based on magnetic-field-assisted separation

Yunlian Zhang et al.

Summary: An upconversion nanosensor for detecting tetracycline was developed using magnetic separation and electrostatic adsorption, with a linear detection range of 0.5-1000 ng mL(-1) and a detection limit of 0.17 ng mL(-1). This method showed great potential for tetracycline detection in food samples, providing simple operation, high sensitivity, excellent repeatability, and selectivity.

FOOD CHEMISTRY (2022)

Review Biochemistry & Molecular Biology

Structural Changes in Aptamers are Essential for Synthetic Riboswitch Engineering

Janis Hoetzel et al.

Summary: Synthetic riboswitches, which consolidate sensing and execution functions in a single RNA molecule, are powerful tools in synthetic biology. However, there is a scarcity of in vitro selected aptamers suitable for engineering synthetic riboswitches. Studies have shown that the key characteristics of regulatory active RNAs, such as structural switching abilities and binding dynamics, are insufficiently represented in conventional SELEX approaches. This review proposes a combination of capture-SELEX and subsequent functional screening for a more successful in vitro selection of aptamers that can be applied in synthetic riboswitch engineering.

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Review Biochemistry & Molecular Biology

Targeted modifications of neomycin and paromomycin: Towards resistance-free antibiotics?

J. Obszynski et al.

Summary: This article discusses the importance of antibiotics and their impact on bacteria, particularly in terms of aging and resistance. It focuses on the chemical synthesis of aminoglycosides and the structure-activity relationships in order to identify efficient modifications that can convert them into future drugs. These studies are of great significance for the development of clinically viable drug candidates.

BIOORGANIC CHEMISTRY (2022)

Article Biophysics

Colorimetric aptasensor targeting zearalenone developed based on the hyaluronic Acid-DNA hydrogel and bimetallic MOFzyme

Yuhan Sun et al.

Summary: In this study, a colorimetric aptasensor based on metal-organic frameworks nanozyme and hyaluronic acid-DNA hydrogel was developed for the quantification of ZEN in food. The aptasensor demonstrated superior analytical performance and ease of use, and was successfully applied for the quantitative detection of ZEN in various food samples.

BIOSENSORS & BIOELECTRONICS (2022)

Review Biotechnology & Applied Microbiology

Dynamic control in metabolic engineering: Theories, tools, and applications

Christopher J. Hartline et al.

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Characterization of synthetic riboswitch in cell-free protein expression systems

Yaroslav Chushak et al.

Summary: Riboswitches are RNA-based regulatory elements that control gene expression through ligand-induced structural changes in mRNA. Synthetic riboswitches have been mainly tested in cell-based systems, but cell-free protein expression systems offer advantages such as eliminating interactions with cellular networks. Studying a theophylline-responsive synthetic riboswitch in E. coli cellular extract and PURE cell-free systems revealed lower protein expression levels due to reduced mRNA fraction in the 'ON' state and lower translation initiation rate compared to a control construct.

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Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection

Piotr Chyzy et al.

Summary: Short, structured fragments of non-coding mRNA may act as molecular switches upon binding specific ligands, regulating the translation of proteins encoded downstream this mRNA sequence. The study reveals that nucleobase mutations in the riboswitch can significantly affect the affinity and efficiency of ligand regulation, with specific mutations altering the binding site position of neomycin and increasing its flexibility.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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What defines a synthetic riboswitch? - Conformational dynamics of ciprofloxacin aptamers with similar binding affinities but varying regulatory potentials

Christoph Kaiser et al.

Summary: Among the many in vitro-selected aptamers, only a small fraction can be applied for synthetic riboswitch engineering. A comparative study was conducted on three aptamers binding to ciprofloxacin, revealing differences in binding kinetics between regulating and non-regulating aptamers. The study suggests that a highly favored structural adaptation of RNA to the ligand during the final binding step is essential for turning an aptamer into a riboswitch.

NUCLEIC ACIDS RESEARCH (2021)

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Tunable Multiplexed Whole-Cell Biosensors as Environmental Diagnostics for ppb-Level Detection of Aromatic Pollutants

Rohita Roy et al.

Summary: By utilizing synthetic biology approaches and structure-guided design, a series of whole-cell biosensors were created, with one sensor capable of detecting harmful substances in drinking water at a sensitivity of 1 ppb. By engineering mutations into the gene, a variety of sensors for detecting different pollutants were generated.

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A malachite green light-up aptasensor for the detection of theophylline

Arghya Sett et al.

Summary: A dual aptasensor for theophylline was designed based on light-up aptamers, which can discriminate between theophylline and its analogues through a fluorescence signal triggered by their specific structure in the presence of theophylline.

TALANTA (2021)

Correction Biochemical Research Methods

RNA-based Capture-SELEX for the selection of small molecule-binding aptamers (vol 161, pg 10, 2019)

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Xiangyang Liu et al.

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Point-of-Use Detection of Environmental Fluoride via a Cell-Free Riboswitch-Based Biosensor

Walter Thavarajah et al.

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The Theophylline Aptamer: 25 Years as an Important Tool in Cellular Engineering Research

Alexandra Wrist et al.

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Peng Zhang et al.

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Adrien Boussebayle et al.

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Next-level riboswitch development-implementation of Capture-SELEX facilitates identification of a new synthetic riboswitch

Adrien Boussebayle et al.

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Riboswitch distribution, structure, and function in bacteria

Nikolet Pavlova et al.

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Real time detection of adenosine and theophylline in urine and blood samples using graphene modified electrode

Srinivasan Kesavan et al.

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Highly sensitive and specific on-site detection of serum cocaine by a low cost aptasensor

Rania Oueslati et al.

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Detection of theophylline using molecularly imprinted mesoporous silica spheres

Tian Gan et al.

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A Fluorescent Split Aptamer for Visualizing RNA-RNA Assembly In Vivo

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Naringenin-responsive riboswitch-based fluorescent biosensor module for Escherichia coli co-cultures

Yu Xiu et al.

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Amin Espah Borujeni et al.

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Mi-Sun Ha et al.

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Applications and advances of metabolite biosensors for metabolic engineering

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Imaging metabolite dynamics in living cells using a Spinach-based riboswitch

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Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine

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