Article
Chemistry, Analytical
Tatiana Zimina, Nikita Sitkov, Vladimir Karasev, Yury Skorik, Alexey Kolobov, Alexander Kolobov, Nikolay Bunenkov, Viktor Luchinin
Summary: The study used in silico modelling to simulate peptides complementary to lactoferrin, specifically focusing on the bonding site between pneumococcal surface protein (PSP) and lactoferrin (LF). The proposed peptide, EEVAPQAQAKIAELENQVHRLE, was synthesized and analyzed to confirm its purity. Experimental results showed that the peptide formed a complex with LF, leading to a change in mobility. However, no binding was observed with homomyeloperoxidase and myoglobin.
Review
Chemistry, Analytical
Bu-yue Zhang, Lei Shi, Xiao-ying Ma, Lu Liu, Yao Fu, Xiu-feng Zhang
Summary: This review focuses on functional nucleic acid-based biosensors for detecting Pb2+ from 2010 to 2020. The biosensors are categorized into colorimetric, fluorometric, and electrochemical biosensors based on different reported signals. The mechanism of action and detection effectiveness of each biosensor are explained, and the current situation and future research direction of nucleic acid biosensors for Pb2+ detection are summarized.
CRITICAL REVIEWS IN ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Multidisciplinary
Haixiang Yu, Obtin Alkhamis, Juan Canoura, Yingzhu Liu, Yi Xiao
Summary: This review discusses the challenges and advances in isolating and characterizing small-molecule-binding DNA aptamers, including in vitro methodologies for isolation, strategies for optimal binding properties, techniques for characterizing aptamer-target binding and structure, and various small-molecule sensing platforms and detection applications based on aptamers.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Zhichu Xiang, Jian Zhao, Deyu Yi, Zhenghan Di, Lele Li
Summary: The study introduces a protease-activatable aptamer system for molecular sensing and imaging in a tumor-specific manner. By utilizing a PNA-peptide-PNA triblock copolymer to lock the structure-switching activity of the aptamer, protease-mediated cleavage of the peptide substrate can reduce binding affinity and recover the biosensing function. This work demonstrates the potential of bridging the gap between functional DNA and peptides for precise biomedical applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Chemistry, Analytical
Yichen Zhao, Kayvan Yavari, Yihao Wang, Kunfu Pi, Philippe Van Cappellen, Juewen Liu
Summary: This review highlights the efforts to develop field-deployable water quality biosensors. Various types of biosensor devices, including microfluidic, lateral flow, and paper-based devices, as well as the conversion of glucometers for environmental analyte detection, are discussed. The review also covers DNA-functionalized hydrogels and their use in diffusive gradients in thin films (DGT) devices. However, future work should focus on testing real environmental samples and comparing DNA-based sensors to standard analytical methods.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Adeem Alshammari, Harm van Zalinge, Ian Sandall
Summary: The dissolution behavior of zinc oxide is investigated using spectroscopic ellipsometry to assess its suitability as a biosensing platform. The results show that functionalized zinc oxide surfaces are well-protected and do not dissolve significantly. The binding kinetics of the SARS-CoV-2 spike protein on aptamer-functionalized zinc oxide surfaces are studied, revealing fluctuation in surface density upon initial exposure and a stable increase in density with increasing protein concentration. The technique and setup demonstrate a limit-of-detection of 1 nanomole (nM) and a linear response up to 100 nM.
Article
Biochemistry & Molecular Biology
Heinz Fabian Raber, Dennis Horst Kubiczek, Nicholas Bodenberger, Ann-Kathrin Kissmann, Deena D'souza, Hu Xing, Daniel Mayer, Pengfei Xu, Uwe Knippschild, Barbara Spellerberg, Tanja Weil, Frank Rosenau
Summary: This study highlights the development and characterization of DNA aptamers for fast labeling of human gut bacterium Akkermansia muciniphila and their potential impact on Alzheimer's disease. The results demonstrate the universal applicability of aptamers in modern microbiology techniques, including fluorimetry, confocal laser scanning microscopy, and flow cytometry. The findings suggest that these aptamers may have promising prospects for developing novel assays in clinical microbiology and electronic biosensors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Chemistry, Analytical
Jiuxing Li, Zijie Zhang, Rudi Liu, Ryan Amini, Bruno J. Salena, Yingfu Li
Summary: Functional nucleic acids (FNAs) are short, single-stranded nucleic acids derived from synthetic libraries that have the potential to overcome limitations in pathogen diagnostics. This review summarizes the development of FNA-based biosensors for viral and bacterial detection in clinical samples, discussing the selection of FNAs for biomarker recognition and their integration into various biosensors. The challenges of using FNA-based biosensors for infectious diseases are also addressed.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Hanxiao Zhang, Albert Zehan Li, Juewen Liu
Summary: Using DNA staining dyes for label-free detection of aptamer binding has been done for a long time, but the cationic nature of the dyes can lead to unstable signals and false interpretations of results due to adsorption. This study evaluated the stability of the signal and found that a quartz cuvette provided a more stable signal compared to a polystyrene microplate, and equilibrating the system improved signal stability. The surfactant Triton X-100 was found to have the best protective effect against fluorescence signal decrease due to dye adsorption, and its use improved signal stability for different aptamers.
Article
Chemistry, Multidisciplinary
Yuqing Li, Hang Gao, Zengyao Qi, Zhicheng Huang, Lingzi Ma, Juewen Liu
Summary: Unmodified DNA can achieve high conjugation efficiency under freezing conditions, and diblock DNA design containing A(5) block allows attachment of various functional DNA sequences, suitable for ultrasensitive DNA hybridization and Hg2+ detection.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Po-Jung Jimmy Huang, Juewen Liu
Summary: In this study, DNA aptamers for L-lactate were obtained through library-immobilization selection method with high affinity and selectivity. A fluorescent biosensor based on the strand displacement method was constructed, allowing simultaneous detection of lactate and glucose in the same solution. This research expands the application of aptamers to simple metabolites and provides a useful tool for continuous and multiplexed monitoring.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Chemistry, Analytical
Zheng Wang, Xinhui Lou
Summary: Fiber optic evanescent wave (FOEW) sensor using functional nucleic acids (FNAs) as specific recognition ligands has shown great potential in the onsite and continuous detection of various targets. This review summarizes the progress of fluorescent FNA-based FOEW biosensor and its sensing mechanisms for different types of targets, including small molecules, heavy metal ions, proteins, nucleic acids, and pathogens. The challenges and prospects for the development of FOEW biosensors capable of onsite and continuous detection are also discussed.
Article
Chemistry, Analytical
Uraiwan Kositanont, Chatchawan Srisawat, Sirinapa Sripinitchai, Charin Thawornkuno, Thanyarat Chaibun, Sinthu Karunaithas, Chamras Promptmas, Benchaporn Lertanantawong
Summary: Researchers developed an electrochemical aptasensor to detect the electron transfer flavoprotein subunit beta (ETFB) for diagnosing leptospiral infection.
Review
Chemistry, Analytical
Somayeh Vandghanooni, Zohreh Sanaat, Raheleh Farahzadi, Morteza Eskandani, Hossein Omidian, Yadollah Omidi
Summary: Early diagnosis of cancer is crucial, and aptamer-based biosensors have been developed as reliable tools for detecting various cancer markers, increasing the chances of successful treatment.
MICROCHEMICAL JOURNAL
(2021)
Article
Chemistry, Analytical
Yichen Zhao, Biwen Gao, Peihuan Sun, Jiawen Liu, Juewen Liu
Summary: This study investigated the effect of pH and metal ions on the fluorescence enhancement sensor OTC5 that binds to tetracycline, oxytetracycline, and doxycycline. The results showed that Mg2+ ions are crucial for the binding of OTC5 to its target and that lower pH values lead to better fluorescence enhancement.
Article
Plant Sciences
Luca Tadini, Carlotta Peracchio, Andrea Trotta, Monica Colombo, Ilaria Mancini, Nicolaj Jeran, Alex Costa, Franco Faoro, Milena Marsoni, Candida Vannini, Eva-Mari Aro, Paolo Pesaresi
Review
Biochemistry & Molecular Biology
Francesca Caselli, Fabio Zanarello, Martin M. Kater, Raffaella Battaglia, Veronica Gregis
BIOCHEMICAL SOCIETY TRANSACTIONS
(2020)
Article
Plant Sciences
Michela Osnato, Luis Matias-Hernandez, Andrea Elizabeth Aguilar-Jaramillo, Martin M. Kater, Soraya Pelaz
Article
Plant Sciences
Michela Osnato, Elia Lacchini, Alessandro Pilatone, Ludovico Dreni, Andrea Grioni, Matteo Chiara, David Horner, Soraya Pelaz, Martin M. Kater
Summary: Floral homeotic genes in angiosperms, such as OsMADS13 in rice, play a crucial role in determining ovule identity. The interaction between OsMADS13 and other genes, like those in the SEP family, may control a common set of target genes involved in ovule development. This study sheds light on the regulatory pathways in rice gynoecium development and provides insights into the role of OsMADS13 as a repressor of the carpel pathway during ovule development.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Mara Cucinotta, Alex Cavalleri, Andrea Guazzotti, Chiara Astori, Silvia Manrique, Aureliano Bombarely, Stefania Oliveto, Stefano Biffo, Dolf Weijers, Martin M. Kater, Lucia Colombo
Summary: The plant hormone auxin regulates gene expression through the canonical AUXIN RESPONSE FACTOR (ARF) and AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) combinatorial system. ARF5/MONOPTEROS (MP) can activate gene transcription in cells with elevated auxin levels and in ovules with low auxin levels, expressing a splice variant that lacks the Aux/IAA interaction domain and can function as a transcriptional activator in subthreshold auxin concentration regions.
Article
Plant Sciences
Dario Paolo, Lisa Rotasperti, Arp Schnittger, Simona Masiero, Lucia Colombo, Chiara Mizzotti
Summary: Seed size is controlled by complex molecular networks in Arabidopsis, with the MADS-domain transcription factor SEEDSTICK playing a key role in regulating it. STK acts as a maternal activator of growth in the earlier phases of seed development by positively regulating cell cycle progression via activating the expression of E2Fa.
Review
Plant Sciences
Sara Forlani, Chiara Mizzotti, Simona Masiero
Summary: Fruits and seeds resulting from fertilization of flowers play a critical role in angiosperms, with transcription factors regulating various cellular processes during fruit ripening. The NAC superfamily of transcription factors is known to be involved in multiple aspects of fruit development and maturation. This review summarizes the current knowledge on NACs that modulate fruit ripening in model species and commercial crops.
Correction
Plant Sciences
Michela Osnato, Elia Lacchini, Alessandro Pilatone, Ludovico Dreni, Andrea Grioni, Matteo Chiara, David Horner, Soraya Pelaz, Martin M. Kater
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Multidisciplinary Sciences
Eugenio Azpeitia, Gabrielle Tichtinsky, Marie Le Masson, Antonio Serrano-Mislata, Jeremy Lucas, Veronica Gregis, Carlos Gimenez, Nathanael Prunet, Etienne Farcot, Martin M. Kater, Desmond Bradley, Francisco Madueno, Christophe Godin, Francois Parcy
Summary: This study reveals that the fractal-like forms in cauliflowers emerge from the combination of key, defined perturbations of floral developmental programs and growth dynamics. The self-similarity of curds is due to meristems failing to form flowers but retaining the memory of their floral state. Additional mutations affecting meristem growth can induce the production of conical structures reminiscent of the Romanesco shape.
Review
Biotechnology & Applied Microbiology
Stefano Rosa, Paolo Pesaresi, Chiara Mizzotti, Vincent Bulone, Bruno Mezzetti, Elena Baraldi, Simona Masiero
Summary: Fungicide use is crucial in intensive agriculture to combat pathogens and prevent production losses. However, some active compounds currently used may be banned due to concerns about their impact on the environment and human health. To ensure food security, it is important to develop new biomolecules that effectively control pathogens while being safe for the environment and human health. This review discusses the use of novel low-risk biological compounds, such as small RNAs and short peptides, as promising alternatives to contentious fungicides.
TRENDS IN BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Nicolaj Jeran, Lisa Rotasperti, Giorgia Frabetti, Anna Calabritto, Paolo Pesaresi, Luca Tadini
Summary: During a plant's life cycle, plastids undergo various modifications, and plastid proteome rearrangements, protein homeostasis, and communication pathways are crucial for proper plastid differentiation and functioning. The study on Arabidopsis gun1-102 ftsh5-3 mutants revealed the significant role of PUB4 E3 ubiquitin ligase in degrading damaged chloroplasts, contributing to the variegated phenotype in seedlings.
Review
Biology
Stefano Rosa, Chiara Bertaso, Paolo Pesaresi, Simona Masiero, Andrea Tagliani
Summary: Protein-protein interactions play a key role in regulating cell physiology and metabolism. By utilizing protein domains in genetic circuits, synthetic biology has enabled the design of circuits that can impact transcriptional outputs and cellular metabolism, with potential applications in biosensing and diagnostics. Additionally, engineered PPIs can be utilized in the development of new drugs targeting specific cellular and extracellular proteins.
Correction
Multidisciplinary Sciences
E. Azpeitia, G. Tichtinsky, M. Le Masson, A. Serrano-Mislata, J. Lucas, V. Gregis, C. Gimenez, N. Prunet, E. Farcot, M. M. Kater, D. Bradley, F. Madueno, C. Godin, F. Parcy
Article
Biochemistry & Molecular Biology
Francesca B. Lopez, Antoine Fort, Luca Tadini, Aline Probst, Marcus McHale, James Friel, Peter Ryder, Frederic Pontvianne, Paolo Pesaresi, Ronan Sulpice, Peter McKeown, Galina Brychkova, Charles Spillane
Summary: In this study, the researchers used Cas9-mediated genome editing in Arabidopsis to reduce the copy number of 45S rRNA genes to around 10%, creating low copy number (LCN) lines. Despite the significant reduction in rDNA copies, the transcriptional rates and steady-state levels of rRNA remained the same as wild-type plants. Furthermore, editing rRNA repeats using Cas9 technology provides insights into the mechanisms of rDNA dosage compensation and the impacts of low rDNA copy number on genome stability, development, and cellular processes.