Article
Biochemistry & Molecular Biology
Wenjing Wang, Yumin He, Yunling Gao, Hongrui Gao, Lei Deng, Qingwen Gui, Zhong Cao, Yulong Yin, Zemeng Feng
Summary: An enzyme-free amperometric biosensor based on a peptide was developed for specific detection of L-glutamate. The biosensor showed excellent sensitivity and specificity, making it suitable for measuring L-Glu in serum samples.
BIOELECTROCHEMISTRY
(2022)
Article
Chemistry, Physical
Yuxi Cheng, Junji Ren, Shumin Fan, Peiyao Wu, Wenshu Cong, Yuxing Lin, Shaojie Lan, Siyang Song, Bin Shao, Wenbing Dai, Xueqing Wang, Hua Zhang, Bo Xu, Wenzhe Li, Xia Yuan, Bing He, Qiang Zhang
Summary: It is observed that nanoparticles bind closely to specific types of extracellular matrix components, namely retraction fibers and migrasomes, which are located at the rear of tumor cells during their migration. This interaction alters cell morphology, limits cell motion range, and changes cell adhesion. Nanoparticles inhibit tumor cell removal and anti-metastasis potential is confirmed in vitro. Mechanically, nanoparticles form a rigid shell on the surface of migrasomes and retraction fibers, blocking their recognition, endocytosis, and elimination by surrounding tumor cells. This interference reduces the promotion effect of migrasomes on cell movement.
NANOSCALE HORIZONS
(2022)
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.
Article
Chemistry, Multidisciplinary
Hao Qu, Manyi Zheng, Qihui Ma, Lu Wang, Yu Mao, Michael Eisenstein, Hyongsok Tom Soh, Lei Zheng
Summary: The ability to modulate aptamer affinity with precision is crucial for a wide range of applications. In this study, we introduce a simple and generalizable strategy for allosteric modulation of aptamer affinity by using a double-stranded molecular clamp. Through mechanical tension, this clamp destabilizes the aptamer secondary structure, allowing for significant changes in affinity. We demonstrate the effectiveness of this approach using a thrombin-binding aptamer and propose a design strategy for achieving even more finely-tuned affinity modulation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Analytical
Diana Soukarie, Philippe Rousseau, Maya Salhi, Alexia de Caro, Jean-Marc Escudier, Catherine Tardin, Vincent Ecochard, Laurence Salome
Summary: This study successfully developed an aptasensor based on high-throughput single-molecule techniques, which enables rapid, simple, and sensitive detection of single target molecules. The presence and concentration of the target molecules can be monitored in real time by combining videomicroscopy and image analysis.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Jessica M. Hong, Michael Gibbons, Ali Bashir, Diana Wu, Shirley Shao, Zachary Cutts, Mariya Chavarha, Ye Chen, Lauren Schiff, Mikelle Foster, Victoria A. Church, Llyke Ching, Sara Ahadi, Anna Hieu-Thao Le, Alexander Tran, Michelle Dimon, Marc Coram, Brian Williams, Phillip Jess, Marc Berndl, Annalisa Pawlosky
Summary: We demonstrate the progress made in developing a high-throughput, single-molecule protein sequencing technology using barcoded DNA aptamers to identify terminal amino acids of peptides on a next-generation sequencing chip. Successful target identification was achieved with two sets of target-binder pairs, and computational simulation suggests that a small set of semi-selective DNA binders can provide significant coverage of the human proteome.
Article
Nanoscience & Nanotechnology
Xiang Wang, Zhenyu Liu, Yang He, Susheng Tan, Guofeng Wang, Scott X. Mao
Summary: The study investigates the atomic-scale friction of a single tungsten asperity through high-resolution transmission electron microscopy, revealing discrete stick-slip friction and providing insights into the sliding pathway of interface atoms through molecular dynamics simulations.
NATURE NANOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Janett Goehring, Florian Kellner, Lukas Schrangl, Rene Platzer, Enrico Klotzsch, Hannes Stockinger, Johannes B. Huppa, Gerhard J. Schuetz
Summary: This study introduces a FRET-based sensor that directly measures the magnitude and kinetics of forces imposed by TCR at the single molecule level. Results showed that when T cells were confronted with gel-phase SLBs, there was a single force peak of around 5pN prior and upon activation, with force loading rates around 1.5pN per second on the TCR; while facing fluid-phase SLBs, T cells exerted tensile forces prior to activation but not afterwards, although of reduced magnitude compared to gel-phase SLBs.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Lijuan Zhu, Jiapei Yang, Yuan Ma, Xinyuan Zhu, Chuan Zhang
Summary: Aptamer-drug conjugates (ApDCs) are a promising drug delivery system for targeted cancer therapy. However, the conventional ApDC has limited drug loading capacity. To address this challenge, researchers have developed drugtamers, whole drug-constituted DNA-like oligomers, which have 100% drug loading ratio, active targeting capability, and enzyme-mediated release of active therapeutics.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Yu-Peng Zhang, Zhi-Gang Wang, Yi-Fan Tian, Lin-Han Jiang, Liang Zhao, De-Ming Kong, Xing Li, Dai-Wen Pang, Shu-Lin Liu
Summary: Real-time visualization of individual viral mRNA translation activities in live cells is achieved using genetically encoded turn-on DFHBI-binding RNA nanozipper, which allows monitoring the mobility and dynamic translation of individual viral mRNAs, providing insights into their spatial dynamics and translational elongation rate.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Medicinal
Angelo Santoro, Manuela Grimaldi, Michela Buonocore, Ilaria Stillitano, Antonio Gloria, Matteo Santin, Fabrizio Bobba, Matilde Sublimi Saponetti, Elena Ciaglia, Anna Maria D'Ursi
Summary: Alzheimer's disease is a common neurodegenerative disorder characterized by the accumulation of amyloid plaques. Many molecules targeting A beta peptides and anti-A beta monoclonal antibodies have been screened as potential drug candidates. In this study, short peptide sequences were designed based on the binding sites of A beta(1-42)/antibodies, and two peptides, WAibH and SYSTPGK, were identified as mimics of solanezumab and aducanumab, respectively. These antibody-derived peptides were found to interact with soluble A beta(1-42) and control its aggregation.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
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)
Article
Chemistry, Multidisciplinary
Yulin Du, Yifan Lyu, Shiquan Li, Ding Ding, Jianghuai Chen, Cai Yang, Yang Sun, Fengli Qu, Zeyu Xiao, Jianhui Jiang, Weihong Tan
Summary: Cell-specific aptamers are a strong tool for studying membrane receptors at the single-molecule level. Ligand dilution analysis (LDA) is proposed as a random sampling-based strategy to study aptamer-based receptors. This strategy allows for the calculation of receptor density, colocalization and differentiation of aptamer and monoclonal antibody binding, and determination of binding site and aptamer-receptor binding mode.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Microbiology
Malgorzata Lisowska, Fiona Lickiss, Maria Gil-Mir, Anne-Sophie Huart, Zuzanna Trybala, Luke Way, Lenka Hernychova, Adam Krejci, Petr Muller, Radovan Krejcir, Igor Zhukow, Przemyslaw Jurczak, Sylwia Rodziewicz-Motowidlo, Kathryn Ball, Borivoj Vojtesek, Ted Hupp, Umesh Kalathiya
Summary: The identification of peptide sequences using next-generation sequencing technology from protein libraries provides a potential tool for studying protein-protein interactions in enzymatic reactions. These peptide sequences can be used as chemical tools to inhibit specific protein targets in complex multi-enzyme reactions.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Yuan Zhou, Jinrun Dong, Pinlong Zhao, Jingkang Zhang, Min Zheng, Jiandong Feng
Summary: Rapid and accurate identification of pathogens is essential for public healthcare and patient treatment. In this study, electrochemiluminescence (ECL) microscopy is introduced as a powerful imaging tool to identify and classify single bacteria with a high level of accuracy. The researchers also reported a novel tunable ECL imaging mode, which allows for both negative and positive contrast imaging of bacteria. This work demonstrates the potential of ECL microscopy for quantitative imaging and characterization of bacteria.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Guillermo J. Amador, Dennis van Dijk, Roland Kieffer, Marie-Eve Aubin-Tam, Daniel Tam
Summary: The study introduced an active microrheology technique to investigate the physical properties of lipid membranes, revealing the significant impact of lipid structure on viscosity and fluid transmission properties. Ordered-phase and liquid disordered-phase lipid bilayers exhibit distinct differences in viscosity and intermonolayer friction.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Physical
Mikhail Soloviev, Giuliano Siligardi, Danilo Roccatano, Enrico Ferrari
Summary: A new geometrical model was developed to study the adsorption of proteins on nanoparticles, and findings showed a 32% surface occupancy of RBD on silica nanoparticles with 25% of RBD secondary structures undergoing conformational changes. These findings contribute to understanding protein-surface interactions and controlling the spread of SARS-CoV-2 through contaminated objects.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Saikat Saha, Francis Pagaud, Bernard P. Binks, Valeria Garbin
Summary: Oil foams stabilized by crystallizing agents have excellent stability and potential applications in consumer products. The behavior of the interfacial layer at different time scales plays a crucial role in product shelf life and processing conditions. Experimental investigation reveals that the dynamics of deformation significantly affect the fate of the interfacial layer.
Article
Chemistry, Physical
Brice Saint-Michel, George Petekidis, Valeria Garbin
Summary: The dynamics of a deformable inclusion, such as a bubble, can be used to locally tune the microstructure of a colloidal gel. Bubble dissolution leads to the formation of a solvent pocket, while ultrasound-induced bubble oscillations rearrange the gel particles into a microstructure with increased local ordering.
Article
Biochemical Research Methods
Srikkanth Balasubramanian, Kui Yu, Diana Vasquez Cardenas, Marie-Eve Aubin-Tam, Anne S. Meyer
Summary: Biofilms are three-dimensional bacterial communities with a highly self-organized nature and resistance properties. The structural elements of biofilms play a crucial role in the development of their emergent biological properties.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
William T. Ferreira, Huynh A. Hong, James R. G. Adams, Mateusz Hess, Natalia K. Kotowicz, Sisareuth Tan, Enrico Ferrari, Alain Brisson, Jurgen Zentek, Mikhail Soloviev, Simon M. Cutting
Summary: Clostridioides difficile is a spore-forming bacterium that causes disease after disruption of the intestinal microbiota. This study demonstrates the role of Bacillus in colonization resistance to C. difficile. Animals with reduced environmental exposure are more susceptible to CDI due to a loss of Bacillus. Heterogeneous lipopeptide lytic micelles (HELMs) produced by Bacillus in the small intestine enhance inhibitory activity against C. difficile.
Article
Genetics & Heredity
Nathalie Schneider, Ellen Reed, Faddy Kamel, Enrico Ferrari, Mikhail Soloviev
Summary: This study predicts molecular biomarkers for breast cancer using a data mining approach. It explores the relationship between subtype-specific and pan-cancer biomarkers and suggests potential extracellular markers for early non-invasive detection of the disease.
Article
Chemistry, Multidisciplinary
Yaroslav Odarchenko, Anna Kazmierczak-Balata, Jerzy Bodzenta, Enrico Ferrari, Mikhail Soloviev
Summary: Nanocalorimetry is a powerful tool for fast thermal processing and thermodynamic analysis at the nanoscale, but faces challenges when applied to biological systems. While successful in material sciences, traditional techniques are not always appropriate for biological objects and do not allow for micro- or nano-scale thermal analysis in bulk liquid media.
Article
Chemistry, Multidisciplinary
Richard D. Perrins, Lee-Anne Mccarthy, Angela Robinson, Kelly L. Spry, Valentin Cognet, Avelino Ferreira, John Porter, Cristina Espinosa Garcia, Miguel Angel Rodriguez, Diana Lopez, Ibon Perera, Kelly Conlon, Africa Barrientos, Tom Coulter, Alessandro Pace, Sarah J. M. Hale, Enrico Ferrari, Csanad Z. Bachrati
Summary: The study aimed to design a targeted delivery system for cytotoxic payload using cyclic arginyl-glycyl-aspartic acid peptide (cRGD) peptides with high affinity towards alpha V beta 3 integrin and the versatility of ultrasmall gold nanoparticles (usGNP). The functionalized usGNPs with cRGD demonstrated enhanced cellular uptake by cells expressing alpha V beta 3 integrin, internalized via clathrin-dependent endocytosis, accumulated in lysosomes, and showed increased cytotoxicity when loaded with mertansine.
Article
Biochemical Research Methods
Ellen Reed, Enrico Ferrari, Mikhail Soloviev
Summary: This study aimed to address issues related to the quality of gene expression data and devise improved quality control and data processing procedures. Linear regression analysis was used to process gene expression datasets, resulting in an increase in the number of identifiable differentially regulated genes and a reduction in false positives. The approach reduced technical errors and improved the accuracy and precision of determining the degree of differential gene expression.
CURRENT BIOINFORMATICS
(2023)
Review
Chemistry, Analytical
Enrico Ferrari
Summary: One of the emerging technologies in molecular diagnostics is the use of gold nanoparticles (AuNPs) for biosensors. AuNPs can be functionalized with biomolecules to recognize and bind specific targets. AuNPs have unique optical properties, such as a distinctive plasmonic band and high extinction coefficient, which allow for visual detection even at low concentrations. This review focuses on the design and molecular mechanisms of AuNP-based plasmonic biosensors, highlighting their applications in point-of-care testing for various analytes.
Article
Chemistry, Multidisciplinary
Jeong-Joo Oh, Satya Ammu, Vivian Dorine Vriend, Roland Kieffer, Friedrich Hans Kleiner, Srikkanth Balasubramanian, Elvin Karana, Kunal Masania, Marie-Eve Aubin-Tam
Summary: This study investigates the growth and photosynthetic productivity of C.reinhardtii cells in three-dimensionally shaped hydrogels. The cells grow faster when located near the material's periphery, and photosynthetic ELMs with increased CO2 capturing rate were successfully designed and printed.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Susannah Emily Cornwell, Sarah Ogechukwu Okocha, Enrico Ferrari
Summary: This study used dynamic light scattering to determine the dissociation constant and thickness of the protein corona formed in solutions of silica or gold nanoparticles mixed with different types of proteins. The results showed that the nanoparticle material had a greater impact on binding properties than the protein type, and serum albumin had a distinct binding pattern compared to other proteins. This pilot study provides a blueprint for future investigations into the complexity of the soft protein corona, which is crucial for the development of nanomedicines.
Article
Chemistry, Physical
Yanyan Liu, Mingjun Xu, Luis M. Portela, Valeria Garbin
Summary: Emulsions stabilized by nanoparticles, known as Pickering emulsions, show remarkable stability and have various applications. The layer of nanoparticles at the interface of Pickering droplets acts as a semi-permeable barrier, affecting the release rate of encapsulates and the interfacial transfer of reactants. However, our understanding of diffusion in multiphase systems with particle-laden interfaces is limited.
Article
Chemistry, Multidisciplinary
Kui Yu, Ewa M. Spiesz, Srikkanth Balasubramanian, Dominik T. Schmieden, Anne S. Meyer, Marie-Eve Aubin-Tam
Summary: The research demonstrates a layered structural material composed of bacterial cellulose and bacterially precipitated calcium carbonate, which exhibits high toughness, impact resistance, and fire resistance, capable of being easily fabricated, recyclable, and suitable for applications such as furniture, helmets, and protective garments.
CELL REPORTS PHYSICAL SCIENCE
(2021)
