Editorial Material
Optics
Zhiyuan Zhang, Daniel Ahmed
Summary: Researchers have developed a new optical technique for high-precision measurement of cell lateral adhesion kinetics in complex clinical samples.
LIGHT-SCIENCE & APPLICATIONS
(2022)
Article
Engineering, Multidisciplinary
Ivan Lenicek, Luka Ferkovic
Summary: This paper presents the establishment of a magnetic flux density standard in the national calibration laboratory in Croatia. The process includes constructing a magnetic field source, determining the error margin, parameterizing the electrical model, and verifying the correction experimentally. The laboratory now has the capability to calibrate environmental magnetometers with a relative uncertainty of 0.8%.
Article
Chemistry, Multidisciplinary
Yi Luo, Jeffrey Chang, Darren Yang, J. Shepard Bryan IV, Molly MacIsaac, Steve Presse, Wesley P. Wong
Summary: Population-level heterogeneity is important for many biomolecules, but is difficult to fully characterize due to various reasons. In this study, a combination of a DNA nanoswitch construct, a benchtop centrifuge force microscope (CFM), and a Bayesian nonparametric (BNP) inference method was used to overcome these difficulties and resolve separate subpopulations with distinct kinetics. This approach was applied to commercially available antibodies and revealed that polyclonal antibody from rabbit serum can be modeled as a mixture of three subpopulations. The results demonstrate the effectiveness of the spatially and temporally multiplexed nanoswitch-CFM assay combined with BNP analysis in resolving complex biomolecular interactions in heterogenous samples.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Yi Luo, Jeffrey Chang, Darren Yang, J. Shepard Bryan, Molly MacIsaac, Steve Presse, Wesley P. Wong
Summary: Currently, the heterogeneity of biomolecules is studied using single-molecule methods, which provide information distinct from ensemble-level averaging. This study introduces a new approach that combines three techniques to overcome the challenges in studying biomolecular heterogeneity. The results demonstrate that this method can effectively resolve complex biomolecular interactions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Ane Kritzinger, Andrew Forbes, Patricia B. C. Forbes
Summary: In this study, micro-scaled polymer beads were functionalized with nano-scaled quantum dots to enable optical trapping and tweezing in an all-digital all-optical configuration, with in-situ fluorescence measurement. The chemistry required for this process, including deactivating the optical trapping environment and controlling size, adhesion, and agglomeration, is outlined. A novel holographic optical trapping set-up utilizing vectorially structured light is introduced, allowing for the delivery of tuneable forms of light and advancing the application of optics in chemistry.
SCIENTIFIC REPORTS
(2022)
Article
Biophysics
James L. Flewellen, Sophie Minoughan, Isabel Llorente Garcia, Pavel Tolar
Summary: We present a 3D imaging technique for tracking microscopic objects in a fluid environment. Our method reconstructs 3D volumes from single-plane images, simplifying image acquisition and allowing for tracking higher densities of microscopic particles.
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Haiyan Hong, Zilong Guo, Hao Sun, Ping Yu, Huanhuan Su, Xuening Ma, Hu Chen
Summary: Research on Csp protein shows that it mainly folds and unfolds in a single step over a force range from 5 pN to 50 pN. The unfolding rates exhibit different force sensitivities below and above 8 pN, indicating a free energy landscape with two barriers and a transient intermediate state between them. These findings provide new insights into the protein folding mechanism of two-state proteins.
COMMUNICATIONS CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Magnus S. Bauer, Sophia Gruber, Adina Hausch, Priscila S. F. C. Gomes, Lukas F. Milles, Thomas Nicolaus, Leonard C. Schendel, Pilar Lopez Navajasg, Erik Procko, Daniel Lietha, Marcelo C. R. Melo, Rafael C. Bernardi, Hermann E. Gaub, Jan Lipfert
Summary: This study introduces a new assay that can quantitate the interaction between SARS-CoV-2 and ACE2 under mechanical load. Through experimental and simulation approaches, the researchers provide important insights into the RBD:ACE2 interaction, which is crucial for understanding the infection mechanism of SARS-CoV-2 and developing targeted pharmaceutical interventions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Engineering, Electrical & Electronic
Sonia Marrara, David Bronte Ciriza, Alessandro Magazzu, Roberto Caruso, Giuseppe Lupo, Rosalba Saija, Antonino Foti, Pietro Giuseppe Gucciardi, Andrea Mandanici, Onofrio Maria Marago, Maria Grazia Donato
Summary: Recently, acoustic tweezers inspired by holographic optical tweezers have been developed. The calibration of optical trap stiffnesses is essential in the latter technique, but seldom carried out in acoustic tweezers. In this work, the calibration protocols used in optical tweezers are adapted for acoustic tweezers based on ultrasonic transducer arrays. The measured trap stiffnesses are consistent with theoretical estimates, providing a common framework for optical and acoustic manipulation communities and enabling consistent calibration of hybrid acoustooptical setups.
IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT
(2023)
Article
Multidisciplinary Sciences
Ian L. Morgan, Omar A. Saleh
Summary: This article introduces how to calibrate forces in single-molecule force spectroscopy experiments using the Tweezepy software package, and estimates parameters and their uncertainties through methods like PSD and AV. Tweezepy is well-documented, fast, and easy to use, effectively addressing common biases in experiments.
Article
Physics, Multidisciplinary
J. J. Hernandez-Sarria, Osvaldo N. Oliveira Jr, J. R. Mejia-Salazar
Summary: Researchers have designed an all-dielectric platform to optically trap small dielectric nanoparticles without heating the nanostructure in the infrared regime. By creating a strong electromagnetic hot spot, nanoparticles as small as 20 nm can be captured without heating.
PHYSICAL REVIEW LETTERS
(2021)
Article
Physics, Applied
Jie Huang, Qinxin Zhou, Xuemei Ren, Zheng Xu, Xiaojun Liu
Summary: Non-diffracting Bessel acoustic beams with self-healing, self-bending, and self-acceleration properties have potential applications for directional transportation of microbubbles. By adjusting the acoustic frequency, the maximum point of acoustic intensity on the beam mainlobe can be changed, and the curved trajectory and adjustable destination of microbubble transportation have been experimentally proven. The proposed method utilizes the conservative part of the radiation force to control the trajectory of microbubbles, making it suitable for in vivo applications.
APPLIED PHYSICS LETTERS
(2021)
Article
Biology
Zhen Wang, Jerome Maluenda, Laurene Giraut, Thibault Vieille, Andreas Lefevre, David Salthouse, Gael Radou, Remi Moulinas, Sandra Astete, Pol D'Avezac, Geoff Smith, Charles Andre, Jean-Francois Allemand, David Bensimon, Vincent Croquette, Jimmy Ouellet, Gordon Hamilton
Summary: In this study, the researchers successfully detected genetic sequence and base modifications simultaneously on single molecules of both DNA and RNA using a magnetic tweezer platform. They also developed a highly specific amplification-free CRISPR/Cas9-based strategy for isolating target regions from native DNA, demonstrating its utility in enriching genomic regions from E. coli and human DNA samples. This approach allows for the simultaneous detection of various genetic, epigenetic, and base modification changes within the same single molecules.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jiangcheng Zhao, Chuanbiao Bai, Zhiguo Zhang, Qingchuan Zhang
Summary: Optical tweezers are important for trapping cells, and it is crucial to analyze their movement. We proposed a fast deep-learning-based method to automatically determine the rotation of ellipsoidal-like cells without additional optical design. By applying this method, we analyzed the planar rotation of trapped sperm cells and investigated variations in sperm rotation rates under different conditions. Our findings demonstrate the feasibility and potential clinical application of this method for sperm quality evaluation.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Arnav Solanki, Zak Griffin, Purab Ranjan Sutradhar, Karisha Pradhan, Caiden Merritt, Amlan Ganguly, Marc Riedel
Summary: This paper introduces an integrated circuit based on microfluidics that can perform complex operations on data stored in DNA. The system is suitable for high-density, throughput-demanding bio-compatible applications.
Article
Biophysics
Sebastian F. Konrad, Willem Vanderlinden, Jan Lipfert
Summary: Nucleosomes are crucial for the storage and expression of eukaryotic genomes. The mode of action and structural implications of nucleosomes at the single-molecule level are still poorly understood. This study investigates the conformational landscape of nucleosome variants and provides insights into the effects of histone modifications on nucleosome structure.
BIOPHYSICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Anssi M. Malinen, Jacob Bakermans, Emil Aalto-Setala, Martin Blessing, David L. Bauer, Olena Parilova, Georgiy A. Belogurov, David Dulin, Achillefs N. Kapanidis
Summary: This study used single-molecule fluorescence microscopy to investigate the conformational dynamics and reaction kinetics during real-time RPO formation. The results revealed that the opening of the promoter may occur in a single step or involve intermediates. The formed RPO complexes showed differences in transcription bubble stability, and the interactions between RNAP and the promoter upstream sequence facilitated the formation of stable forms of RPO.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Ariadna Boloix, Natalia Feiner-Gracia, Mariana Kober, Javier Repetto, Rosa Pascarella, Aroa Soriano, Marc Masanas, Nathaly Segovia, Guillem Vargas-Nadal, Josep Merlo-Mas, Dganit Danino, Inbal Abutbul-Ionita, Laia Foradada, Josep Roma, Alba Cordoba, Santi Sala, Josep Sanchez Toledo, Soledad Gallego, Jaume Veciana, Lorenzo Albertazzi, Miguel F. Segura, Nora Ventosa
Summary: The engineering of non-liposomal lipid nanovesicles, known as quatsomes (QS), for delivering miRNAs and other small RNAs into tumor cells' cytosol, triggering a tumor-suppressive response, offers a promising platform for the clinical delivery of miRNA therapeutics.
Article
Nanoscience & Nanotechnology
Sara Battista, Mariana Koeber, Pierangelo Bellio, Giuseppe Celenza, Luciano Galantini, Guillem Vargas-Nadal, Lorenza Fagnani, Jaume Veciana, Nora Ventosa, Luisa Giansanti
Summary: The newly developed nanovesicle system of the quatsome family shows noticeable antibacterial activity, demonstrating great potential for the treatment of bacterial infections and can also serve as nanocarriers of pharmaceutical actives.
ACS APPLIED NANO MATERIALS
(2022)
Article
Chemistry, Physical
Mariana Kober, Silvia Illa-Tuset, Lidia Ferrer-Tasies, Evelyn Moreno-Calvo, Witold I. Tatkiewicz, Natascia Grimaldi, David Pina, Alejandro Perez Perez, Vega Lloveras, Jose Vidal-Gancedo, Donatella Bulone, Imma Ratera, Jan Skov Pedersen, Dganit Danino, Jaume Veciana, Jordi Faraudo, Nora Ventosa
Summary: This study investigates the stability and formation mechanism of CHOL/CTAB quatsomes, which are nanovesicles formed through the self-assembly of cholesterol and cetyltrimethylammonium bromide in water. Experimental and simulation results show that CHOL/CTAB quatsomes are thermodynamically stable nanovesicles, but they do not exhibit the classical membrane curvature induced by composition asymmetry.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Letter
Chemistry, Multidisciplinary
Pauline J. Kolbeck, Mihir Dass, Irina V. Martynenko, Relinde J. A. van Dijk-Moes, Kelly J. H. Brouwer, Alfons van Blaaderen, Willem Vanderlinden, Tim Liedl, Jan Lipfert
Summary: Atomic force microscopy (AFM) is a powerful technique for high-resolution imaging of molecules, macromolecular complexes, and nanoparticles. However, the shape of the AFM tip can distort the images. In this study, we use a 3D DNA origami structure as a fiducial for tip reconstruction and image correction. The fiducial has sharp steps at different heights, allowing reliable tip reconstruction with as few as ten fiducials. This fiducial enables accurate and precise AFM imaging for a wide range of applications.
Review
Pharmacology & Pharmacy
Guillem Vargas-Nadal, Mariana Kober, Audrey Nsamela, Francesca Terenziani, Cristina Sissa, Silvia Pescina, Fabio Sonvico, Amirah Mohd Gazzali, Habibah A. Wahab, Luca Grisanti, Maria Eugenia Olivera, Maria Celeste Palena, Maria Laura Guzman, Laura Carolina Luciani-Giacobbe, Alvaro Jimenez-Kairuz, Nora Ventosa, Imma Ratera, Kevin D. Belfield, Ben M. Maoz
Summary: Fluorescent organic nanoparticles (FONs) are a class of nanostructures made up of organic components, which have high tunability and multifunctionality for diagnostic and therapeutic applications in biology and medicine. This review provides a tutorial overview of the design, preparation, characterization, and applications of FONs, as well as recent biomedical applications.
Article
Chemistry, Multidisciplinary
Pauline J. Kolbeck, Dihia Benaoudia, Leia Chazot-Franguiadakis, Gwendoline Delecourt, Jeirome Mathei, Sha Li, Romeo Bonnet, Pascal Martin, Jan Lipfert, Anna Salvetti, Mordjane Boukhet, Veironique Bennevault, Jean-Christophe Lacroix, Philippe Guegan, Fabien Montel
Summary: Researchers have developed a selective and switchable nanopore by grafting polymers within artificial nanopores to control the transport of biomolecules. Using fluorescence microscopy with a zero-mode waveguide set up, they measured transport at the scale of individual biomolecules. They demonstrated tight control over DNA and viral capsid transport with a sharp transition based on temperature, and proposed a simple physical model to predict key features of this transition. This approach offers the potential for controllable and responsive nanopores in various applications.
Article
Biochemistry & Molecular Biology
Clement Rouillon, Bruna Eckhardt, Leonie Kollenstart, Fabian Gruss, Alexander E. E. Verkennis, Inge Rondeel, Peter H. L. Krijger, Giulia Ricci, Alva Biran, Theo van Laar, Charlotte M. Delvaux de Fenffe, Georgiana Luppens, Pascal Albanese, Koichi Sato, Richard A. Scheltema, Wouter de Laat, Puck Knipscheer, Nynke H. Dekker, Anja Groth, Francesca Mattiroli
Summary: During cell cycle, CAF-1 plays a crucial role in chromatin replication, and its interaction with the DNA replication machinery remains unknown. The study reveals that the interaction between CAF-1 and replication forks differs between the leading and lagging strand. Biochemical reconstructions demonstrate that DNA and histones promote CAF-1 recruitment to its binding partner PCNA, and two CAF-1 complexes are required for efficient nucleosome assembly. In the context of the replisome, CAF-1 competes with Pol epsilon for PCNA binding on the leading strand, while it does not affect the activity of Pol delta on the lagging strand.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Pharmacology & Pharmacy
Nicolo Bordignon, Mariana Kober, Giorgia Chinigo, Carlotta Pontremoli, Ettore Sansone, Guillem Vargas-Nadal, Maria Jesus Moran Plata, Alessandra Fiorio Pla, Nadia Barbero, Judit Morla-Folch, Nora Ventosa
Summary: Photodynamic therapy is a non-invasive therapeutic strategy that uses external light and a photosensitizer to destroy abnormal cells. The main challenges in this therapy are the photosensitivity, hydrophobicity, and tumor target avidity of the photosensitizer. In this study, brominated squaraine was successfully incorporated into Quatsome nanovesicles to overcome the solubility limitation and maximize the PDT effectiveness. This approach allows for a lower concentration of squaraine compared to traditional PDT, making it a promising photosensitizer for PDT.
Article
Materials Science, Multidisciplinary
Adriana R. Kyvik, Ramon Roca-Pinilla, Karla Mayolo-Deloisa, Xavier Rodriguez Rodriguez, Marc Martinez-Miguel, Marta Martos, Mariana Kober, Nora Ventosa, Jaume Veciana, Judith Guasch, Elena Garcia-Fruitos, Anna Aris, Imma Ratera
Summary: In this study, novel biofunctionalized gold surfaces with the antimicrobial multidomain recombinant protein JAMF1 were developed. The immobilized JAMF1 protein successfully reduced biofilm formation of both Escherichia coli and carbapenem-resistant Klebsiella pneumoniae. This strategy provides new possibilities for biomolecule immobilization in fundamental biological studies and biotechnological applications.
MATERIALS ADVANCES
(2023)
Meeting Abstract
Biophysics
Nynke H. Dekker
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Pauline J. Kolbeck, Milos Tisma, Brian T. Analikwu, Willem Vanderlinden, Cees Dekker, Jan Lipfert
Summary: In this article, the authors propose a quantitative model for the modulation of DNA binding by DNA topology and demonstrate its accuracy through experiments. They focus on the binding of fluorescent intercalators to DNA and directly observe the impact of different intercalator densities on DNA through single-molecule assays. The model has wide implications for the detection and quantification of DNA.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Willem Vanderlinden, Enrico Skoruppa, Pauline J. Kolbeck, Enrico Carlon, Jan Lipfert
Summary: DNA supercoiling is a key regulatory mechanism for DNA readout, recombination, and genome maintenance. This study presents a real-time, single-molecule level method to quantitatively measure the size and dynamics of topological domains in supercoiled DNA. By measuring DNA extension fluctuations, the formation and size of topological domains are determined. In addition, the dynamics and reaction pathways of protein-plectoneme interactions are revealed.
Article
Biochemical Research Methods
Louis Kuijpers, Theo van Laar, Richard Janissen, Nynke H. Dekker
Summary: This article presents a protocol for simultaneously probing the RNA synthesis dynamics of hundreds of single polymerases using multiplexed single-molecule magnetic tweezers (MT). The protocol provides a detailed description of the dsRNA construct preparation and the measurement of RdRp RNA synthesis kinetics using MT. This method is suitable for high-throughput screening of RdRp-targeting antiviral compounds for mechanistic function and efficacy.
