Article
Chemistry, Multidisciplinary
Raphael P. B. Jacquat, Georg Krainer, Quentin A. E. Peter, Ali Nawaz Babar, Oliver Vanderpoorten, Catherine K. Xu, Timothy J. Welsh, Clemens F. Kaminski, Ulrich F. Keyser, Jeremy J. Baumberg, Tuomas P. J. Knowles
Summary: This paper presents an approach called nanocavity diffusional sizing (NDS) that relies on nanocavity confinement to measure the size of nanoscale particles and single biomolecules in solution. It uses particle residence times within nanofluidic cavities to determine their hydrodynamic radii. Experimental results show that the residence times scale linearly with the sizes of nanoscale colloids, protein aggregates, and single DNA oligonucleotides. NDS offers a new optofluidic approach for rapid and quantitative sizing of nanoscale particles with potential applications in nanobiotechnology, biophysics, and clinical diagnostics.
Article
Chemistry, Multidisciplinary
Zheng Yuan, Dapeng Zhang, Fangzhi Yu, Yangde Ma, Yan Liu, Xiangjun Li, Hailin Wang
Summary: This study demonstrates a new supernuclease's capability for highly efficient cutting of DNA segments, leading to the development of a method that allows precise sequencing of single protected-DNA fragment molecules, and the direct measurement of RecA filament length. This innovative assay shows promise as an analytical tool for studying various protein-DNA interactions involved in DNA replication, transcription, recombination, repair, and gene editing.
Article
Electrochemistry
Masaru Kato, Yuya Masuda, Narumi Yoshida, Takehiko Tosha, Yoshitsugu Shiro, Ichizo Yagi
Summary: The reconstitution of protein tethered bilayer lipid membranes in protein film electrochemistry has a significant impact on functionality and stability at electrolyte/electrode interfaces. Protein-lipid interactions affect the formation kinetics of phospholipid bilayers and the electrocatalytic stability of protein-modified electrodes, but not the fluidity of the phospholipid bilayer.
ELECTROCHIMICA ACTA
(2021)
Article
Biochemistry & Molecular Biology
Sabrina Koch, Anne-Bart Seinen, Michael Kamel, Daniel Kuckla, Cornelia Monzel, Alexej Kedrov, Arnold J. M. Driessen
Summary: This study uses total internal reflection fluorescence microscopy to investigate the oligomeric state and diffusion of SecYEG translocons in supported lipid bilayers at the single-molecule level. The findings suggest that the complex mobility of SecYEG arises from the conformational dynamics of the translocon and protein-lipid interactions.
Review
Biophysics
Karolin Frykholm, Vilhelm Muller, K. K. Sriram, Kevin D. Dorfman, Fredrik Westerlund
Summary: Nanofluidic structures provide a powerful platform for detailed analysis of DNA. By confining DNA to nanochannels, it can be stretched to near its full length without any chemical modifications. The versatility of nanofabrication allows for the design of devices tailored for specific applications, such as controlling confinement or enabling exchange of reagents. The two important applications discussed in this review are optical DNA mapping and DNA-protein interactions, showcasing the power of DNA confinement and nanofluidics in genomics, molecular biology, and biophysics.
QUARTERLY REVIEWS OF BIOPHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Mukesh Kumar Thakur, Golam Haider, Farjana J. Sonia, Jan Plsek, Alvaro Rodriguez, Vipin Mishra, Jaganandha Panda, Ondrej Gedeon, Martin Mergl, Oleksandr Volochanskyi, Vaclav Vales, Otakar Frank, Jana Vejpravova, Martin Kalbac
Summary: Tailoring the physicochemical properties of graphene through functionalization while addressing the issue of defect formation has been a major interest. This study introduces a two-step fluorination process to stabilize fluorinated graphene and control the induced defects. The study provides a comprehensive analysis on fluorination sites, C-F bond stability, and the utilization of fluorinated graphenic carbon in practical applications such as a field-effect phototransistor.
Article
Biochemistry & Molecular Biology
Eneko Largo, Maria Queralt-Martin, Pablo Carravilla, Jose L. Nieva, Antonio Alcaraz
Summary: Our study shows that CSFV p7 channels are controlled by equilibrium conformational dynamics involving protein-lipid interactions. Atomic force microscopy confirms the existence of a variety of pore sizes regulated by solution pH. The findings suggest that p7 viroporin forms subnanometric channels involved in virus propagation, as well as larger pores with potentially significant roles in virus pathogenicity.
BIOELECTROCHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Jangyup Son, Huije Ryu, Junyoung Kwon, Siyuan Huang, Jaehyung Yu, Jingwei Xu, Kenji Watanabe, Takashi Taniguchi, Eunji Ji, Sol Lee, Yongjun Shin, Jong Hun Kim, Kwanpyo Kim, Arend M. van der Zande, Gwan-Hyoung Lee
Summary: The study explores functionalization of multilayer graphene and demonstrates a method to fabricate fluorinated bilayer graphene through tailoring substrate interactions. The type of functionalization affects electronic properties, with double-sided fluorinated bilayer graphene showing insulating behavior and single-sided fluorinated graphene maintaining conductivity.
Article
Chemistry, Multidisciplinary
Yusuke Takashima, Yuki Komoto, Takahito Ohshiro, Kazuhiko Nakatani, Masateru Taniguchi
Summary: Chemical properties have been determined using statistical averages, but the lack of suitable counting methods for single molecules has been a challenge. This study presents a new approach using single-molecule electrical measurements and AI to quantify important parameters like binding selectivity and microscopic hydrogen bonds. The results provide insights into the nature of DNA and its interaction with small molecules.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Wenzhe Liu, Jie Li, Yongping Xu, Dongbao Yin, Xin Zhu, Huanyan Fu, Xiaodong Su, Xuefeng Guo
Summary: The study utilized high-gain silicon nanowire field-effect transistors for label-free detection of DNA-protein interaction, visualizing the binding process with single-base resolution. The swinging of hydrogen bonds between amino acid residues and DNA bases induced dynamic collective motion between DNA-binding protein and DNA.
Article
Multidisciplinary Sciences
Gaurav Goyal, Elina Ekedahl, My Nyblom, Jens Krog, Erik Frobrant, Magnus Brander, Tsegaye Sewunet, Teerawit Tangkoskul, Christian G. Giske, Linus Sandegren, Visanu Thamlikitkul, Tobias Ambjornsson, Fredrik Westerlund
Summary: Antimicrobial resistance is a growing threat to global health, and effective methods for detecting antimicrobial resistance genes on bacterial plasmids are necessary. In this study, researchers propose a simple and inexpensive assay based on CRISPR/Cas9 excision and DNA combing to detect these genes.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Fabian C. Herbert, Sameera S. Abeyrathna, Nisansala S. Abeyrathna, Yalini H. Wijesundara, Olivia R. Brohlin, Francesco Carraro, Heinz Amenitsch, Paolo Falcaro, Michael A. Luzuriaga, Alejandra Durand-Silva, Shashini D. Diwakara, Ronald A. Smaldone, Gabriele Meloni, Jeremiah J. Gassensmith
Summary: This study demonstrates the successful generation and immobilization of metastable lipid, protein-detergent, and protein-lipid supramolecular complexes within a zeolitic-imidazole framework (ZIF) to enhance stability against various stressors. The immobilized complexes exhibit resistance to elevated temperatures, chemical denaturants, aging, and mechanical stresses, maintaining their native morphology, structure, and activity. Immobilizing lipid nanoparticles and lipid-protein assemblies remains challenging due to lipid dynamics and protein instability, but this work shows promise for long-term storage at room temperature.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Jhoan Toro-Mendoza, Lucia Maio, Marta Gallego, Ferdinand Otto, Florian Schulz, Wolfgang J. Parak, Carlos Sanchez-Cano, Ivan Coluzza
Summary: Nanoparticles and other nano-materials have potential as nanodrugs or nanomedical devices, but their therapeutic response can be significantly affected by protein adsorption. By combining experimental and computational approaches, we have developed nanoparticles with polyethylene glycol (PEG) coatings that mimic the surface charge distribution of proteins in blood, showing low aggregation under normal blood conditions.
Article
Biophysics
Surajit Ghosh, Zeinab Mohamed, Jung-Ho Shin, Samavi Farnush Bint E. Naser, Karan Bali, Tobias Dorr, Roisin M. Owens, Alberto Salleo, Susan Daniel
Summary: Antibiotic resistance is a global health concern due to the decreasing number of available antibiotics and the development of drug-resistant bacteria. Understanding the interactions between the bacterial membrane and antibiotics is crucial for designing novel antimicrobial drugs. By creating a surface-supported planar bacterial outer membrane model, researchers can study these interactions and gain insights into membrane properties for drug design.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Nanoscience & Nanotechnology
Milana Pikula, M. Monsur Ali, Carlos Filipe, Todd Hoare
Summary: The hydrogel-printed RCA microarray offers improved RCA immobilization and resistance to denaturation, as well as size-discriminative sensing of DNA probes based on the internal porosity of the hydrogel.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Multidisciplinary Sciences
Gaurav Goyal, Elina Ekedahl, My Nyblom, Jens Krog, Erik Frobrant, Magnus Brander, Tsegaye Sewunet, Teerawit Tangkoskul, Christian G. Giske, Linus Sandegren, Visanu Thamlikitkul, Tobias Ambjornsson, Fredrik Westerlund
Summary: Antimicrobial resistance is a growing threat to global health, and effective methods for detecting antimicrobial resistance genes on bacterial plasmids are necessary. In this study, researchers propose a simple and inexpensive assay based on CRISPR/Cas9 excision and DNA combing to detect these genes.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Evan S. H. Kang, K. K. Sriram, Inho Jeon, Jehan Kim, Shangzhi Chen, Kyoung-Ho Kim, Ka-Hyun Kim, Hyun Seok Lee, Fredrik Westerlund, Magnus P. Jonsson
Summary: Optical nanoantennas provide control of light at the nanoscale and have diverse applications. Traditional metallic and dielectric nanostructures can only support plasmonic and Mie resonances, respectively, while nanostructures of organic J-aggregate excitonic materials can support both plasmon-like resonances and dielectric resonances. These structures are highly anisotropic, enabling them to support hyperbolic localized surface exciton resonances and elliptic Mie resonances.
Article
Chemistry, Multidisciplinary
Teng Wang, Jiaojiao Hu, Yanan Li, Lulu Bi, Lijuan Guo, Xinshuo Jia, Xia Zhang, Dan Li, Xi-Miao Hou, Mauro Modesti, Xu-Guang Xi, Cong Liu, Bo Sun
Summary: The study reveals that Bloom syndrome protein (BLM) possesses the intrinsic ability for phase separation and can co-phase separate with single-stranded DNA (ssDNA) to form co-condensates. ATP enhances BLM's condensation capability on ssDNA and promotes ssDNA compression against a resistive force. BLM can also condense replication protein A (RPA)- or RAD51-coated ssDNA by dismantling these ssDNA-binding proteins.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Sune Levin, Sarah Lerch, Astrid Boje, Joachim Fritzsche, K. K. Sriram, Henrik Strom, Kasper Moth-Poulsen, Henrik Sunden, Anders Hellman, Fredrik Westerlund, Christoph Langhammer
Summary: Catalytic activity can be significantly influenced by the size and shape of nano-particles. In this study, single-particle resolution experiments were conducted using nanofluidic channels to selectively trap individual spherical, cubic, and octahedral colloidal Au nanocrystals. The results show distinct structure sensitivity of the catalytic reactions, which can be attributed to the different edge site abundance on the three particle types.
Article
Chemistry, Multidisciplinary
Maria Bespalova, Robin Oz, Fredrik Westerlund, Madhavi Krishnan
Summary: This study demonstrates the use of surfaces coated with charged lipid bilayers as a system with tunable surface properties for molecular electrometry experiments, and explores the relevance of lipid bilayer formation and wetting dynamics on nanostructured surfaces.
Article
Multidisciplinary Sciences
Tsegaye Sewunet, K. K. Sriram, Ha Hoang Nguyen, Noikaseumsy Sithivong, Ngoc Thi Bich Hoang, Vanphanom Sychareun, Kokasia Nengmongvang, Mattias Larsson, Linus Olson, Fredrik Westerlund, Christian G. Giske
Summary: In this study, the colonization rate of carbapenemase-producing Enterobacterales (CPE) on admission to intensive care units in Vientiane, Lao PDR was determined. The prevalence of extended-spectrum beta-lactamases (ESBLs) was high, while carbapenemases were less common. However, clonal dissemination of bla(NDM-1)-producing Klebsiella pneumoniae isolates in one of the intensive care units was detected, highlighting the need for stringent infection prevention and antimicrobial stewardship strategies.
Review
Biophysics
Karolin Frykholm, Vilhelm Muller, K. K. Sriram, Kevin D. Dorfman, Fredrik Westerlund
Summary: Nanofluidic structures provide a powerful platform for detailed analysis of DNA. By confining DNA to nanochannels, it can be stretched to near its full length without any chemical modifications. The versatility of nanofabrication allows for the design of devices tailored for specific applications, such as controlling confinement or enabling exchange of reagents. The two important applications discussed in this review are optical DNA mapping and DNA-protein interactions, showcasing the power of DNA confinement and nanofluidics in genomics, molecular biology, and biophysics.
QUARTERLY REVIEWS OF BIOPHYSICS
(2022)
Article
Multidisciplinary Sciences
Sagar Mahale, Meenakshi Setia, Bharat Prajapati, Santhilal Subhash, Mukesh Pratap Yadav, Subazini Thankaswamy Kosalai, Ananya Deshpande, Jagannath Kuchlyan, Mirco Di Marco, Fredrik Westerlund, L. Marcus Wilhelmsson, Chandrasekhar Kanduri, Meena Kanduri
Summary: The study reveals the critical role of HnRNPK in regulating double-stranded RNA formation in loci with overlapping sense and antisense transcripts, maintaining them in a single-stranded form and determining their oncogenic functions through blocking RNA-RNA interactions.
NATURE COMMUNICATIONS
(2022)
Article
Nanoscience & Nanotechnology
John Andersson, Julia Jarlebark, K. K. Sriram, Andreas Schaefer, Rebekah Hailes, Chonnipa Palasingh, Bagus Santoso, Van-Truc Vu, Chun-Jun Huang, Fredrik Westerlund, Andreas Dahlin
Summary: In nanobiotechnology, controlling the interactions between biological molecules and surfaces is crucial. This study presents a simple method for passivating or selectively functionalizing silica surfaces, without the need for complex reactions. The modified surfaces show superior properties compared to existing options, with low fouling and the ability to detect specific molecules. This method is compatible with various surface-based sensors and analytical devices, making it highly valuable for the field of nanobiotechnology.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Microbiology
Adrien Camus, Elena Espinosa, Penelope Zapater Baras, Parul Singh, Nicole Quenech'Du, Elise Vickridge, Mauro Modesti, Francois Xavier Barre, Olivier Espeli
Summary: DNA damage repair is crucial for genome maintenance and evolution. By studying two genotoxic antibiotics, it was found that only a small set of DNA repair proteins are involved in the repair of the lesions induced by these drugs. RecN, a SMC-like protein, plays an important role in controlling sister chromatids dynamics and genome morphology during the repair processes. However, the influence of RecN on sister chromatids dynamics is different in the processing of lesions induced by the two drugs.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Bjorn Altenburger, Carl Andersson, Sune Levin, Fredrik Westerlund, Joachim Fritzsche, Christoph Langhammer
Summary: This study introduces nanofluidic scattering microscopy to measure the activity of single nanoparticles during catalytic reactions. By detecting minuscule refractive index changes in the liquid, the concentration changes of reactants can be accurately measured. The turnover frequency of the particles is derived from the growth rate of gas bubbles formed during the reaction.
Article
Biochemistry & Molecular Biology
Madison B. Adolph, Atharv S. Garje, Swati Balakrishnan, Florian Morati, Mauro Modesti, Walter J. Chazin, David Cortez
Summary: RAD51 forms nucleoprotein filaments to promote DNA repair and replication processes, and its stability is regulated by RADX. Mutants of RADX with separation of function exhibit impaired ATP hydrolysis activity of RAD51, leading to accumulation of DNA damage and replication defects in cells.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Medicine, Research & Experimental
My Nyblom, Anna Johnning, Karolin Frykholm, Marie Wrande, Vilhelm Mueller, Gaurav Goyal, Miriam Robertsson, Albertas Dvirnas, Tsegaye Sewunet, K. K. Sriram, Tobias Ambjornsson, Christian G. Giske, Linus Sandegren, Erik Kristiansson, Fredrik Westerlund
Summary: We have developed a method to directly identify bacteria from patient samples, which can accurately identify different strains or subtypes. This method can be used for mixed bacterial samples and urine samples, providing fast diagnostic information for choosing the most suitable antibiotics and reducing the risk of death and suffering.
COMMUNICATIONS MEDICINE
(2023)
Article
Biochemical Research Methods
Oskar E. Stroem, Jason P. Beech, Jonas O. Tegenfeldt
Summary: Regular patterns emerge in high-concentration DNA solutions in microfluidic pillars at low Reynolds numbers and high Deborah numbers. Interacting vortices between pillars lead to long-range traveling waves consisting of DNA. The position of the pillars in each unit cell plays a role in the formation of waves. Elastic effects are identified as central to the origin of these waves, and this research may contribute to improving sample processing in microfluidics and understanding viscoelastic mechanisms.
Article
Chemistry, Multidisciplinary
Nima Sasanian, Rajhans Sharma, Quentin Lubart, K. K. Sriram, Marziyeh Ghaeidamini, Kevin D. Dorfman, Elin K. Esbjorner, Fredrik Westerlund
Summary: Amyloid fibrils play a central role in the pathology of many diseases and have significant structural polymorphism. A nanofluidic channel analysis technique was introduced to study single, fluorescently-labeled amyloid fibrils and determine their physical properties. The method allowed for accurate determination of fibril persistence length and revealed differences in physical properties between amyloid-beta(1-42) and alpha-synuclein fibrils.
