Article
Oncology
Yang Wang, Wen-Yi Gao, Li-Li Wang, Ruo-Lei Wang, Zhi-Xia Yang, Fu-Qiang Luo, Yu-Hao He, Zi-Bin Wang, Fu-Qiang Wang, Qing-Yuan Sun, Jing Li, Dong Zhang
Summary: This study revealed that knockout of the FBXW24 gene in female mice significantly affected fertility, follicle reserve, oocyte quality, meiotic prophase progression of female germ cells, and oocyte meiosis primarily by regulating the stability of SYCP3, ultimately leading to oocyte death and infertility.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
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
Biochemistry & Molecular Biology
Soma Mondal, Padmaja P. Mishra
Summary: The conformation of DNA is influenced by cellular conditions, nucleotide sequence, and environmental effects, including osmotic stress, while the presence of molecular crowding alters the structural integrity and flexibility of DNA, affecting its breathing dynamics. These changes in DNA structure, monitored by single-molecule FRET microspectroscopy, have implications for enzyme kinetics and nucleic acid structure elucidation.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Andrew J. Lee, Masayuki Endo, Jamie K. Hobbs, A. Giles Davies, Christoph Walti
Summary: The study used DNA nanostructure-augmented high-speed AFM to directly observe the RecA-orchestrated alignment of homologous DNA strands, revealing transient sampling of micro-homology by RecA during the search for sequence alignment. These transient interactions are early steps in the search for sequence homology.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Analytical
Xiaojia Jiang, Tiezheng Pan, Chao Lang, Chao Zeng, Jinxing Hou, Jiayun Xu, Quan Luo, Chunxi Hou, Junqiu Liu
Summary: In this study, a semisynthetic selenoenzyme nanoreactor was created to monitor and analyze intermediates in enzymatic reactions, revealing the mysteries of selenoenzyme catalysis at the single-molecule level.
ANALYTICAL CHEMISTRY
(2022)
Article
Biology
Soham Chakraborty, Deep Chaudhuri, Souradeep Banerjee, Madhu Bhatt, Shubhasis Haldar
Summary: The role of chaperones in talin mechanics and stability is investigated. Chaperones were found to affect adhesion proteins' stability by changing their folding mechanics, with unfoldases reducing the unfolding force and foldases increasing it. Chaperones directly reshape the energy landscape of talin, influencing its force-dependent interactions and adhesion dynamics.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Meenakshi Sharma, Eva de Alba
Summary: This study investigates the association and dissociation rates of the AIM2-DNA complex at the single molecule level using optical traps and confocal fluorescence microscopy. The results reveal distinct mechanisms for the growth of AIM2 oligomers and show that the size of the oligomers can increase fourfold within seconds. Additionally, it is found that single AIM2 molecules do not diffuse/scan along the DNA, suggesting that oligomerization depends on stochastic encounters with DNA and/or DNA-bound AIM2.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Lars Richter, Alan M. Szalai, C. Lorena Manzanares-Palenzuela, Izabela Kaminska, Philip Tinnefeld
Summary: The study explores the use of fluorescence-based single-molecule techniques in the research of 2D materials and the application of DNA as an anchor for single dye molecules. It reviews the existing literature on the combination of these two fields and discusses the potential synergies that can be achieved.
ADVANCED MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Lei Tian, Niannian Ding, Xuehui Liu, Yuanyuan Chen, Zhenfeng Zhang
Summary: This study analyzed the critical role of F41 in protein folding of Cren7. Mutation analysis revealed that the mutation of F41 led to misfolding and reduced stability of Cren7, but had minimal effect on the activities of DNA binding and supercoiling. Furthermore, F41A lost the ability to form oligomers/polymers on DNA.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Multidisciplinary
Lu Zhang, Satoshi Kaneko, Shintaro Fujii, Manabu Kiguchi, Tomoaki Nishino
Summary: This study investigated a single-molecule reaction of DNA intercalation as an example of a bimolecular association reaction, measuring single-molecule conductance values of the product and reactant molecules adsorbed on an Au surface to identify and quantify these molecules, and determining the association constant of the reaction on a single-molecule basis.
CHEMICAL COMMUNICATIONS
(2021)
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
Chemistry, Multidisciplinary
Juan Zhou, Qing Lan, Wang Li, Li-Na Ji, Kang Wang, Xing-Hua Xia
Summary: Obtaining sequential and conformational information on proteins is important for understanding their functions. This study combines surface enhanced Raman scattering (SERS) with a nanopore to observe the unfolding and multistep sequential translocation of single molecule (SM) cytochrome c (cyt c). The high bias voltage unfolds the SM protein, slowing down the translocation and allowing specific SERS traces of different SM cyt c segments to be recorded. This research provides insight into protein segments and accelerates the development of nanopore-based SM protein sequencing.
Article
Biochemistry & Molecular Biology
Wonje Heo, Jeonghwan Seo, Yoonhee Lee, Yoori Kim
Summary: This paper reviews the advances in single-molecule tools for imaging long genomic DNA and studying dynamic protein interactions. It focuses on three representative techniques: molecular combing, nanochannel confinement, and DNA curtain assays, which elongate individual DNA using fluid-driven force. The paper provides an integrated perspective and direction for future use in dissecting protein function.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Stefan H. Mueller, Lucy J. Fitschen, Afnan Shirbini, Samir M. Hamdan, Lisanne M. Spenkelink, Antoine M. van Oijen
Summary: Traditional enzyme characterization methods only provide population averages, while single-molecule methods can reveal kinetics and population heterogeneity but are often complex and time-consuming. We present a high-throughput single-molecule assay for rapidly characterizing DNA metabolism-related proteins by measuring changes in fluorescence intensity. Our method, combined with automated data analysis, can provide enzymatic activity data for thousands of molecules in less than an hour. We demonstrated three different enzyme activities and discovered a previously unknown activity of the UvrD helicase.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Jinyue Zhang, Yu Wang, Yuqin Wang, Panke Zhang, Hong-Yuan Chen, Shuo Huang
Summary: DNA lesions induced by alkylating agents can be directly distinguished by observing the enzymatic stalling kinetics, which is not interfered with by the sequence context.
Editorial Material
Biochemistry & Molecular Biology
Aniruddha Mitra, Erwin J. G. Peterman
Summary: Directional changes in intraflagellar transport do not rely on tip-associated machinery.
Article
Cell Biology
Christine W. Bruggeman, Guus H. Haasnoot, Noemie Danne, Jaap van Krugten, Erwin J. G. Peterman
Summary: Cilia are membrane-enveloped organelles protruding from cell surfaces, crucial for sensing external environment. Chemical stimulation causes changes in ciliary structure and intra-flagellar transport, leading to different neuronal activity responses. The findings suggest cilia can sense and respond to external cues in distinct ways, highlighting their flexible nature as sensing hubs.
Review
Cell Biology
Wouter Mul, Aniruddha Mitra, Erwin J. G. Peterman
Summary: In this review, the authors explore the regulation of intraflagellar transport (IFT) in cilia from three different perspectives: the motor track, motor proteins, and kinases. By discussing these factors, the authors provide mechanistic insights into IFT regulation in cilia and suggest directions for future research.
Article
Biology
James M. Dunce, Lucy J. Salmon, Owen R. Davies
Summary: Meiosis protein TEX12 plays a vital role in homologous chromosome synapsis and centrosome function. This study reveals the structural basis of TEX12 and its interaction with SYCE2 within the synaptonemal complex. The conformational change of TEX12 upon C-terminal tip mutations suggests its role in regulating SC assembly and its functions in meiotic centrosomes and cancer.
COMMUNICATIONS BIOLOGY
(2022)
Review
Pharmacology & Pharmacy
Matthew T. J. Halma, Jack A. Tuszynski, Gijs J. L. Wuite
Summary: The time and cost of developing new therapeutic drugs is a significant burden, involving computational screening, compound assays, and expensive clinical trials. This review highlights the value of dynamic conformational information obtained through optical tweezers for targeting "undruggable" proteins. Optical tweezers provide insights into the relationship between biological mechanisms and structural conformations, aiding in drug discovery. Developing workflows and tools for optical tweezers will improve efficiency, allowing for greater adoption in the biopharmaceutical industry. As a complementary tool, optical tweezers increase the number of potential drug candidates, enhance understanding of a target's complex structural dynamics, and elucidate compound-target interactions.
DRUG DISCOVERY TODAY
(2023)
Review
Biochemistry & Molecular Biology
Longfu Xu, Matthew T. J. Halma, Gijs J. L. Wuite
Summary: Single-stranded DNA-binding proteins (SSBs) are essential for DNA metabolism and play crucial roles in maintaining genome integrity and coordinating with other proteins involved in DNA replication, recombination, and repair. Recent advances in single-molecule techniques and structural methods have greatly improved our understanding of the binding dynamics and interaction of SSBs with ssDNA and other protein partners. We highlight the central coordination role of SSBs in directly modulating the activities of other proteins and discuss the various modes of interaction between SSBs and their protein partners, providing a comprehensive view of the interaction network shaped by SSBs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
James H. Crichton, James M. Dunce, Orla M. Dunne, Lucy J. Salmon, Paul S. Devenney, Jennifer Lawson, Ian R. Adams, Owen R. Davies
Summary: During meiosis, the synaptonemal complex (SC), a supramolecular protein structure, forms between homologous chromosomes to aid in recombination. In mammals, SC formation involves the hierarchical assembly of an SYCP1 protein lattice. However, our study shows that the CE protein SYCE3 actively remodels the SYCP1 lattice during synapsis, rather than stabilizing it. SYCE3 interacts with other CE complexes and establishes a new lattice, leading to long-range synapsis and the formation of a mature SC.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Dian Spakman, Tinka V. M. Clement, Andreas S. Biebricher, Graeme A. King, Manika I. Singh, Ian D. Hickson, Erwin J. G. Peterman, Gijs J. L. Wuite
Summary: In this study, an in vitro single-molecule assay was used to mimic chromatin under tension and it was demonstrated that PICH is a tension- and ATP-dependent nucleosome remodeler.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Kirsten E. L. Garner, Anna Salter, Clinton K. Lau, Manickam Gurusaran, Cecile M. Villemant, Elizabeth P. Granger, Gavin McNee, Philip G. Woodman, Owen R. Davies, Brian E. Burke, Victoria J. Allan
Summary: During prophase I of mammalian meiosis, dynein-driven movement of chromosomes is crucial for synapsis and genetic exchange. KASH5 acts as an activating adaptor for dynein, promoting its motility in vitro. However, cytosolic KASH5 inhibits dynein's interphase functions.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Longfu Xu, Jordi Cabanas-Danes, Matthew T. J. Halma, Iddo Heller, Sarah A. Stratmann, Antoine M. van Oijen, Seung-Joo Lee, Erwin J. G. Peterman, Gijs J. L. Wuite
Summary: In vitro experiments show that bacteriophage T7 single-stranded DNA-binding protein (gp2.5) can protect transiently exposed regions of single-stranded DNA (ssDNA) through its dynamic interaction. Furthermore, the sequence of T7 gp2.5, the ssDNA conformation induced by template tension, and the acidic C-terminal domain of T7 gp2.5 significantly affect its DNA binding properties. Finally, a unique template-catalyzed recycling behavior of T7 gp2.5 is revealed, facilitating efficient spatial redistribution during the synthesis of successive Okazaki fragments.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Optics
Aniruddha Mitra, Elizaveta Loseva, Guus H. Haasnoot, Erwin J. G. Peterman
Summary: Single-particle imaging using laser-illuminated widefield epi-fluorescence microscopy is a powerful tool to investigate molecular processes in vivo. By exciting only a small region in chemosensory neurons in live C. elegans, long-duration single-particle imaging with improved quality can be achieved. Small-window illumination microscopy (SWIM) allows for reduced photobleaching and improved signal-to-background ratio, and can be applied to study intracellular transport or cytoskeletal dynamics in elongated protrusions.
OPTICS COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Robert Appleby, Daniel Bollschweiler, Dimitri Y. Chirgadze, Luay Joudeh, Luca Pellegrini
Summary: In this study, the researchers investigated the role of RAD51 in homologous recombination. They found that ATP binding to RAD51 promotes its folding into a conformation that allows DNA binding. The presence of a second metal ion at the ATP-binding site explains how RAD51 regulates its interaction with DNA. Loss of the second metal ion upon ATP hydrolysis weakens the stability of RAD51 filament and contributes to its disassembly.
Meeting Abstract
Biophysics
Vadim Bogatyr, Andreas S. Biebricher, Giulia Bergamaschi, Erwin J. G. Peterman, Gijs J. L. Wuite
BIOPHYSICAL JOURNAL
(2023)
Meeting Abstract
Biophysics
Gijs Wuite
BIOPHYSICAL JOURNAL
(2023)
Article
Nanoscience & Nanotechnology
Vadim Bogatyr, Andreas S. Biebricher, Giulia Bergamaschi, Erwin J. G. Peterman, Gijs J. L. Wuite
Summary: Studying cellular mechanics provides important insights into cell structure and health. The quantitative acoustophoresis (QAP) method allows simultaneous measurement of compressibility and density of multiple cells in a contact-free manner, offering a simple and effective alternative for studying biological particles. This technique not only measures mechanical properties of living cells, but can also sense artificial cytoskeletons, showing potential for a new approach in studying cellular mechanics.
ACS NANOSCIENCE AU
(2022)
