Article
Biochemistry & Molecular Biology
Aleksandr Alekseev, Natalia Morozova, Alexey Vedyaykin, Alexander Yakimov, Mikhail Khodorkovskii, Georgii Pobegalov
Summary: RecA is a central enzyme in bacteria that is involved in homologous recombination, DNA repair, natural transformation, and SOS-response activation. This study explores the features of inactive RecA nucleoprotein filaments formed without nucleotide cofactors, demonstrating that compressed RecA-DNA filaments can exist with different binding stoichiometry and only the 3:1 stoichiometry allows direct interconvertibility with the active ATP-bound conformation.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Review
Cell Biology
Muwen Kong, Eric C. Greene
Summary: DNA double strand breaks are highly deleterious forms of DNA damage that, if left unrepaired, can lead to a high risk of cancer. Homologous recombination and nonhomologous end joining are the two major mechanisms responsible for repairing DSBs, and single-molecule studies have provided detailed insights into the repair processes at each step.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Katerina Zakharova, Brian J. Caldwell, Shalya Ta, Carter T. Wheat, Charles E. Bell
Summary: Red beta is a protein from bacteriophage lambda that promotes repair of double-stranded DNA breaks through single-strand annealing. Lysine residues within the DNA binding domain were found to be critical for DNA binding and recombination in vitro and in vivo, while lysines within the C-terminal domain were mainly involved in recombination. Specific lysine residues, such as K61 and K148, played important roles in DNA annealing and oligomer formation, respectively.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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
Multidisciplinary Sciences
Jason C. Bell, Christopher C. Dombrowski, Jody L. Plank, Ryan B. Jensen, Stephen C. Kowalczykowski
Summary: Mutations in the BRCA2 gene increase the risk of breast and ovarian cancers. This study shows that BRCA2 accelerates the formation of the RAD51 nucleoprotein filament, which plays a crucial role in DNA repair. BRCA2 also eliminates the kinetic barrier imposed by replication protein-A (RPA), allowing efficient and regulated recombination.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Shunsuke Takahashi, Masahiko Oshige, Shinji Katsura
Summary: DNA replication, repair, and recombination in cells regulate genetic information transfer. Single-molecule imaging provides new insights into the dynamic behaviors of individual biomolecules, helping analyze the interaction between DNA and proteins.
Article
Chemistry, Physical
Roaa Mahmoud, Soma Dhakal
Summary: This article systematically investigates the effects of cell-mimic solvent composition and crowding on DNA Holliday junctions (HJs) branch migration (BM) using single-molecule fluorescence analysis. The results show that BM is affected by cosolutes in a concentration-dependent manner, and it is significantly accelerated under crowding environments. The enhanced mobility of HJs in cell-like environments may provide new avenues for therapeutic interventions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
Chaoyou Xue, Lucia Molnarova, Justin B. Steinfeld, Weixing Zhao, Chujian Ma, Mario Spirek, Kyle Kaniecki, Youngho Kwon, Ondrej Belan, Katerina Krejci, Simon J. Boulton, Patrick Sung, Eric C. Greene, Lumir Krejci
Summary: RECQ5 is identified as an ATP-dependent single-stranded DNA motor protein that can translocate on various nucleoprotein complexes and dismantle RAD51-ssDNA filaments. Protein-protein interaction with RAD51 is crucial for RECQ5's functions, but its substrate specificity and ability to remove certain mutant RAD51 proteins suggest a complex regulatory role in genome maintenance.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biophysics
Dalton R. Gibbs, Roaa Mahmoud, Anisa Kaur, Soma Dhakal
Summary: This study used an optical-tweezers-based single-molecule manipulation assay to investigate the mechanical and thermodynamic properties of the RuvA-Holliday junction complex. The results showed that RuvA protein stabilizes the Holliday junction and increases its unfolding force, facilitating refolding under high force. This approach can be applied to study other junction-binding proteins involved in critical DNA repair processes.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Aurimas Kopustas, Sarune Ivanovaite, Tomas Rakickas, Ernesta Pocevicitue, Juste Paksaite, Tautvydas Karvelis, Mindaugas Zaremba, Elena Manakova, Marijonas Tutkus
Summary: Over the past 20 years, single-molecule methods in combination with new nanotechnological platforms have become extremely important for biophysical studies, facilitating experimental design and faster data acquisition. Utilizing a nanotechnological platform called DNA Curtains, which involves a flow-stretch of immobilized DNA molecules, allowed for stable immobilization and orientation of DNA molecules using a protein template-directed assembly. This method improves immobilization stability and enables the study of protein-DNA interactions under more controllable conditions, demonstrating potential applications in nucleic acid-interacting protein binding assays.
Review
Oncology
Alexander M. A. van der Wiel, Lesley Schuitmaker, Ying Cong, Jan Theys, Arne Van Hoeck, Conchita Vens, Philippe Lambin, Ala Yaromina, Ludwig J. Dubois
Summary: This review discusses more accurate methods to detect homologous recombination deficiency (HRD) and how these can be applied for more personalized cancer treatment. Current methods to assess HRD are insufficient, leading to an underestimation of patients with HRD. Detection of HRD scar might be a more reliable biomarker for HRD.
Review
Chemistry, Multidisciplinary
Hsiu-Fang Fan
Summary: Single-molecule techniques are powerful tools to investigate protein-DNA interactions that are challenging to study using conventional biochemical techniques. By using single-molecule tethered particle motion, we have studied various protein-DNA interactions and obtained valuable information about homologous recombination, site-specific recombination, DNA packaging, and nucleosome remodeling processes.
JOURNAL OF THE CHINESE CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Donna R. Whelan, Eli Rothenberg
Summary: Using single-molecule localization super-resolution imaging assays, we observed the spatiotemporal behavior of key mediator and nuclease proteins during DNA resection at single-ended double-strand breaks. Multiple simultaneous resection events were demonstrated, with recruitment of various proteins and completion of resection 2 to 4 hours after break induction. Additionally, we identified potential roles of BRCA1 and BLM in homology search and repair resolution during HR.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Mi Ae Kang, Jong-Soo Lee
Summary: CTCF, a highly conserved multifunctional DNA-binding protein with 11 zinc fingers, plays crucial roles in diverse genomic processes such as transcriptional regulation, insulation, genome imprinting, and maintenance of genome organization. Recent findings reveal that CTCF is involved in DNA double-strand break (DSB) repair through homologous recombination (HR), facilitating accurate restoration of broken DNA sequences. Understanding the functional crosstalks between CTCF and other HR factors may shed light on the molecular basis of various human diseases and the diverse functions of CTCF in genome biology.
Review
Biochemistry & Molecular Biology
Xingchen Xiong, Zhiwen Lu, Lixin Ma, Chao Zhai
Summary: Programmable endonucleases, such as Cas and pAgo, can recognize and cleave DNA sequences at nearly any arbitrary site by base pairing with guide RNA or DNA. This review focuses on the use of these enzymes in in vivo and in vitro recombination-based gene cloning methods, and the advantages and disadvantages of using programmable endonucleases for gene cloning are discussed.
Article
Multidisciplinary Sciences
Chih-Ying Lee, Guan-Chin Su, Wen-Yen Huang, Min-Yu Ko, Hsin-Yi Yeh, Geen-Dong Chang, Sung-Jan Lin, Peter Chi
NATURE COMMUNICATIONS
(2019)
Article
Geosciences, Multidisciplinary
W. Bruce Banerdt, Suzanne E. Smrekar, Don Banfield, Domenico Giardini, Matthew Golombek, Catherine L. Johnson, Philippe Lognonne, Aymeric Spiga, Tilman Spohn, Clement Perrin, Simon C. Staehler, Daniele Antonangeli, Sami Asmar, Caroline Beghein, Neil Bowles, Ebru Bozdag, Peter Chi, Ulrich Christensen, John Clinton, Gareth S. Collins, Ingrid Daubar, Veronique Dehant, Melanie Drilleau, Matthew Fillingim, William Folkner, Raphael F. Garcia, Jim Garvin, John Grant, Matthias Grott, Jerzy Grygorczuk, Troy Hudson, Jessica C. E. Irving, Guenter Kargl, Taichi Kawamura, Sharon Kedar, Scott King, Brigitte Knapmeyer-Endrun, Martin Knapmeyer, Mark Lemmon, Ralph Lorenz, Justin N. Maki, Ludovic Margerin, Scott M. McLennan, Chloe Michaut, David Mimoun, Anna Mittelholz, Antoine Mocquet, Paul Morgan, Nils T. Mueller, Naomi Murdoch, Seiichi Nagihara, Claire Newman, Francis Nimmo, Mark Panning, W. Thomas Pike, Ana-Catalina Plesa, Sebastien Rodriguez, Jose Antonio Rodriguez-Manfredi, Christopher T. Russell, Nicholas Schmerr, Matt Siegler, Sabine Stanley, Eleanore Stutzmann, Nicholas Teanby, Jeroen Tromp, Martin Van Driel, Nicholas Warner, Renee Weber, Mark Wieczorek
Editorial Material
Multidisciplinary Sciences
Hannah L. Klein
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Multidisciplinary Sciences
Wei-Hsuan Lan, Sheng-Yao Lin, Chih-Yuan Kao, Wen-Hsuan Chang, Hsin-Yi Yeh, Hao-Yen Chang, Peter Chi, Hung-Wen Li
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Hao-Yen Chang, Chia-Yi Lee, Chih-Hao Lu, Wei Lee, Han-Lin Yang, Hsin-Yi Yeh, Hung-Wen Li, Peter Chi
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Xinxing Lyu, Kai-Hang Lei, Pau Biak Sang, Olga Shiva, Megan Chastain, Peter Chi, Weihang Chai
Summary: The CST complex protects stalled replication forks from degradation by the MRE11 nuclease by inhibiting MRE11 binding to reversed forks, thus preventing excessive nascent-strand degradation and preserving genome integrity under replication stress, particularly in BRCA2 deficient cells.
Article
Multidisciplinary Sciences
Shih-Chi Luo, Hsin-Yi Yeh, Wei-Hsuan Lan, Yi-Min Wu, Cheng-Han Yang, Hao-Yen Chang, Guan-Chin Su, Chia-Yi Lee, Wen-Jin Wu, Hung-Wen Li, Meng-Chiao Ho, Peter Chi, Ming-Daw Tsai
Summary: RAD51 and DMC1 recombinases catalyse high-fidelity and mismatch tolerant recombination, processes that are indispensable for the maintenance of genomic integrity. The study elucidates the structural difference between RAD51 and DMC1 with regard to mismatch tolerance, showing that key residues in Loop 1 and Loop 2 play a crucial role in determining the fidelity of DNA recombinases.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Wan-Chen Li, Chia-Yi Lee, Wei-Hsuan Lan, Tai-Ting Woo, Hou-Cheng Liu, Hsin-Yi Yeh, Hao-Yen Chang, Yu-Chien Chuang, Chiung-Ya Chen, Chi-Ning Chuang, Chia-Ling Chen, Yi-Ping Hsueh, Hung-Wen Li, Peter Chi, Ting-Fang Wang
Summary: Most eukaryotes possess two RecA-like recombinases for interhomolog recombination during meiosis, but some have lost Dmc1. TrRad51 in Trichoderma reesei plays a crucial role in interhomolog recombination and has better mismatch tolerance than ScRad51, evolving ScDmc1-like properties through structural variations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Albert W. Hinman, Hsin-Yi Yeh, Baptiste Roelens, Kei Yamaya, Alexander Woglar, Henri-Marc G. Bourbon, Peter Chi, Anne M. Villeneuve
Summary: Meiotic recombination plays essential roles in genetic diversity and genome inheritance, with DSB-3 identified as a protein promoting DSB formation in the nematode Caenorhabditis elegans. DSB-3 is interdependent with other DSB proteins and its localization supports its role as a homolog of MEI4 in conserved DSB-promoting complexes. Variations in meiotic programs across diverse organisms may contribute to the diversification of essential meiotic machinery components.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Vincent Blay, Saule Gailiunaite, Chih-Ying Lee, Hao-Yen Chang, Douglas R. Houston, Ted Hupp, Peter Chi
Summary: In this study, we explore various ATPases to find attractive binding pockets for drug discovery. Through computational design, we identified two novel inhibitors against RAD51, a promising target in cancer treatment.
BIOORGANIC & MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Chia-Chun Liu, Hsin-Ru Chan, Guan-Chin Su, Yan-Zhu Hsieh, Kai-Hang Lei, Tomoka Kato, Tai-Yuan Yu, Yu-wen Kao, Tzu-Hao Cheng, Peter Chi, Jing-Jer Lin
Summary: The non-coding RNA TERRA regulates telomere recombination. Mutations in DNA2, EXO1, MRE11, and SAE2 cause delay in type II survivor formation, while mutation in RAD27 results in early formation of type II recombination. Rad27 cleaves TERRA in the context of an R-loop or flapped RNA-DNA duplex and regulates C-circles during telomere recombination.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Chia-Lun Guh, Kai-Hang Lei, Yi-An Chen, Yi-Zhen Jiang, Hao-Yen Chang, Hungjiun Liaw, Hung-Wen Li, Hsin-Yung Yen, Peter Chi
Summary: This study provides evidence for an unknown function of RAD51 paralogs in synergizing with RAD51 nucleoprotein filament to prevent degradation of stressed replication forks.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Cell Biology
Hannah L. Klein, Kenny K. H. Ang, Michelle R. Arkin, Emily C. Beckwitt, Yi-Hsuan Chang, Jun Fan, Youngho Kwon, Michael J. Morten, Sucheta Mukherjee, Oliver J. Pambos, Hafez el Sayyed, Elizabeth S. Thrall, Joao P. Vieira-da-Rocha, Quan Wang, Shuang Wang, Hsin-Yi Yeh, Julie S. Biteen, Peter Chi, Wolf-Dietrich Heyer, Achillefs N. Kapanidis, Joseph J. Loparo, Terence R. Strick, Patrick Sung, Bennett Van Houten, Hengyao Niu, Eli Rothenberg
Review
Cell Biology
Hannah L. Klein, Giedre Bacinskaja, Jun Che, Anais Cheblal, Rajula Elango, Anastasiya Epshtein, Devon M. Fitzgerald, Belen Gomez-Gonzalez, Sharik R. Khan, Sandeep Kumar, Bryan A. Leland, Lea Marie, Qian Mei, Judith Mine-Hattab, Alicja Piotrowska, Erica J. Polleys, Christopher D. Putnam, Elina A. Radchenko, Anissia Ait Saada, Cynthia J. Sakofsky, Eun Yong Shim, Mathew Stracy, Jun Xia, Zhenxin Yan, Yi Yin, Andres Aguilera, Juan Lucas Argueso, Catherine H. Freudenreich, Susan M. Gasser, Dmitry A. Gordenin, James E. Haber, Grzegorz Ira, Sue Jinks-Robertson, Megan C. King, Richard D. Kolodner, Andrei Kuzminov, Sarah A. E. Lambert, Sang Eun Lee, Kyle M. Miller, Sergei M. Mirkin, Thomas D. Petes, Susan M. Rosenberg, Rodney Rothstein, Lorraine S. Symington, Pawel Zawadzki, Nayun Kim, Michael Lisby, Anna Malkova