Article
Biochemistry & Molecular Biology
Amedeo Capobianco, Alessandro Landi, Andrea Peluso
Summary: Molecular dynamics simulations and quantum mechanical/molecular mechanics methods predict that short, single-stranded DNA oligonucleotides adopt conformations similar to crystallographic B-DNA in solution. Single strands rich in adjacent purine nucleobases have more regular arrangements, and poly-thymine single strands also retain helical structure in solution.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Maria Cano-Linares, Aurora Yanez-Vilches, Nestor Garcia-Rodriguez, Marta Barrientos-Moreno, Roman Gonzalez-Prieto, Pedro San-Segundo, Helle D. Ulrich, Felix Prado
Summary: This study reveals that the HR protein Rad52 works in conjunction with the TLS machinery to repair MMS and UV light-induced ssDNA gaps. Rad52 facilitates DNA damage-induced mutagenesis and PCNA ubiquitylation through Rad51/Rad57-dependent and -independent processes, providing a novel role for recombination proteins in maintaining genome integrity.
Article
Biochemical Research Methods
Stephan Riesenberg, Philipp Kanis, Dominik Macak, Damian Wollny, Dorothee Duesterhoeft, Johannes Kowalewski, Nelly Helmbrecht, Tomislav Maricic, Svante Paeaebo
Summary: The study introduces a high-precision method, HDRobust, for repairing DNA double-stranded breaks through homology-directed repair (HDR). By transiently inhibiting nonhomologous end joining and microhomology-mediated end joining, HDRobust achieved point mutations by HDR in up to 93% of chromosomes. Insertions, deletions, rearrangements, and unintended changes at other genomic sites were largely eliminated. The efficient correction of pathogenic mutations in cells derived from patients with anemia, sickle cell disease, and thrombophilia was validated.
Article
Multidisciplinary Sciences
Brian J. Caldwell, Andrew S. Norris, Caroline F. Karbowski, Alyssa M. Wiegand, Vicki H. Wysocki, Charles E. Bell
Summary: Some bacteriophages encode a recombinase that catalyzes single-stranded DNA annealing (SSA). In this study, a Red beta homolog from a prophage of Listeria innocua in complex with two complementary DNA strands was determined using cryo-electron microscopy. The structure revealed a helical protein filament bound to an extended and unwound DNA duplex. The protein shares similarity in fold and single-stranded DNA-binding mode with RAD52, providing insights into the mechanism of protein-catalyzed SSA.
NATURE COMMUNICATIONS
(2022)
Review
Genetics & Heredity
Felix Prado
Summary: The DNA damage tolerance (DDT) response aims to complete DNA replication timely and safely by facilitating the advance of replication forks through blocking lesions. Accumulation of single-strand DNA (ssDNA), lesion bypass, and ssDNA filling are key processes involving low-fidelity polymerases and Rad51/ssDNA nucleofilament. Rad51, BRCA2, and Rad52 play critical roles in homologous recombination (HR) and have been shown to perform various functions in DDT mechanisms without requiring the strand exchange activity of Rad51.
Article
Cell Biology
Emilie Ma, Laurent Maloisel, Lea Le Falher, Raphael Guerois, Eric Coic
Summary: Rad52 SUMOylation or mutations disrupting the Rad52-Rad51 interaction can suppress Rad51 filament toxicity, while mutations in the Rad52 N-terminal domain can also reduce DNA damage sensitivity of Srs2-deficient cells. These mutations affect the Rad52 oligomeric ring structure and play a crucial role in protecting Rad51 filaments from Srs2, but they may also increase Rad51 filament stability and toxicity in Srs2-deficient cells. The stabilization function of Rad52 ring structure is distinct from its mediator and annealing activities.
Article
Biochemistry & Molecular Biology
Tasnim Ahmad, Ryotaro Kawasumi, Tomoya Taniguchi, Takuya Abe, Kazuhiro Terada, Masataka Tsuda, Naoto Shimizu, Toshiki Tsurimoto, Shunichi Takeda, Kouji Hirota
Summary: This study identifies the PARP1-CTF18-Pol ε exonuclease axis that acts independently of homology-directed repair (HDR) to prevent fork collapse at single-ended double-strand breaks (seDSBs). The findings also show that olaparib inhibits this axis and has pronounced cytotoxic effects on HDR-deficient cells.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Alison C. Carley, Manisha Jalan, Shyamal Subramanyam, Rohini Roy, Gloria E. O. Borgstahl, Simon N. Powell
Summary: Loss of RAD52 in BRCA-deficient cells is synthetically lethal due to its role in backup homologous recombination repair. We demonstrate that phosphorylation of RPA is necessary for RAD52 to function as a mediator in HR, especially in BRCA-deficient cells.
MOLECULAR AND CELLULAR BIOLOGY
(2022)
Article
Chemistry, Medicinal
Federica Battistini, Alba Sala, Adam Hospital, Modesto Orozco
Summary: The properties of DNA duplex have been accurately described using molecular dynamics simulations, but there lacks equivalent simulations for RNA duplex which is usually represented as a rigid rod. In this study, a massive simulation effort was conducted to derive the properties of RNA duplex and a simplified model for long RNA duplexes. Despite high chemical similarity, the local and global elastic properties of DNA and RNA duplexes are significantly different. Statement about the relative flexibility or stability of both polymers is meaningless and a detailed description depending on the sequence and deformation type should be used.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Multidisciplinary Sciences
Guangxue Liu, Jimin Li, Boxue He, Jiaqi Yan, Jingyu Zhao, Xuejie Wang, Xiaocong Zhao, Jingyan Xu, Yeyao Wu, Simin Zhang, Xiaoli Gan, Chun Zhou, Xiangpan Li, Xinghua Zhang, Xuefeng Chen
Summary: The yeast ubiquitin ligase Bre1 and its human homolog RNF20 function as recombination mediator proteins by promoting Rad51-ssDNA assembly and antagonizing the activities of Srs2 or FBH1 anti-recombinase. They interact with Rad51, direct Rad51 to ssDNA, and facilitate Rad51-ssDNA filament assembly and strand exchange. In addition, they counteract the disrupting effect of Srs2 or FBH1 helicase on the Rad51 filament. These findings reveal the important role of Bre1/RNF20 in homologous recombination repair.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Goro Doi, Satoshi Okada, Takehiro Yasukawa, Yuki Sugiyama, Siqin Bala, Shintaro Miyazaki, Dongchon Kang, Takashi Ito
Summary: In this study, it was found that dCas9 can impede replication fork progression and destabilize tandem repeats in budding yeast. This effect involves a complex interplay of genetic and biochemical mechanisms to counteract replication fork stalling.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Haibo Yang, Emily M. Lachtara, Xiaojuan Ran, Jessica Hopkins, Parasvi S. Patel, Xueping Zhu, Yao Xiao, Laiyee Phoon, Boya Gao, Lee Zou, Michael S. Lawrence, Li Lan
Summary: This study reveals the crucial role of RNA m5C modification in R-loops in regulating DNA damage repair pathways, promoting TC-HR and suppressing Alt-NHEJ. Simultaneous disruption of TC-HR and Alt-NHEJ exhibits synergistic cytotoxic effects on cancer cells, suggesting a potential strategy for cancer therapy.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Valeria Dolce, Sabrina Dusi, Michele Giannattasio, Chinnu Rose Joseph, Marco Fumasoni, Dana Branzei
Summary: In this study, the connections between Ctf4-mediated processes involved in drug resistance were investigated by conducting a suppressor screen of ctf4 Delta sensitivity to the methylating agent MMS. The findings demonstrate a chromatin-based drug resistance mechanism in which defects in parental histone transfer after replication fork passage impair error-free recombination bypass and lead to up-regulation of TLS-mediated mutagenesis and drug resistance.
GENES & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Anjali Mann, Miguel Angel Ramirez-Otero, Anna De Antoni, Yodhara Wijesekara Hanthi, Vincenzo Sannino, Giorgio Baldi, Lucia Falbo, Anna Schrempf, Sara Bernardo, Joanna Loizou, Vincenzo Costanzo
Summary: POLO plays an important role in repairing DNA double-strand breaks in HR-defective tumors. It is found that POLO processes stalled Okazaki fragments, preventing the accumulation of ssDNA gaps on lagging strands in the absence of RAD51. Inhibition of POLO's DNA polymerase activity leads to unprotected fork gaps, which are cleaved by the MRE11-NBS1-CtIP endonuclease, causing asymmetric single-ended DSBs that impede the survival of BRCA2-defective cells.
Article
Multidisciplinary Sciences
Elodie Hatchi, Liana Goehring, Serena Landini, Konstantina Skourti-Stathaki, Derrick K. DeConti, Fieda O. Abderazzaq, Priyankana Banerjee, Timothy M. Demers, Yaoyu E. Wang, John Quackenbush, David M. Livingston
Summary: Strong connections are found between R-loops, genome instability, and human disease. R-loops play a role in maintaining homeostasis by regulating certain physiological processes, such as the synthesis of antisense transcripts through transcription termination pause sites. A species of single-stranded, DNA-damage-associated small RNA (sdRNA) generated by a BRCA1-RNAi complex promotes DNA repair at transcriptional termination pause sites forming R-loops.
Article
Multidisciplinary Sciences
Julia A. M. Bakx, Andreas S. Biebricher, Graeme A. King, Panagiotis Christodoulis, Kata Sarlos, Anna H. Bizard, Ian D. Hickson, Gijs J. L. Wuite, Erwin J. G. Peterman
Summary: Topoisomerase IIIa is a type 1A topoisomerase that forms a complex with RMI1 and RMI2 called TRR in human cells. In this study, the authors used optical tweezers and fluorescence microscopy to investigate the catalytic steps of TRR. They found that TRR forms an open gate in single-stranded DNA and can bind a second single-stranded or double-stranded DNA molecule, leading to catenation. Interestingly, double-stranded DNA binding increases the gate size and the helicase BLM affects the flexibility of the gate. These findings suggest that TRR-mediated transfer of double-stranded DNA may be more important than previously believed.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Florian Chardon, Aleksandre Japaridze, Hannes Witt, Leonid Velikovsky, Camellia Chakraborty, Therese Wilhelm, Marie Dumont, Wayne Yang, Carlos Kikuti, Stephane Gangnard, Anne-Sophie Mace, Gijs Wuite, Cees Dekker, Daniele Fachinetti
Summary: Chromosome inheritance relies on centromeres, which are regulated through DNA topology. The DNA-binding protein CENP-B compacts centromeres by forming DNA loops, maintaining centromere position and integrity.
Article
Multidisciplinary Sciences
Lulu Bi, Zhenheng Qin, Teng Wang, Yanan Li, Xinshuo Jia, Xia Zhang, Xi-Miao Hou, Mauro Modesti, Xu-Guang Xi, Bo Sun
Summary: In this study, the relationship between helicase oligomerization and functional switching was investigated using single-molecule techniques and Bloom syndrome helicase. It was found that helicases can promptly oligomerize during DNA unwinding and transition from unwinding double-stranded DNA to translocating along single-stranded DNA. This transition allows for the displacement of single-stranded DNA-binding proteins, contributing to the maintenance of genome stability.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Nicole Kaminski, Anne R. Wondisford, Youngho Kwon, Michelle Lee Lynskey, Ragini Bhargava, Jonathan Barroso-Gonzalez, Laura Garcia-Exposito, Boxue He, Meng Xu, Dattatreya Mellacheruvu, Simon C. Watkins, Mauro Modesti, Kyle M. Miller, Alexey Nesvizhskii, Huaiying Zhang, Patrick Sung, Roderick J. O'Sullivan
Summary: In this study, the researchers found that RAD51AP1 interacts with TERRA and utilizes it to generate D and R-loop HR intermediates. RAD51AP1 binds to and stabilizes TERRA-containing R-loops, playing a role in the suppression of TERRA and prevention of TRCs during ALT-HDR. These findings provide insights into the important role of RAD51AP1 in the ALT mechanism and regulation of TERRA.
Article
Biochemistry & Molecular Biology
Noah J. Goff, Manon Breniere, Christopher J. Buehl, Abinadabe J. de Melo, Hana Huskova, Takashi Ochi, Tom L. Blundell, Weifeng Mao, Kefei Yu, Mauro Modesti, Katheryn Meek
Summary: Studies show that inactive Lig4 can promote DNA repair by enhancing the activity of DNA ligase III, with repair products showing both alternative end-joining utilizing micro-homology and joints without micro-homology.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Rohit Prakash, Yashpal Rawal, Meghan R. Sullivan, McKenzie K. Grundy, Helene Bret, Michael J. Mihalevic, Hayley L. Rein, Jared M. Baird, Kristie Darrah, Fang Zhang, Raymond Wang, Tiffany A. Traina, Marc R. Radke, Scott H. Kaufmann, Elizabeth M. Swisher, Raphael Guerois, Mauro Modesti, Patrick Sung, Maria Jasin, Kara A. Bernstein
Summary: In this study, the authors investigated the mutations in RAD51C and found a cluster of variants that lead to HR deficiency and disruption of interactions with other RAD51 paralogs. Structural models were generated to explain the mechanisms of RAD51C interactions and ATP binding. Ovarian cancer patients with variants in this cluster showed longer survival, which may be relevant to the reversion potential of the variants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(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
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
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
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)
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)