Article
Multidisciplinary Sciences
Anthony D. Rish, Zhangfei Shen, Zhenhang Chen, Nan Zhang, Qingfei Zheng, Tian-Min Fu
Summary: This study reports two cryo-EM structures of RuvB, revealing the mechanism of HJ branch migration. RuvB assembles into a spiral staircase, ring-like hexamer, enveloping double-stranded DNA. The asymmetric assembly of RuvB explains the 6:4 stoichiometry of the RuvB/RuvA complex in coordinating HJ migration in bacteria. These findings provide a mechanistic understanding of HJ branch migration facilitated by RuvB, which may be universally shared by prokaryotic and eukaryotic organisms.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Binh Nguyen, Min Kyung Shinn, Elizabeth Weiland, Timothy M. Lohman
Summary: Research reveals that PriC can activate both the monomeric and dimeric helicase activity of Rep, confirming PriC as an important processivity factor for Rep and highlighting its role in DNA unwinding.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Tribhuwan Yadav, Jia-Min Zhang, Jian Ouyang, Wendy Leung, Antoine Simoneau, Lee Zou
Summary: This study reveals that the telomere non-coding RNA TERRA can form dynamic telomeric R-loops and contribute to ALT activity. This process is mediated by the formation of G-quadruplexes (G4s), independent of RAD52. The findings shed light on the mechanism of the R-loop to D-loop switch in the ALT pathway and provide new insights into the function and homeostasis of telomeres.
Article
Oncology
Alizhah J. Watson, Michaela L. Shaffer, Renee A. Bouley, Ruben C. Petreaca
Summary: This study investigated the relationship between mutations in the FBH1 gene and mutations in other DNA damage repair genes, such as BRCA2. The findings suggest that FBH1 mutations co-occur with mutations in BRCA2 and other genes, and that certain mutations destabilize the FBH1 protein structure. Overall, this research highlights the contribution of mutations in DNA damage repair genes to cellular transformation and immortalization.
Article
Biochemistry & Molecular Biology
Min Kyung Shinn, Alexander G. Kozlov, Timothy M. Lohman
Summary: Escherichia coli RecO is a recombination mediator protein that interacts with RecR to play a crucial role in homologous recombination. Analytical ultracentrifugation studies reveal a pH-dependent dimer-tetramer equilibrium for RecR and positive cooperativity between RecO and RecR resulting in the formation of RecR(4)O and RecR(4)O(2) complexes. Binding of RecO to SSB-Ct peptides induces an allosteric effect, shifting the equilibrium towards RecR(4)O complex formation. These findings suggest a mechanism for how SSB binding influences the distribution of RecOR complexes to facilitate homologous recombination initiation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Swagata Halder, Lepakshi Ranjha, Angelo Taglialatela, Alberto Ciccia, Petr Cejka
Summary: SMARCAL1, ZRANB3 and HLTF are important factors in remodeling replication forks to maintain genome stability. RAD51 and the RAD51 paralog complex have recombination-independent functions in fork reversal, possibly through physical interactions with SMARCAL1 and ZRANB3.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Anupam Singh, Gayatri Patel, Smita S. Patel
Summary: Strand exchange between homologous nucleic acid sequences is essential for DNA repair, recombination, and genome editing. In this study, the authors demonstrate that human mitochondrial DNA helicase Twinkle can accelerate the spontaneous toehold-mediated strand displacement (TMSD) reaction, leading to faster response times.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Natalia S. Adler, Leila A. Cababie, Carolina Sarto, Claudio N. Cavasotto, Leopoldo G. Gebhard, Dario A. Estrin, Andrea Gamarnik, Mehrnoosh Arrar, Sergio B. Kaufman
Summary: This article presents a detailed mechanistic analysis of the product release stage in the catalytic cycle of the dengue virus NS3h. The study supports a model in which ATP hydrolysis proceeds through an ordered sequential mechanism involving the NS3h-Pi-ADP ternary complex intermediate. The results indicate that a novel open-loop conformation plays an important role in the product release stage of NS3h.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Linxuan Hao, Rui Zhang, Timothy M. Lohman
Summary: E. coli RecBCD, a helicase/nuclease involved in double stranded (ds) DNA break repair, binds to a DNA end and melts several base pairs using its binding free energy. The interactions with ssDNA and structural characteristics of RecBCD-DNA complexes were studied, revealing conformational heterogeneities in RecB(Nuc) and RecD. The extent of DNA melting regulates initiation of helicase activity within RecBCD complexes.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Alicia K. Byrd, Emory G. Malone, Lindsey Hazeslip, Maroof Khan Zafar, David K. Harrison, Matthew D. Thompson, Jun Gao, Senthil K. Perumal, John C. Marecki, Kevin D. Raney
Summary: Helicases are molecular motors that unwind double-stranded nucleic acids using ATP hydrolysis. They can also remove proteins from nucleic acids.
Article
Optics
Seiichiro Izawa, Masahiro Hiramotot
Summary: A novel upconversion system with heterojunctions of organic semiconductors has been reported. The system achieves photon conversion through charge separation and recombination, with an efficiency two orders of magnitude higher than traditional systems. This allows for efficient photon upconversion from near-infrared to visible light on flexible organic thin films under weak LED-induced excitation, visible to the naked eye.
Article
Multidisciplinary Sciences
Shikai Jin, Carlos Bueno, Wei Lu, Qian Wang, Mingchen Chen, Xun Chen, Peter G. Wolynes, Yang Gao
Summary: The study used AWSEM and 3SPN.2C force fields to simulate the translocation of gp4 helicase. The research found that ATP at the subunit interface stabilizes subunit-subunit interactions and inhibits translocation, whereas hydrolysis of ATP enables subunit translocation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Tianpeng Zhang, Yashpal Rawal, Haoyang Jiang, Youngho Kwon, Patrick Sung, Roger A. Greenberg
Summary: Break-induced telomere synthesis (BITS) is a RAD51-independent mechanism that contributes to alternative lengthening of telomeres. This process utilizes a minimal replisome comprising PCNA and DNA polymerase-d to perform conservative DNA repair synthesis over long stretches. The response of this repair synthesis to complex secondary DNA structures and whether additional DNA repair events are orchestrated by the break-induced replisome remain unclear. In this study, the telomeric DNA damage response proteome during BITS was captured using a combination of synchronous double-strand break induction and proteomics of isolated chromatin segments (PICh). The findings revealed a replication stress-dominant response, with repair synthesis-driven DNA damage tolerance signaling through RAD18-dependent PCNA ubiquitination. The SNM1A nuclease was identified as the major effector of ubiquitinated PCNA-dependent DNA damage tolerance, playing a critical role in resection-dependent lesion bypass in mammalian cells.
Article
Chemistry, Multidisciplinary
Yihuai Huang, Bo Huang, Huichao Zhang, Xinmiao Lu, Yu Zhang, Xiumin Gao, Songlin Zhuang
Summary: The study focuses on the optical properties of nitrogen-doped carbon quantum dot films using spectro-electrochemical methods, revealing a distinctive photoluminescence enhancement phenomenon with both positive and negative electrochemical potential sweeps. Positive potential has a greater effect on photoluminescence enhancement than negative potential. By increasing electrolyte fluidity with argon gas bubbling, a low hysteresis reversible electrochemistry regulation of the photoluminescence spectrum can be achieved.
Article
Chemistry, Medicinal
Jia-Li Tu, Bi-Han Wu, Heng-Bo Wu, Jia-En Wang, Zi-Lin Zhang, Kun-Yu Gao, Lu-Xuan Zhang, Qin-Rui Chen, Ying-Chen Zhou, Jia-Heng Tan, Zhi-Shu Huang, Shuo-Bin Chen
Summary: A new series of quinazolinone derivatives with N3-substitution was designed and synthesized to improve the anticancer activity. Compound 21 was identified as a promising BLM inhibitor, which effectively suppressed the proliferation and invasion of CRC cells, along with cell cycle arrest and apoptosis.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)