Article
Genetics & Heredity
Ellen B. Higgs, Roger Godschalk, Sabine A. S. Langie, Frederik-Jan van Schooten, Nikolas J. Hodges
Summary: Reactive oxygen species formation and oxidative damage to DNA are common events in cells, which can be dysregulated in pathological conditions. The study on Ogg1-null cells revealed that upregulation of components in NER and Neil3 pathways play important roles in preventing genomic accumulation of 8-oxoG.
Article
Oncology
Jiajing Niu, Jiamei Wang, Qi Zhang, Zhihua Zou, Yushuang Ding
Summary: The study revealed that sublethal doses of cinobufagin suppressed the viability of cancer cells by inducing oxidative stress, leading to DNA damage and cell cycle regulation that ultimately resulted in the induction of apoptosis.
CANCER CELL INTERNATIONAL
(2021)
Article
Chemistry, Analytical
Elizabeth R. LaFave, Michael D. Tarpey, Nicholas P. Balestrieri, Espen E. Spangenburg, Eli G. Hvastkovs
Summary: BRCA1 gene mutations impact skeletal muscle functions, resulting in loss of muscle quality. Electrochemical and LC-MS/MS analysis of mtDNA and nDNA extracted directly from mouse skeletal muscles revealed reduced guanine content and elevated oxidative damage in KO mice.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Dorsa Moezzi, Yifei Dong, Rajiv W. Jain, Brian M. Lozinski, Samira Ghorbani, Charlotte D'Mello, V. Wee Yong
Summary: Oxidative stress can cause tissue injury in the central nervous system in neurological disorders such as multiple sclerosis. To combat this, antioxidant enzymes may be upregulated, and it has been found that the elevation of these enzymes in mouse models of neurodegeneration is similar to their expression in human diseases like MS.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Jialuo Jiang, Yan Huang, Wenlin Wang, Chen Sun, Qiuyan Liu, Yan Chen, Tingting Hu, Xiaoju Ma, Cheng Peng, Yuntong Ma, Shukun Liu, Chaolong Rao
Summary: Zanthoxylum armatum DC, a traditional medicinal plant widely used in clinical treatment and disease prevention, has been reported to induce DNA damage and G1/S cell cycle arrest in BRL 3A cells through triggering oxidative stress. This study provides evidence for its potential development as an antitumor drug via activation of ATM/Chk2 pathway.
JOURNAL OF ETHNOPHARMACOLOGY
(2022)
Article
Cell Biology
Letizia Granieri, Federica Marocchi, Marine Melixetian, Neda Mohammadi, Paola Nicoli, Alessandro Cuomo, Tiziana Bonaldi, Stefano Confalonieri, Federica Pisati, Giuseppina Giardina, Giovanni Bertalot, Daniela Bossi, Luisa Lanfrancone
Summary: This study identifies USP7 as a regulator of melanoma and shows that its downregulation induces cellular senescence, inhibiting tumor growth and proliferation. Transcriptomic and proteomic analysis reveals the targets and networks affected by USP7 depletion. RRM2 is identified as a target of USP7 and is regulated by USP7 during the S phase of the cell cycle. Combination therapy using a USP7 inhibitor and a histone deacetylase (HDAC)/LSD1 inhibitor eliminates senescent cells.
Article
Biochemistry & Molecular Biology
Chao Dong, Liwei An, Cheng-han Yu, Michael S. Y. Huen
Summary: The DYRK1B kinase plays a crucial role in maintaining rDNA stability, nucleolar reorganization, and inhibition of rRNA synthesis. Inhibition of DYRK1B results in sustained nucleolar transcription, hypersensitivity to DSBs at rDNA arrays, and requirement for DSB repair and rDNA copy number maintenance. These findings highlight the importance of DYRK1B as a key signaling intermediate in coordinating DSB repair and rDNA transcriptional activities within the nucleolus.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Changjiang Fan, Xinyue Meng, Wei Yang, Peiyan Wang, Wenguang Chang, Peifeng Li, Jianxun Wang
Summary: A labeling chemistry-based method, APSC-8-oxoGua-seq, is developed for sequencing 8-oxoGua in the microRNA transcriptome. The method uses N-(3-azidopropyl)-spermine-5-carboxamide (APSC) for selective labeling of 8-oxoGua, allowing the conjugation of a cleavable linker via the click reaction for 8-oxoGua pull-down and sequencing. APSC-8-oxoGua-seq enables identification of 8-oxoGua at single-base resolution.
CHEMICAL COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Ke Shi, Nicholas H. Moeller, Surajit Banerjee, Jennifer L. McCann, Michael A. Carpenter, Lulu Yin, Ramkumar Moorthy, Kayo Orellana, Daniel A. Harki, Reuben S. Harris, Hideki Aihara
Summary: EndoQ repairs DNA mutations caused by deamination through cleaving the DNA backbone with selectivity depending on DNA distortion and hydrogen bonds with deaminated bases. The enzyme clamps down on a sharply bent DNA substrate with a zinc-binding and C-terminal helical domain swing motion, shaping a deep active-site pocket for accommodating the extruded deaminated base.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Juntaek Oh, Jun Xu, Jenny Chong, Dong Wang
Summary: This review summarizes recent research progress on the molecular basis of transcriptional pausing and stalling caused by different types of obstacles, and discusses new insights into Pol II-mediated lesion recognition and the roles of CSB in TC-NER.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2021)
Review
Biochemistry & Molecular Biology
Vladimir Shafirovich, Nicholas E. Geacintov
Summary: Base excision repair (BER) and nucleotide excision repair (NER) are two major mechanisms that remove DNA lesions. Experimental evidence shows that oxidatively generated DNA lesions can be repaired by both competitive BER and NER pathways. The interaction between BER and NER pathways in repairing oxidatively generated DNA lesions is crucial for understanding DNA repair mechanisms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Michel Fasnacht, Norbert Polacek
Summary: Since the great oxidation event, Earth's cellular life forms have had to deal with reactive oxygen species (ROS) affecting biomolecules and cellular metabolism. Increased ROS levels in the biosphere represent growing stress and shape species evolution. Systems have evolved to remove ROS and repair damage, but oxidative stress occurs if ROS surpass the cell's capacity.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Iwona Bukowska-Osko, Dorota Sulejczak, Katarzyna Kaczynska, Patrycja Kleczkowska, Karol Kramkowski, Marta Popiel, Ewa Wietrak, Pawel Kowalczyk
Summary: Structural abnormalities can cause DNA modifications, leading to various diseases including cancer. Cells defend and repair damaged genetic material through lactoferrin, an endogenous protein with antibacterial, antiviral, antifungal, and anticancer properties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Food Science & Technology
Robin Mesnage, Scarlett Ferguson, Inger Brandsma, Nynke Moelijker, Gaonan Zhang, Francesca Mazzacuva, Anna Caldwell, John Halket, Michael N. Antoniou
Summary: The co-formulant POE-15 tallow amine (POE-15) and the active ingredient glyphosate in herbicides have been found to be cytotoxic, causing cell necrosis and oxidative stress. The study highlights the importance of comprehensive testing of both co-formulants and active ingredients of commercial pesticides to ensure better regulation and protection of public health and the environment.
FOOD AND CHEMICAL TOXICOLOGY
(2022)
Article
Multidisciplinary Sciences
Michael Schmalz, Xiao- Xuan Liang, Ines Wieser, Caroline Gruschel, Lukas Muskalla, Martin Thomas Stoeckl, Roland Nitschke, Norbert Linz, Alfred Leitenstorfer, Alfred Vogel, Elisa Ferrando-May, Wei Yang
Summary: Understanding and predicting the outcome of light-DNA interaction is crucial for DNA repair and radiotherapy. This study combines laser microirradiation, imaging, and modeling to investigate the damage pathways in live cells. The results show that photochemical damage dominates at 515 nm, while electron-mediated damage dominates at wavelengths ≥620 nm. The study provides a conceptual framework for interpreting the wavelength-dependent DNA damage induced by laser and electron interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Rodrigo Galindo-Murillo, Lauren Winkler, Jingwei Ma, Fatjon Hanelli, Aaron M. Fleming, Cynthia J. Burrows, Thomas E. Cheatham
Summary: This study investigates the specific ligand recognition of abasic sites in G-quadruplex using riboflavin and guanine as examples. The results show that riboflavin can only stabilize abasic site-containing G-quadruplex in the presence of an adjacent OG-modified base.
Editorial Material
Chemistry, Organic
Cynthia J. Burrows, Jason B. Harper, Wolfram Sander, Dean J. Tantillo
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Letter
Biology
Cynthia Burrows, Aaron Fleming
INTERNATIONAL JOURNAL OF RADIATION BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Aaron M. Fleming, Cynthia J. Burrows
Summary: Direct RNA sequencing using a commercial nanopore platform was utilized to sequence RNA molecules with uridine (U), pseudouridine (psi) or N1-methylpseudouridine (m(1)psi) in various contexts. The base calling data for psi and m(1)psi differed from U, allowing their detection. The study examined the selection of UTP, psi TP, or m(1)psi TP by T7 RNA polymerase in different adjacent sequence contexts, finding a significant dependency on sequence context.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Juntaek Oh, Michiko Kimoto, Haoqing Xu, Jenny Chong, Ichiro Hirao, Dong Wang
Summary: This study reveals the mechanism of how T7 RNA polymerase recognizes unnatural base pairs, providing a theoretical basis for synthesizing RNA molecules with synthetic modifications and unnatural base pairs.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Shereen A. Howpay A. Manage, Judy Zhu, Aaron M. M. Fleming, Cynthia J. J. Burrows
Summary: This study focused on the topological properties of AP-bearing G4 folds and their impact on APE1 interaction. The results showed that APE1 preferentially binds to telomere sequences with hybrid or basket folds, while the binding to promoter G4s is weaker. These findings suggest that the topological features of G4s in gene promoters are critical for APE1 recognition and gene regulation.
RSC CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Aaron M. Fleming, Praneeth Bommisetti, Songjun Xiao, Vahe Bandarian, Cynthia J. Burrows
Summary: This study successfully identified the signatures of almost all modifications in the 16S and 23S rRNA strands of Escherichia coli using nanopore direct RNA sequencing. Furthermore, the study also revealed the impact of metabolic and cold-shock stress on rRNA modifications.
ACS CHEMICAL BIOLOGY
(2023)
Editorial Material
Chemistry, Multidisciplinary
Jillian M. Buriak, Deji Akinwande, Natalie Artzi, C. Jeffrey Brinker, Cynthia Burrows, Warren C. W. Chan, Chunying Chen, Xiaodong Chen, Manish Chhowalla, Lifeng Chi, William Chueh, Cathleen M. Crudden, Dino Di Carlo, Sharon C. Glotzer, Mark C. Hersam, Dean Ho, Tony Y. Hu, Jiaxing Huang, Ali Javey, Prashant V. Kamat, Il-Doo Kim, Nicholas A. Kotov, T. Randall Lee, Young Hee Lee, Yan Li, Luis M. Liz-Marzan, Paul Mulvaney, Prineha Narang, Peter Nordlander, Rahmi Oklu, Wolfgang J. Parak, Andrey L. Rogach, Mathieu Salanne, Paolo Samori, Raymond E. Schaak, Kirk S. Schanze, Tsuyoshi Sekitani, Sara Skrabalak, Ajay K. Sood, Ilja K. Voets, Shu Wang, Shutao Wang, Andrew T. S. Wee, Jinhua Ye
Editorial Material
Cell Biology
Aaron M. Fleming, Cynthia J. Burrows
Summary: In the study of DNA modifications, the disciplines of epigenetics and of DNA damage and repair have traditionally been separate. However, it is now recognized that epigenetic modifications require DNA repair pathways for erasure and recent discoveries have shown that oxidative DNA damage can affect gene expression, blurring the lines between these two areas.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Review
Chemistry, Multidisciplinary
Cynthia J. Burrows, Aaron M. Fleming
Summary: This article discusses the reaction mechanism of bisulfite with pseudouridine and introduces a chemical method for sequencing modified bases in the epitranscriptome. Through the study of structure and mechanism, a sequencing reaction specific to pseudouridine was designed, and psi sites were mapped using nanopore direct RNA sequencing.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Aaron M. Fleming, Carla A. Omaga, Cynthia J. Burrows
Summary: Oxidative stress leads to the oxidation of G nucleotides in the genome and affects the expression of the NEIL3 gene. The study found that the modified G-quadruplex (G4) can stall DNA polymerases, and the concentration of Mg2+ and the location of the modification have an impact on this process.
Article
Chemistry, Multidisciplinary
Songjun Xiao, Aaron M. Fleming, Cynthia J. Burrows
Summary: The previously reported click-code-seq method has been redesigned to enable the sequencing of many damage types by making simple changes to the protocol (i.e., click-code-seq v2.0), which could aid in understanding the cellular outcomes of oxidative damage to DNA nucleotides.
CHEMICAL COMMUNICATIONS
(2023)