Article
Biochemistry & Molecular Biology
Alexandra A. Kuznetsova, Svetlana Senchurova, Alexander A. Ishchenko, Murat Saparbaev, Olga S. Fedorova, Nikita A. Kuznetsov
Summary: The study revealed that structurally different AP endonucleases Nfo and APE1 utilize a common strategy of damage recognition controlled by enzyme conformational transitions after initial DNA binding. Local stability of the DNA duplex near the lesion affects catalytic-complex formation and DNA cleavage efficacy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
William Rostain, Theophile Grebert, Danylo Vyhovskyi, Paula Thiel Pizarro, Gatwa Tshinsele-Van Bellingen, Lun Cui, David Bikard
Summary: Off-target binding of Cas9 to essential gene promoters can occur with as little as 4 nt of identity in the PAM-proximal sequence, leading to toxicity. This potential for off-target effects must be considered in CRISPR-Cas experiments in bacteria.
NUCLEIC ACIDS RESEARCH
(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)
Article
Biochemistry & Molecular Biology
Grant A. Rybnicky, Nicholas A. Fackler, Ashty S. Karim, Michael Kopke, Michael C. Jewett
Summary: Researchers have developed a software package called Spacer2PAM to predict and guide the experimental determination of functional PAM sequences for CRISPR-Cas systems. This package can generate targeted PAM libraries small enough to screen in difficult-to-transform organisms, thereby facilitating the use of endogenous CRISPR-Cas systems in industrial biotechnology and synthetic biology.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Jungmin Yoo, Donghun Lee, Hyeryeon Im, Sangmi Ji, Sanghoon Oh, Minsang Shin, Daeho Park, Gwangrog Lee
Summary: The study reveals that during base excision repair, Exonuclease III creates a gap and transient ssDNA loop through an AP site anchor-based mechanism. The size of the gap is determined by the rigidity of the ssDNA loop and the duplex stability of the DNA.
Article
Biochemistry & Molecular Biology
Katherine A. Paulin, David Cortez, Brandt F. Eichman
Summary: AP sites in DNA are common forms of DNA damage, and the replication-associated AP site repair protein HMCES plays a role in the repair of AP site-derived interstrand DNA cross-links. This study provides insights into the mechanisms of DPC formation and resolution by HMCES.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Jonathan Dorival, Brandt F. Eichman
Summary: This study reveals the nuclease activities of human TatD paralogs TATDN1 and TATDN3, which include both 3'-5' exonuclease activity and AP endonuclease activity. The two nuclease activities are exhibited in different types of DNA and are regulated by divalent metal cofactors. The study also shows that the three E. coli TatD paralogs also possess AP endonuclease activity.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Kazuki Kato, Sae Okazaki, Cian Schmitt-Ulms, Kaiyi Jiang, Wenyuan Zhou, Junichiro Ishikawa, Yukari Isayama, Shungo Adachi, Tomohiro Nishizawa, Kira S. Makarova, Eugene V. Koonin, Omar O. Abudayyeh, Jonathan S. Gootenberg, Hiroshi Nishimasu
Summary: The type III-E CRISPR-Cas7-11 effector can catalyze crRNA-guided RNA cleavage by binding crRNA and Csx29, and the binding of tgRNA induces conformational changes in Csx29. Csx29 cleaves Csx30 through a tgRNA-dependent pathway, resulting in the generation of toxic protein fragments and growth arrest, which is regulated by Csx31. Csx30 modulates the cellular response to infection by binding Csx31 and the associated sigma factor RpoE. Additionally, the Cas7-11-Csx29-Csx30 system has been engineered for programmable RNA sensing in mammalian cells.
Article
Biochemistry & Molecular Biology
Andras Talas, Krisztina Huszar, Peter Istvan Kulcsar, Julia K. Varga, Eva Varga, Eszter Toth, Zsombor Welker, Gergely Erdos, Peter Ferenc Pach, Agnes Welker, Zoltan Gyorgypal, Gabor E. Tusnady, Ervin Welker
Summary: Detailed target-selectivity information and experiment-based efficacy prediction tools are primarily available for Streptococcus pyogenes Cas9 (SpCas9). One obstacle to develop such tools is the rarity of accurate data. The researchers have developed a method called 'Self-targeting sgRNA Library Screen' (SLS) to analyze the activity of Cas9 nucleases in bacteria, providing a more affordable and efficient alternative to current approaches. The algorithm created for predicting the activity of SpCas9-HF1 matches the accuracy of existing tools.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Nada Farag, Rosanna Mattossovich, Rosa Merlo, Lukasz Nierzwicki, Giulia Palermo, Alessandro Porchetta, Giuseppe Perugino, Francesco Ricci
Summary: A new class of DNA-based nanoswitches capable of undergoing conformational changes upon enzymatic repair, leading to changes in fluorescent signals, has been presented. These nanoswitches, designed to fold into optically active structures after enzymatic demethylation, can serve as specific substrates for various methyltransferase enzymes and aid in screening potential inhibitors.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Kyung W. Yoo, Manish Kumar Yadav, Qianqian Song, Anthony Atala, Baisong Lu
Summary: Fusing Escherichia coli DNA polymerase I or the Klenow fragment to Cas9 increases the frequencies of 1-bp deletions and decreases >1-bp deletions or insertions. This strategy also greatly reduces the generation of long deletions (>2 kb) and increases templated insertions. Targeting DNA polymerase to double-strand breaks does not increase off-targets or base substitution rates, but improves editing efficiency in primary cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Liang Chen, Mengjia Hong, Changming Luan, Hongyi Gao, Gaomeng Ru, Xinyuan Guo, Dujuan Zhang, Shun Zhang, Changwei Li, Jun Wu, Peyton B. Randolph, Alexander A. Sousa, Chao Qu, Yifan Zhu, Yuting Guan, Liren Wang, Mingyao Liu, Bo Feng, Gaojie Song, David R. Liu, Dali Li
Summary: This article reports on a class of gene editors that can efficiently convert adenine bases and successfully achieve high-efficiency repair of pathogenic mutations in mouse embryos and human cell lines. This technology brings new possibilities for the capabilities and applications of gene editing.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Wen Wei, Wei-Chin Ho, Megan G. Behringer, Samuel F. Miller, George Bcharah, Michael Lynch
Summary: Ecological and demographic factors can significantly shape the evolution of microbial populations, including the mutation rate. This study provides direct evidence that the mutation rate of Escherichia coli evolves rapidly in response to different transfer volumes and resource-replenishment intervals.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Xiaoshen Wang, Guimei Yu, Yanan Wen, Qiyin An, Xuzichao Li, Fumeng Liao, Chengwei Lian, Kai Zhang, Hang Yin, Yong Wei, Zengqin Deng, Heng Zhang
Summary: The type III-E CRISPR-Cas systems are newly discovered adaptive immune systems in prokaryotes that can cleave target RNA using a single Cas7-11 protein. This study demonstrated the functional linkage between the RNase and protease activities in type III-E systems and elucidated the mechanisms underlying the target RNA-guided proteolytic activity of Csx29. The findings will guide further developments leveraging this simple RNA targeting system for RNA and protein-related applications.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Xiaoying Wei, Zhishuo Wang, Caroline Hinson, Kun Yang
Summary: The study found that human tyrosyl-DNA phosphodiesterase 1 (TDP1), AP endonuclease 1 (APE1), and three-prime repair exonuclease 1 (TREX1) can repair 3'-PUA-protein crosslinks, providing new repair pathways for maintaining genome integrity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Sandrine Ragu, Nathalie Droin, Gabriel Matos-Rodrigues, Aurelia Barascu, Sylvain Caillat, Gabriella Zarkovic, Capucine Siberchicot, Elodie Dardillac, Camille Gelot, Josee Guirouilh-Barbat, J. Pablo Radicella, Alexander A. Ishchenko, Jean-Luc Ravanat, Eric Solary, Bernard S. Lopez
Summary: In human primary cells, a noncanonical cellular response specific to nonblocking replication stress is discovered. This response generates reactive oxygen species (ROS) and activates detoxification genes. ROS are produced by DUOX1/DUOX2 and controlled by NF-kappa B.
CELL DEATH AND DIFFERENTIATION
(2023)
Article
Genetics & Heredity
Artemiy S. Bakman, Aleksandra A. Kuznetsova, Lyudmila V. Yanshole, Alexander A. Ishchenko, Murat Saparbaev, Olga S. Fedorova, Nikita A. Kuznetsov
Summary: The base excision repair (BER) pathway involves a step-by-step process in which DNA glycosylases and AP endonucleases work together to repair damaged DNA. This study aimed to verify the passing-the-baton model of DNA intermediates transfer between enzymes by creating an experimental system. The findings of the study confirm that Pol beta plays a key role in coordinating the activities of APE1 and Pol beta in the initial steps of BER.
Article
Biochemistry & Molecular Biology
Olga A. Kladova, Timofey E. Tyugashev, Elena S. Mikushina, Nikita O. Soloviev, Nikita A. Kuznetsov, Daria S. Novopashina, Aleksandra A. Kuznetsova
Summary: The expression of DNA polymerase beta (Pol beta) is essential for the cell's response to DNA damage. Mutations in Pol beta can lead to cancer, neurodegenerative diseases, or premature aging. Some polymorphic variants in the Pol beta sequence reduce the efficiency of DNA repair, increasing the frequency of mutations in the genome. In this study, two polymorphic variants (G118V and R149I) were found to affect Pol beta's DNA-binding region, weakening its ability to maintain base excision repair efficiency.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Anna Yudkina, Nikita A. Bulgakov, Daria Kim, Svetlana Baranova, Alexander A. Ishchenko, Murat K. Saparbaev, Vladimir V. Koval, Dmitry O. Zharkov
Summary: AP sites are DNA lesions that can trap DNA-bound proteins, forming DNA-protein cross-links called APPXLs. The fate of APPXLs, however, is unclear. In this study, we synthesized two in vitro models of APPXLs using DNA glycosylases Fpg and OGG1. These APPXLs strongly blocked various DNA polymerases, but were efficiently hydrolyzed by specific AP endonucleases. Our findings suggest that the BER pathway may be responsible for removing APPXLs in bacterial and yeast cells.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Artemiy S. Bakman, Stanislav S. Boichenko, Aleksandra A. Kuznetsova, Alexander A. Ishchenko, Murat Saparbaev, Nikita A. Kuznetsov
Summary: Base excision repair (BER) is an important system for maintaining genome stability by repairing DNA lesions. It involves multiple enzymes, including DNA glycosylases, endonucleases, DNA polymerase beta, and DNA ligase. Protein-protein interactions play a crucial role in coordinating BER, but their mechanisms and roles are poorly understood.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Anatoly A. Bulygin, Victoria N. Syryamina, Aleksandra A. Kuznetsova, Darya S. Novopashina, Sergei A. Dzuba, Nikita A. Kuznetsov
Summary: This study investigated the molecular events in the process of damage recognition by Apurinic/apyrimidinic endonuclease 1 (APE1) through DEER spectroscopy and kinetic analysis. The results showed that specific mutants of APE1 had higher activity in recognizing and repairing damaged DNA, revealing the factors that affect its substrate specificity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Anastasiia T. T. Davletgildeeva, Timofey E. E. Tyugashev, Mingxing Zhao, Nikita A. A. Kuznetsov, Alexander A. A. Ishchenko, Murat Saparbaev, Aleksandra A. A. Kuznetsova
Summary: ABH2 is an important protein involved in DNA repair and the oxidation of 5-methylcytosine. This study investigated the role of active-site amino acid residues in the substrate specificity of ABH2 and revealed their significant impact on the catalytic activity of the enzyme.
Review
Optics
Nikita A. Kuznetsov
Summary: This review presents a comprehensive method for studying DNA repair enzymes, focusing on DNA glycosylases and apurinic/apyrimidinic endonuclease. The method employs kinetic, thermodynamic, and mutational analyses to investigate the interaction and conformational changes between enzymes and DNA in real time.
Article
Biotechnology & Applied Microbiology
Aleksandra A. Kuznetsova, Ksenia S. Bedritskikh, Anatoly A. Bulygin, Nikita A. Kuznetsov
Summary: In this study, His-tagged Mau DNA polymerase was successfully expressed and purified. The optimal conditions for its polymerase activity were observed at 30°C, pH 8.4-8.8, 2-10 mM MgCl2, and 10-40 mM KCl. The kinetic parameters for correct and incorrect dNTP incorporation as well as DNA-binding affinity were determined. Additionally, the enzyme was found to have 5'→3' and 3'→5' exonuclease activities associated with the main polymerase activity.
FERMENTATION-BASEL
(2023)
Review
Biotechnology & Applied Microbiology
Irina V. Alekseeva, Nikita A. Kuznetsov
Summary: Restriction endonucleases are important components of restriction-modification systems in bacteria, providing protection against foreign DNA. Type II restriction enzymes, which specifically recognize and cleave DNA sequences of 4-8 bp, are the most extensively studied. The discovery and design of new restriction endonucleases with high specificity and unique properties will expand the applications of biotechnology and genetic engineering.
FERMENTATION-BASEL
(2023)
Review
Biotechnology & Applied Microbiology
Aleksandra A. Kuznetsova, Nikita A. Kuznetsov
Summary: DNA-dependent DNA polymerases have been extensively studied and are widely used in biotechnological and diagnostic applications. Understanding their mechanisms and improving their properties are crucial for developing new enzymes for various applications.
BIOENGINEERING-BASEL
(2023)
