Article
Biochemistry & Molecular Biology
Daryl M. Gohl, Benjamin Auch, Amanda Certano, Brice LeFrancois, Anne Bouevitch, Evgueni Doukhanine, Christina Fragel, Jean Macklaim, Emily Hollister, John Garbe, Kenneth B. Beckman
Summary: Proofreading polymerases have the ability to correct errors during DNA replication and edit PCR primers to match template sequences. The editing activity can be measured and compared using synthetic DNA standards, revealing editing extent and effects of different polymerases and cycling conditions. Additionally, primer editing can be tuned by incorporating phosphorothioate linkages and has the potential to rescue mismatches in 16S rRNA gene-targeting primers in microbiome analysis.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Materials Science, Multidisciplinary
Jingjing Liu, Bin Liu
Summary: Organelles play vital roles in cellular communication and their dysfunction leads to various pathological conditions. Exosomes, as extracellular vesicles, have been utilized as natural vehicles for drug delivery. Material-assisted engineering of intracellular organelles using different strategies has gained significant research interest. This Review highlights the potential of modifying organelles with man-made and natural materials for diverse applications.
ACS MATERIALS LETTERS
(2023)
Review
Chemistry, Multidisciplinary
Liangcan He, Jing Mu, Oleg Gang, Xiaoyuan Chen
Summary: DNA serves as a versatile tool for engineering and self-assembling nanostructures, enhancing scalability, programmability, and functionality. This has opened doors for various biomedical applications such as biosensing, bioimaging, drug delivery, and disease therapy. Recent advancements in DNA nanostructure design and construction, including conjugated nanoparticle systems, DNA-based clusters, and DNA origami-templated assemblies, have further expanded its potential in the field.
Review
Neurosciences
Xiaoling Li, Guanghui Cao, Xiaokang Liu, Tie-Shan Tang, Caixia Guo, Hongmei Liu
Summary: This review summarizes the relationship between neurodegenerative diseases and aging with reactive oxygen species (ROS) or other intracellular damaging agents that challenge the genome integrity of neurons. It highlights the important role of DNA and RNA polymerases in sensing and repairing damages, and their diverse functions depending on the cell cycle phase and damage types. The review discusses the biological relevance of polymerases and their interactors with neuronal degeneration observed in patients with hereditary diseases, as well as the vicious cycle of trinucleotide repeat (TNR) and impaired DNA repair pathway.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2022)
Article
Multidisciplinary Sciences
Jianpu Tang, Xuemei Jia, Qian Li, Zhen Cui, Aiqi Liang, Bin Ke, Dayong Yang, Chi Yao
Summary: In this study, a DNA-based hydrogel was developed for the specific and nondestructive separation of exosomes from complex biological media. The separated exosomes were used for breast cancer detection and the therapeutics of myocardial infarction. The DNA hydrogel showed promising potential in the classification of breast cancer patients and the repair of infarcted myocardium in rat models.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Kok Zhi Lee, Juya Jeon, Bojing Jiang, Shri Venkatesh Subramani, Jingyao Li, Fuzhong Zhang
Summary: Protein hydrogels, with their biocompatibility, biodegradability, and versatility for modifications, have become attractive materials for various medical applications. Recent advancements in protein engineering, synthetic biology, and material science have allowed for precise control over protein sequences, hydrogel structures, and mechanical properties, expanding the range of biomedical applications for protein hydrogels. This review focuses on recent progress in protein hydrogels, particularly those produced by microorganisms, discussing different formation strategies, associated properties, and biomedical applications categorized by protein sequence origins. The current challenges and future opportunities in engineering protein-based hydrogels are also discussed, aiming to inspire material innovation and the development of advanced protein hydrogels with desired properties for diverse biomedical applications.
Review
Biotechnology & Applied Microbiology
Liuru Fang, Chen Shi, Yuhua Wang, Zuzhao Xiong, Yumei Wang
Summary: DNA nanoparticles show great potential for various biological applications, such as advanced treatments and diagnostic tests. Their precise modification capabilities make them ideal for targeted delivery and diagnostic instruments. This paper discusses the scalability, programmability, and functionality of DNA nanomaterials, highlighting their potential in disease diagnosis and treatment. Challenges, including improving scalability and reliability, as well as ensuring safety in clinical applications, are addressed, along with the progress and prospects of DNA nanotechnology for biomedical applications.
JOURNAL OF NANOBIOTECHNOLOGY
(2023)
Review
Chemistry, Multidisciplinary
Xiaoyi Ma, Xiaoqiang Li, Gangyin Luo, Jin Jiao
Summary: This review highlights the importance of DNA-modified gold nanoparticles (DNA-AuNPs) in biomedical applications and their potential uses in various fields. By summarizing the methods for immobilizing DNA strands on the surface of AuNPs and discussing representative studies, the advantages and future challenges of DNA-AuNPs are revealed.
FRONTIERS IN CHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Ke Li, Yanfei Liu, Beibei Lou, Yifu Tan, Liwei Chen, Zhenbao Liu
Summary: In the past decades, DNA has been widely utilized in the field of nanostructures due to its programmable properties. This review presents different strategies for the functionalization of DNA on nanoparticle surfaces and discusses the roles of DNA in the assembly of nanostructures as well as the influencing factors. The biomedical applications of DNA-assembled nanostructures are also summarized. This review provides new insights into the application of DNA in nanostructure assembly.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Biochemistry & Molecular Biology
Komal Mehra, Sonia Khurana, Shrikant Kukreti, Mahima Kaushik
Summary: The development of nanoscience and nanotechnology has allowed for the synthesis and characterization of nanomaterials with unique properties. However, nanomaterials do not have the ability to selectively bind with analytes. DNA, a polymorphic genetic material, can form different secondary/multistranded structures and has been used in conjunction with nanomaterials for various applications.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Engineering, Chemical
Carolina Monck, Yuval Elani, Francesca Ceroni
Summary: The use of cell-free protein synthesis (CFPS) has great potential in synthetic biology and biomedical applications, allowing for the production of clinical molecules and vaccines. Integration with other technologies can provide new therapeutic expression methods.
CHEMICAL ENGINEERING RESEARCH & DESIGN
(2022)
Article
Chemistry, Multidisciplinary
Bo Yang, Bini Zhou, Cuifeng Li, Xiaowei Li, Ziwei Shi, Yuxin Li, Chenyou Zhu, Xin Li, Yi Hua, Yufan Pan, Jian He, Tianyang Cao, Yawei Sun, Wanli Liu, Min Ge, Yuhe R. Yang, Yuanchen Dong, Dongsheng Liu
Summary: This article introduces a novel l-DNA hydrogel with outstanding biostability and biocompatibility, which can serve as an ideal 3D cell-culture matrix and implanted bio-scaffold for long-term biomedical applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Jegadheeswari Venkadakrishnan, Ganesh Lahane, Arti Dhar, Wei Xiao, Krishna Moorthi Bhat, Tej K. Pandita, Audesh Bhat
Summary: DNA damage tolerance (DDT) pathway suppresses replication fork arrest-induced DNA double strand breaks (DSBs) through translesion DNA synthesis (TLS) and homology-directed DDT mechanisms, with TLS polymerases playing a crucial role. Defects in TLS pathway can lead to various diseases. Apart from their role in DDT pathway, noncanonical functions of TLS polymerases are also important for maintaining genomic stability.
MOLECULAR AND CELLULAR BIOLOGY
(2023)
Article
Biochemical Research Methods
Fatima Akram, Fatima Iftikhar Shah, Ramesha Ibrar, Taseer Fatima, Ikram ul Haq, Waqas Naseem, Mahmood Ayaz Gul, Laiba Tehreem, Ghanoor Haider
Summary: DNA polymerases are essential enzymes for replicating genetic information in nucleic acids and maintaining its integrity. They play a crucial role in cell division and are necessary for the survival of all organisms using DNA as their genetic material. Thermostable DNA polymerases are particularly important in modern biotechnology and molecular biology, as they enable various techniques such as DNA cloning, sequencing, amplification, diagnostics, PCR, synthetic biology, and SNP detection.
ANALYTICAL BIOCHEMISTRY
(2023)
Review
Biotechnology & Applied Microbiology
Xueting Jian, Xiaoyi Feng, Yuning Luo, Fangjie Li, Junyan Tan, Yuli Yin, Yang Liu
Summary: DNA-based hydrogels have shown great potential in biomedical applications, such as drug delivery, biosensing, and tissue engineering, due to their excellent properties and functional diversity. Researchers have successfully constructed a variety of high-performance DNA hydrogels using different methods, expanding the scope of their applications through the development of multifunctional DNA-based hybrid hydrogels.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sarah S. Henrikus, Camille Henry, Amy E. McGrath, Slobodan Jergic, John P. McDonald, Yvonne Hellmich, Steven T. Bruckbauer, Matthew L. Ritger, Megan E. Cherry, Elizabeth A. Wood, Phuong T. Pham, Myron F. Goodman, Roger Woodgate, Michael M. Cox, Antoine M. van Oijen, Harshad Ghodke, Andrew Robinson
NUCLEIC ACIDS RESEARCH
(2020)
Review
Cell Biology
Gabrielle J. Valles, Irina Bezsonova, Roger Woodgate, Nicholas W. Ashton
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Nicholas W. Ashton, Gabrielle J. Valles, Nancy Jaiswal, Irina Bezsonova, Roger Woodgate
Summary: USP7 is a critical deubiquitinating enzyme with important roles in multiple signaling pathways. The study reveals that DNA polymerase iota is a novel substrate of USP7, which requires binding to both TRAF and UBL1-2 domains for efficient deubiquitination. This discovery establishes a new bipartite mode of substrate binding for USP7.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Milosz Rolinski, Nicola Pietro Montaldo, Merdane Ezgi Aksu, Sarah L. Fordyce Martin, Alessandro Brambilla, Nicolas Kunath, Jostein Johansen, Sten Even Erlandsen, Nina-Beate Liabbak, Kristin Rian, Magnar Bjoras, Pal Saetrom, Barbara van Loon
Summary: The research identified a novel mechanism of alkylation stress response dependent on MED13 and cyclin D1, which can serve as a basis for developing innovative therapeutic strategies.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Mahmood Faraz, Roger Woodgate, Anders R. Clausen
Summary: This study mapped the location of ribonucleotides incorporated into the E. coli genome by pol V variants, revealing a specific role for pol V in lagging strand DNA synthesis during the SOS response.
Article
Cell Biology
Adhirath Sikand, Malgorzata Jaszczur, Linda B. Bloom, Roger Woodgate, Michael M. Cox, Myron F. Goodman
Summary: The study investigates the role of a specialized error-prone DNA polymerase in Escherichia coli and the impact of the beta-sliding processivity clamp on DNA synthesis efficiency. Results suggest that beta clamp enhances primer elongation and translesion DNA synthesis, possibly by stabilizing the polymerase and inhibiting its ATPase activity.
Article
Biochemistry & Molecular Biology
John P. McDonald, Dominic R. Quiros, Alexandra Vaisman, Antonio R. Mendez, Jan Reyelt, Marlen Schmidt, Martin Gonzalez, Roger Woodgate
Summary: RumAB is a potent mutator in low-copy-number expression vectors but poorly mutable in the native 88.5 kb R391, with SetR(R391) and CroS(R391) playing crucial roles in regulating RumA levels and mutagenesis. Inactivating mutations in CroS(R391) have the potential to increase cellular mutagenesis and evolution of antibiotic resistance in pathogenic bacteria harboring R391.
MOLECULAR MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Alexandra Vaisman, Krystian Lazowski, Martin A. M. Reijns, Erin Walsh, John P. McDonald, Kristiniana C. Moreno, Dominic R. Quiros, Marlen Schmidt, Harald Kranz, Wei Yang, Karolina Makiela-Dzbenska, Roger Woodgate
Summary: The Escherichia coli dnaE gene encodes the alpha-catalytic subunit of DNA polymerase III, with the study focusing on the role of residues H760 and S759 in maintaining genome stability. Out of 38 mutants created, only nine were successfully sub-cloned, with three having substitutions at H760 and six having substitutions at S759. Further characterization revealed altered phenotypes in terms of deoxyribonucleotide base selectivity and ribonucleotide discrimination for certain alleles.
MOLECULAR MICROBIOLOGY
(2021)
Correction
Biochemistry & Molecular Biology
Alexandra Vaisman, John P. McDonald, Mallory R. Smith, Sender L. Aspelund, Thomas C. Evans, Roger Woodgate
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Alexandra Vaisman, John P. McDonald, Mallory R. Smith, Sender L. Aspelund, Thomas C. Evans, Roger Woodgate
Summary: Y-family DNA polymerases consist of six phylogenetically separate subfamilies, with representatives found in all three domains of life. Different evolutionary diversity exists within eukaryotes, with different species possessing varying numbers and types of Y-family pols. The Y-family pols from Thermomyces lanuginosus show increased thermostability and share major biochemical properties with their human counterparts, displaying low fidelity during DNA synthesis.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Debika Ojha, Malgorzata M. Jaszczur, Adhirath Sikand, John P. McDonald, Andrew Robinson, Antoine M. van Oijen, Chi H. Mak, Fabien Pinaud, Michael M. Cox, Roger Woodgate, Myron F. Goodman
Summary: Homologs of mutagenic DNA polymerase V are encoded by pathogens and mobile elements. These polymerases can be transferred horizontally into different cells but require activation by host factors.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Agriculture, Dairy & Animal Science
L. Bittner-Schwerda, E. Malama, M. Siuda, B. van Loon, H. Bollwein
Summary: This study investigated the effects of hydrogen peroxide (H2O2) on the chromatin structure of sperm. The results showed that H2O2 adversely affected the sperm's motility, plasma membrane and acrosome integrity, but had a minor impact on chromatin structure. The addition of catalase reversed the chromatin damage caused by H2O2.
ANIMAL REPRODUCTION SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Sunbok Jang, Namrata Kumar, Mathew A. Schaich, Zhou Zhong, Barbara van Loon, Simon C. Watkins, Bennett Van Houten
Summary: This study discovered that UV-DDB has specific recognition for N-6-ethenoadenine and hypoxanthine, besides oxidized bases, and it stimulates AAG activity and helps with the release of AAG from abasic sites, facilitating the repair process.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Rossana Aprigliano, Merdane Ezgi Aksu, Stefano Bradamante, Boris Mihaljevic, Wei Wang, Kristin Rian, Nicola P. Montaldo, Kayla Mae Grooms, Sarah L. Fordyce Martin, Diana L. Bordin, Matthias Bosshard, Yunhui Peng, Emil Alexov, Cindy Skinner, Nina-Beate Liabakk, Gareth J. Sullivan, Magnar Bjoras, Charles E. Schwartz, Barbara van Loon
Summary: The study reveals that increased p53 signaling due to HUWE1 mutations is central to XLID syndromes, particularly affecting neural differentiation in JMS cells. By reducing p53 levels and restoring p53 target gene expression, the neural differentiation defects in JMS cells can be successfully rescued.
CELL REPORTS MEDICINE
(2021)
Article
Multidisciplinary Sciences
Gabrielle J. Valles, Nicholas W. Ashton, Nancy Jaiswal, Roger Woodgate, Irina Bezsonova
Summary: This article presents complete NMR spectroscopy data used to characterize direct interactions between USP7 and its novel substrate DNA polymerase iota (Pol ι), which binds both TRAF and UBL1-2 domains.
Article
Genetics & Heredity
Marit A. E. van Bueren, Aniek Janssen
Summary: Eukaryotic nuclei rely on multiple repair pathways to accurately repair DNA damage, particularly in chromatin domains enriched for repetitive DNA sequences. Tailored repair mechanisms are necessary to maintain genome stability in these domains.
