Editorial Material
Chemistry, Multidisciplinary
[Anonymous]
Summary: The cover of this issue features the research team at McMaster University, led by John Brennan and Yingfu Li, who have discovered a universal DNA aptamer that recognizes spike proteins of various SARS-CoV-2 variants.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Zijie Zhang, Jiuxing Li, Jimmy Gu, Ryan Amini, Hannah D. Stacey, Jann C. Ang, Dawn White, Carlos D. M. Filipe, Karen Mossman, Matthew S. Miller, Bruno J. Salena, Deborah Yamamura, Payel Sen, Leyla Soleymani, John D. Brennan, Yingfu Li
Summary: A unique DNA aptamer, MSA52, has been identified in this study, which exhibits high affinity for the spike proteins of wildtype SARS-CoV-2 and multiple variants. This discovery demonstrates the potential of generating aptamers with high affinity for multiple variants of a single protein, including emerging variants, which makes it a promising tool for molecular recognition of rapidly evolving targets, such as those found in SARS-CoV-2.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Yunwang Zhao, Lei He, Baihai Huang, Weidong Zhang, Ailing Hu, Baolin Li, Shiqi Liao, Na Wang
Summary: Lung cancer is the leading cause of cancer-related deaths globally, and early diagnosis and treatment are crucial for improving survival rates. The use of serum-SELEX to isolate the aptamer Ap-LC-19 with low dissociation constant and high affinity represents a promising approach for early diagnosis and targeted therapy of lung cancer. Additionally, biomarker CLEC3B identified through MS analysis may serve as a useful indicator for early detection and monitoring of lung cancer progression.
Article
Biology
Fengwei Zheng, Roxana Georgescu, Nina Y. Yao, Huilin Li, Michael E. O'Donnell
Summary: The RFC complex has been shown to have a second DNA binding site, located between the N-terminal BRCT domain and AAA+ module of the large Rfc1 subunit. This 5' DNA site exhibits ideal binding to a 7-nt gap and shows enhanced binding to 5 and 10 nt gaps. It is proposed that the 5' site facilitates RFC's PCNA loading activity at DNA damage-induced gaps and plays a potential role in lagging strand DNA synthesis.
Article
Biochemistry & Molecular Biology
Aleem Syed, Frantisek Filandr, Jeffrey Patterson-Fortin, Albino Bacolla, Ramya Ravindranathan, Jia Zhou, Drew T. Mcdonald, Mohammed E. Albuhluli, Amy Verway-Cohen, Joseph A. Newman, Miaw-Sheue Tsai, Darin E. Jones, David C. Schriemer, Alan D. D'Andrea, John A. Tainer
Summary: Polymerase theta (Pol θ) is involved in DNA replication and repair, and its inhibition is deadly for BRCA1 and BRCA2-deficient tumor cells. Novobiocin (NVB), an ATPase inhibitor of Pol θ, is being tested as an anti-cancer drug in clinical trials. This study reveals the molecular mechanism of NVB-mediated Pol θ inhibition, showing that NVB blocks DNA binding by binding to an allosteric site.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biophysics
Taro Saito, Yutaka Shimizu, Kaori Tsukakoshi, Koichi Abe, Jinhee Lee, Kinuko Ueno, Ryutaro Asano, Brian Jones, Tomohiro Yamada, Tatsuki Nakano, Jiaxing Tong, Asami Hishiki, Kodai Hara, Hiroshi Hashimoto, Koji Sode, Toshimasa Toyo'oka, Kenichiro Todoroki, Kazunori Ikebukuro
Summary: A novel anti-idiotype aptamer A14#1 with extraordinary specificity against the anti-vascular endothelial growth factor therapeutic mAb, bevacizumab, was developed. The affinity of A14#1 to bevacizumab markedly increased at pH 4.7, enabling it to be potentially useful for therapeutic drug measurement as a novel ligand of bevacizumab.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Chemistry, Medicinal
Hajime Takahashi, Ryo Okubo, Atsushi Ogawa
Summary: This study constructed efficient eukaryotic ON-riboswitches using high-affinity aptamers of mid-sized Arg-rich peptides. These riboswitches showed higher switching efficiencies at low ligand concentrations compared to small ligand-responsive ON-riboswitches. Additionally, the two best riboswitches were almost insensitive to each other's peptide ligands despite their high sequence similarity. This orthogonal pair of riboswitches could serve as widely useful eukaryotic gene regulators or biosensors due to their high responsiveness and specificity.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Wenxiao Wang, Yu Shen, Fuan Wang, Ying Liu, Xiaoqing Liu
Summary: A versatile approach for fine control of DNA-based hierarchical assembly is developed using dual stimuli and two assembly strategies. By designing functional thrombin aptamer structures on the DNA nanoassembly, precise regulation of thrombin activity can be achieved.
CHEMICAL COMMUNICATIONS
(2021)
Review
Chemistry, Analytical
Marimuthu Citartan
Summary: Light-up aptamers are aptamers that trigger fluorescence emission of specific dyes upon binding, widely used in in vivo imaging and in vitro diagnostic assay development. This study aims to provide an overview of various diagnostic assay formats developed using light-up aptamers, offering insights for researchers interested in developing one-pot in vitro diagnostic assays based on light-up aptamers.
Article
Chemistry, Multidisciplinary
Shuang Wan, Siwen Liu, Miao Sun, Jialu Zhang, Xinyu Wei, Ting Song, Yuhao Li, Xinyang Liu, Honglin Chen, Chaoyong James Yang, Yanling Song
Summary: Researchers have successfully achieved neutralization of SARS-CoV-2 by designing a DNA framework-guided trimer of neutralizing aptamers. The design utilizes the precise spatial organization of the DNA framework to enhance the interaction between the aptamers and the spike protein of the virus, effectively preventing viral infection through the formation of a nanoscale barrier.
Article
Chemistry, Analytical
Dong-Yeon Song, Yu Jin Park, Dong-Myung Kim
Summary: The study presents a novel method for detecting FEN1 that can detect sub-nanomolar concentrations of FEN1 within an hour. It has the potential to be used for cancer diagnosis, prognosis, and drug screening.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biotechnology & Applied Microbiology
Hugo Oliveira, Silvio Santos, Diana P. Pires, Dimitri Boeckaerts, Graca Pinto, Rita Domingues, Jennifer Otero, Yves Briers, Rob Lavigne, Mathias Schmelcher, Andreas Doetsch, Joana Azeredo
Summary: In this study, a newly isolated myovirus CkP1 was found to infect Citrobacter koseri, causing urinary tract infections. The phage showed a broad host range and specifically bound to C. koseri cells through the tail fiber protein. It demonstrated high stability and potential for controlling drug-resistant C. koseri infections.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Chunmin Pu, Xiaoyan Liao, Xianming Shi, Yan Cui, Yalong Bai, Lili Chen
Summary: A novel method based on amino-modified silica-coated magnetic particles (ASMPs) was successfully developed for the extraction of short single-stranded DNA (ssDNA) from agarose gel. The method demonstrated remarkable efficiency and outperformed three commercially available DNA gel extraction products in aptamer screening.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Matilde Clarissa Malfatti, Marta Codrich, Emiliano Dalla, Chiara D'Ambrosio, Francesca Storici, Andrea Scaloni, Gianluca Tell
Summary: The aim of this study is to investigate the existence of modified ribonucleotide monophosphates in genomic DNA under oxidative stress conditions. The research discovered that AUF1 can specifically recognize and promote APE1 endoribonuclease activity on 8-oxo-guanosine embedded in DNA. These findings provide new insights into the genome stability in mammalian cells under oxidative stress-related damages.
ANTIOXIDANTS & REDOX SIGNALING
(2023)
Article
Virology
Prabu Gnanasekaran, Neha Gupta, Kalaiarasan Ponnusamy, Supriya Chakraborty
Summary: This study identified a novel function of the beta C1 protein encoded by geminivirus satellites, demonstrating its ATPase activity and the essential conserved residues for this function. The DNA-binding activity of beta C1 was shown to be influenced by the binding of ATP. Inhibiting the ATPase activity in the presence of other cellular nucleoside triphosphates suggested the broad substrate specificity of beta C1 in vitro.
JOURNAL OF VIROLOGY
(2021)