Article
Biochemistry & Molecular Biology
Qin-Xia Song, Chang -Wei Lai, Na-Nv Liu, Xi-Miao Hou, Xu-Guang Xi
Summary: The G4 DNA binding protein Dbp2 has been found to prefer G-rich substrates and plays a dual role in destabilizing and inducing further folding of MycG4 structures. It may also participate in DNA metabolism.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Andrei G. Loiko, Alexander Sergeev, Adelya Genatullina, Mayya Monakhova, Elena A. Kubareva, Nina G. Dolinnaya, Elizaveta S. Gromova
Summary: This study reveals a potential link between G-quadruplex formation and the function of DNA methyltransferase Dnmt3a in mammals. G4s may play a role in epigenetic regulation by affecting the methylation of specific CpG sites and modulating the enzyme activity. Possible mechanisms include sequestration of Dnmt3a at G4 structures and disruption of Dnmt3a oligomerization on DNA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Ahyun Son, Veronica Huizar Cabral, Zijue Huang, Theodore J. Litberg, Scott Horowitz
Summary: Recent research has found that G-quadruplex (G4) nucleic acids are effective in preventing protein aggregation and improving protein folding in Escherichia coli. Through in vitro protein folding experiments, it was discovered that G4s can accelerate protein folding by rescuing kinetically trapped intermediates. Time-course folding experiments in E. coli further showed that G4s primarily enhance protein folding quality instead of preventing protein aggregation. This study suggests that nucleic acids and ATP-independent chaperones may play important roles in determining the folding fate of proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Inorganic & Nuclear
Hasan Emre Yilmaz, Efkan Bagda, Esra Bagda, Mahmut Durmus
Summary: The study investigated the interaction of TGaPc and OGaPc with different DNA forms, revealing that TGaPc had a higher binding affinity for AS1411 and caused destabilization of Tel21 structure. These compounds have the potential for cancer treatment by interacting with different DNA types at different strengths and mechanisms.
Article
Biochemistry & Molecular Biology
Sara Illodo, Cibran Perez-Gonzalez, Ramiro Barcia, Flor Rodriguez-Prieto, Wajih Al-Soufi, Mercedes Novo
Summary: Guanine quadruplexes (G4s) are four-stranded structures formed within guanine-rich DNA and RNA sequences that play a crucial role in biological processes. The recent discovery of G4 structures within mitochondrial DNA has brought significant advancements to the field. This study investigates the relevant G4 structures formed within CSB II and reveals the stability differences among different sequences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Swati Chaudhary, Mohan Kumar, Mahima Kaushik
Summary: G-quadruplexes play significant roles in various diseases and have been extensively studied. Further understanding of these structures and their stabilizing or destabilizing ligands can facilitate future drug discovery.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Hijiri Hasegawa, Ikkei Sasaki, Kaori Tsukakoshi, Yue Ma, Kazuo Nagasawa, Shusuke Numata, Yuuki Inoue, Yeji Kim, Kazunori Ikebukuro
Summary: Genomic DNA methylation is studied as a potential biomarker for disease diagnosis. This study focuses on detecting CpG methylation in G4-forming oligonucleotides using G4 ligands, which show significant differences in fluorescence and chemiluminescence intensities between methylated and unmethylated DNAs. This research provides a new method for detecting DNA methylation based on structural changes using G4 ligands.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
J. Tassilo Gruen, Anja Bluemler, Ines Burkhart, Julia Wirmer-Bartoschek, Alexander Heckel, Harald Schwalbe
Summary: This study unravels the folding dynamics of a G4 sequence containing five G-tracts from cMYC, a major oncogene, and dissects the individual kinetics and thermodynamics of the spare-tire mechanism of cMYC-G4.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Ying Bao, Xiaonong Zhang, Xiaoxuan Xiang, Yujing Zhang, Xinhua Guo
Summary: G-quadruplexes (G4s) are important molecules that regulate various physiological functions. Surface-enhanced Raman scattering (SERS) technique can quickly provide structural details of G4s and study their interactions with ligands. This study demonstrates that SERS is a powerful tool for revealing specific interactions between G4s and their ligands.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Biochemistry & Molecular Biology
Anzhela Pavlova, Elena A. Kubareva, Mayya Monakhova, Maria Zvereva, Nina G. Dolinnaya
Summary: DNA G-quadruplexes are crucial components of regulatory systems in cells and impact genome integrity by impeding DNA replication. Recent studies have focused on the role of G4s in genomic instability and DNA repair processes, highlighting the intricate balance between stability and instability in the genome.
Review
Multidisciplinary Sciences
Sagar Bag, Mangal Deep Burman, Sudipta Bhowmik
Summary: G-quadruplex is a unique structure in nucleic acids that exists widely in human genome and has attracted great attention in therapeutic investigations. Targeting G-quadruplex structure is a new strategy for drug development. Flavonoids, which are present in various dietary plant-based products, have shown high pharmacological effectiveness with minimal cytotoxicity, making them potential alternatives to synthetic therapeutic medicines. Research on the interaction between G-quadruplex and flavonoids is expected to provide newer perspectives for the development of novel therapeutic agents.
Article
Chemistry, Multidisciplinary
Wenxuan Hu, Haitao Jing, Wenqiang Fu, Zengrong Wang, Jiang Zhou, Na Zhang
Summary: In this study, a new type of G-quadruplex structure, parallel homomeric bimolecular G-quadruplex, was demonstrated to undergo strand displacement reaction with short G-rich DNA fragments at room temperature, resulting in the formation of a parallel heteromeric trimolecular G-quadruplex. This provides new insights into the development of complex architectures in G-quadruplex-based DNA nanotechnology.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Biochemistry & Molecular Biology
Nuria Escaja, Bartomeu Mir, Miguel Garavis, Carlos Gonzalez
Summary: Tetrads are arrangements of four nucleobases commonly used to stabilize nucleic acid structures. In addition to the well-known G-quadruplex, non-G tetrads formed by different nucleobases have been observed in experimental structures. They are mostly found in the context of G-quadruplex structures but also occur in other unusual four-stranded structures.
Article
Polymer Science
Viacheslav Severov, Vladimir Tsvetkov, Nikolay Barinov, Vladislav Babenko, Dmitry Klinov, Galina Pozmogova
Summary: This study reports the spontaneous formation of DNA-DNA junctions in solution without the involvement of proteins, visualized using atomic force microscopy. The positions of synapsis match with potential G-quadruplex (G4) sites, and these conjugates exhibit an affinity for G4 antibodies. Molecular modeling was employed to elucidate the possible structures of G4/IM-synaptic complexes, indicating a novel role of intermolecular noncanonical structures in chromatin architecture and genomic rearrangement.
Article
Biochemistry & Molecular Biology
Maria Marzano, Stefano D'Errico, Francesca Greco, Andrea Patrizia Falanga, Monica Terracciano, Daria Di Prisco, Gennaro Piccialli, Nicola Borbone, Giorgia Oliviero
Summary: G-wires are supramolecular DNA structures obtained through self-assembly based on the G-quadruplex structural motif. Despite their potential applications in DNA nanotechnologies, the self-assembly process to obtain G-wires is not completely understood or controlled.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Immunology
Anthony Kusnadi, Sung Ho Park, Ruoxi Yuan, Tania Pannellini, Eugenia Giannopoulou, David Oliver, Theresa Lu, Kyung-Hyun Park-Min, Lionel B. Ivashkiv
Article
Immunology
Jee Eun Choi, Allysia J. Matthews, Genesis Michel, Bao Q. Vuong
JOURNAL OF IMMUNOLOGY
(2020)
Article
Biochemistry & Molecular Biology
David E. Gordon, Ariane Watson, Assen Roguev, Simin Zheng, Gwendolyn M. Jang, Joshua Kane, Jiewei Xu, Jeffrey Z. Guo, Erica Stevenson, Danielle L. Swaney, Kathy Franks-Skiba, Erik Verschueren, Michael Shales, David C. Crosby, Alan D. Frankel, Alexander Marson, Ivan Marazzi, Gerard Cagney, Nevan J. Krogan
Article
Biochemistry & Molecular Biology
Jessica Sook Yuin Ho, Matthew Angel, Yixuan Ma, Elizabeth Sloan, Guojun Wang, Carles Martinez-Romero, Marta Alenquer, Vladimir Roudko, Liliane Chung, Simin Zheng, Max Chang, Yesai Fstkchyan, Sara Clohisey, Adam M. Dinan, James Gibbs, Robert Gifford, Rong Shen, Quan Gu, Nerea Irigoyen, Laura Campisi, Cheng Huang, Nan Zhao, Joshua D. Jones, Ingeborg van Knippenberg, Zeyu Zhu, Natasha Moshkina, Lea Meyer, Justine Noel, Zuleyma Peralta, Veronica Rezelj, Robyn Kaake, Brad Rosenberg, Bo Wang, Jiajie Wei, Slobodan Paessler, Helen M. Wise, Jeffrey Johnson, Alessandro Vannini, Maria Joao Amorim, J. Kenneth Baillie, Emily R. Miraldi, Christopher Benner, Ian Brierley, Paul Digard, Marta Luksza, Andrew E. Firth, Nevan Krogan, Benjamin D. Greenbaum, Megan K. MacLeod, Harm van Bakel, Adolfo Garcia-Sastre, Jonathan W. Yewdell, Edward Hutchinson, Ivan Marazzi
Article
Biochemistry & Molecular Biology
Benjamin J. Meckiff, Ciro Ramirez-Suastegui, Vicente Fajardo, Serena J. Chee, Anthony Kusnadi, Hayley Simon, Simon Eschweiler, Alba Grifoni, Emanuela Pelosi, Daniela Weiskopf, Alessandro Sette, Ferhat Ay, Gregory Seumois, Christian H. Ottensmeier, Pandurangan Vijayanand
Article
Immunology
Anthony Kusnadi, Ciro Ramirez-Suastegui, Vicente Fajardo, Serena J. Chee, Benjamin J. Meckiff, Hayley Simon, Emanuela Pelosi, Gregory Seumois, Ferhat Ay, Pandurangan Vijayanand, Christian H. Ottensmeier
Summary: CD8(+) T cells in COVID-19 patients exhibit two distinct states – exhausted and non-exhausted, with non-exhausted cells in severe cases showing enhanced memory responses to SARS-CoV-2 infection.
SCIENCE IMMUNOLOGY
(2021)
Article
Immunology
Jung-Yeon Lim, Sascha H. Duttke, Turner S. Baker, Jihye Lee, Kristyne J. Gambino, Nicholas J. Venturini, Jessica Sook Yuin Ho, Simin Zheng, Yesai S. Fstkchyan, Vinodh Pillai, David C. Fajgenbaum, Ivan Marazzi, Christopher Benner, Minji Byun
Summary: DNMT3A is the most frequently mutated gene in age-related clonal hematopoiesis, with heterozygous mutations causing loss of function and impacting DNA methylation and demethylation in mature immune cells. These alterations in enhancer activity due to DNMT3A haploinsufficiency lead to abnormal gene expression and impaired immune response, shedding light on the mechanism of immune dysfunction associated with clonal hematopoiesis and acquired DNMT3A mutations.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Multidisciplinary Sciences
Emily Sible, Simin Zheng, Jee Eun Choi, Bao Q. Vuong
Summary: Somatic hypermutation in germinal centers is a critical process for B cells to generate higher affinity immunoglobulins by introducing untemplated mutations. Methods to quantify intron mutations like JH4 using FACS, PCR, and Sanger sequencing provide valuable tools for studying somatic hypermutation and immunoglobulin diversification.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Review
Immunology
Alec J. Wishnie, Tzippora Chwat-Edelstein, Mary Attaway, Bao Q. Vuong
Summary: Recent studies demonstrate that the affinity of the B cell receptor plays a key role in modulating T-B interactions and the subsequent differentiation of B cells in the extrafollicular and germinal center response. B cells expressing high affinity BCRs preferentially differentiate into antibody-secreting cells, while those expressing low affinity BCRs undergo further affinity maturation or differentiate into memory B cells.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Genetics & Heredity
Mary Attaway, Tzippora Chwat-Edelstein, Bao Q. Vuong
Summary: The article discusses the role of non-coding RNAs, such as miRNAs and lncRNAs, in regulating the expression and activity of transcriptional regulators during B lymphocyte development, highlighting the complex gene regulatory networks and identifying new regulatory RNAs that require further investigation.
FRONTIERS IN GENETICS
(2021)
Article
Immunology
Lucie Fallone, Guilhem Lalle, Manuela Pereira-Abrantes, Emily Sible, Marie-Cecile Michallet, Bao Q. Vuong, Uzma Ayesha Hasan
JOURNAL OF IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Simin Zheng, Allysia J. Matthews, Numa Rahman, Kayleigh Herrick-Reynolds, Emily Sible, Jee Eun Choi, Alec Wishnie, Yan Kee Ng, Daniela Rhodes, Stephen J. Elledge, Bao Q. Vuong
Summary: Class switch recombination (CSR) is the process of B cells switching production from IgM/IgD to other immunoglobulin isotypes. SANBR, identified as a negative regulator of CSR, inhibits CSR through its BTB domain.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)