Article
Biochemistry & Molecular Biology
Valeria Libera, Federico Bianchi, Barbara Rossi, Francesco D'Amico, Claudio Masciovecchio, Caterina Petrillo, Francesco Sacchetti, Alessandro Paciaroni, Lucia Comez
Summary: This study found that during the thermal melting process of G4 structure, the hydrogen-bonded network of water molecules undergoes rearrangement, which is closely related to the DNA rearrangement. Understanding the structural properties of the solvent can contribute to a better understanding of the interaction between G4s and ligands.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Taniya Sharma, Nikita Kundu, Sarvpreet Kaur, Vibha Tandon, J. Shankaraswamy, Sarika Saxena
Summary: This study provides evidence of human telomeric G4 destabilization upon peptide binding in dilute and cell-mimicking conditions, suggesting the potential therapeutic targets for diseases with over-representation of G4 motifs.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
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
Yuanlei Cheng, Yashuo Zhang, Huijuan You
Summary: G-quadruplexes (G4s) are stable secondary nucleic acid structures that are crucial in biological processes, with complex folding/unfolding dynamics. Single-molecule force spectroscopy methods can be used to study their polymorphism and dynamics. Recent studies have utilized this approach to investigate the molecular mechanisms of G4-interacting proteins.
Article
Biochemistry & Molecular Biology
Nikita Kundu, Taniya Sharma, Sarvpreet Kaur, Aman Kumar Mahto, Rikeshwer Prasad Dewangan, J. Shankaraswamy, Sarika Saxena
Summary: This study provides the first evidence of human telomeric G4 destabilization upon peptide binding, which will open new research avenues for treating DNA-related diseases.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Joanna Nowak-Karnowska, Agata Gluszylska, Joanna Kosman, Grazyna Neunert, Anna Dembska
Summary: The highly fluorescent 9-methoxyluminarine ligand 9-MeLM was found to interact with different topologies of G-quadruplexes, selectively quenched by parallel c-MYC G-quadruplex DNA. This suggests that 9-MeLM can potentially be used as a selective probe for parallel G-quadruplexes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Shuntaro Takahashi, Sudipta Bhowmik, Shinobu Sato, Shigeori Takenaka, Naoki Sugimoto
Summary: The relationship between G4 structures and DNA replication was studied, and it was found that different ligands have different effects on the topology of G4. Some ligands can inhibit the replication of G4 with anti-parallel topology, while others selectively inhibit G4 with anti-parallel and hybrid topology. The experiments suggest that native human telomere G4 is more flexible than the modified sequence and can interact with ligands.
Article
Chemistry, Analytical
Ji Zheng, Dayong Li, Jin Jiao, Chengjie Duan, Zhongyun Wang, Yang Xiang
Summary: In this study, a dual-aptamer recognition strategy based on G-quadruplex nanowires was developed for selective analysis of exosomes, allowing sensitive and specific analysis of target exosomes. This method is simple and universal for different types of exosomes, showing great significance for clinical cancer diagnosis.
Article
Biochemistry & Molecular Biology
Robert C. Monsen, Srinivas Chakravarthy, William L. Dean, Jonathan B. Chaires, John O. Trent
Summary: The study used an integrated structural biology approach to characterize the structure of telomeric overhang, revealing that single-stranded sequences fold into multimeric structures with a maximum number of G4 units. The flexibility of these structures was investigated through molecular dynamics simulations, identifying unique sites for drug targeting.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Polymer Science
Weize Yuan, Remi Casier, Jean Duhamel
Summary: The denaturation process of alpha-helical poly(L-glutamic acid) (PLGA) in N,N-dimethyl-formamide with addition of guanidine hydrochloride (GdHCl) was characterized using fluorescence comparison. By taking advantage of pyrene excimer formation (PEF), changes in the conformation of alpha-helical Py-PLGA were probed. Analysis using Fluorescence Blob Model (FBM) revealed a decrease in the average number of glutamic acids located inside a blob as GdHCl concentration increased, indicating the unravelling of the alpha-helix in PLGA.
Article
Chemistry, Physical
K. Laouer, M. Schmid, F. Wien, P. Changenet, F. Hache
Summary: The research utilized a T-jump experiment to study the thermal denaturation and renaturation dynamics of different G-quadruplex topologies, revealing distinct kinetics and ruling out a simple two-state mechanism. The parallel topology exhibited slower dynamics compared to antiparallel topologies, likely due to constrained conformational space hindering movement of the DNA strand and reducing entropy contribution during the renaturation process at high temperatures.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemistry & Molecular Biology
Xiaobin Ling, Yuqi Yao, Lei Ding, Jinbiao Ma
Summary: The study reveals that the nucleic acid binding protein UP1 can bind and unfold the G-quadruplexes in human telomere DNA. The RNA recognition motifs RRM1 and RRM2 in UP1 are responsible for initial binding, unfolding, and completion of G-quadruplexes unfolding, respectively. The TAG binding motif in the telomeric G-quadruplex Loop2 is critical for UP1 recognition and initiation of G-quadruplexes unfolding.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2023)
Article
Spectroscopy
Dilan Guner, Berke Bilgenur Sener, Ceren Bayrac
Summary: Auramine o (AO) is a synthetic dye used in paper and textile industries. Although it has been banned as a food additive in many countries, it is still illegally used in certain food products and pharmaceuticals. Monitoring the presence of AO in food products is important to minimize health risks. This study developed a simple, sensitive, and selective label-free detection method based on G-quadruplex for AO. The method showed high specificity for AO and was successfully applied to detect AO in pasta, bulgur, and curry powder.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Chemistry, Physical
Farkhad Maksudov, Lee K. Jones, Valeri Barsegov
Summary: Single-molecule force spectroscopy is a powerful tool for exploring dynamic processes involving proteins, but interpreting experimental data remains a challenge. This study tested Support Vector Machines and Expectation Maximization approaches for statistical learning from dynamic force experiments using molecular modeling output as training sets. An EM-based method was designed to directly analyze experimental data without the need for data classification, showing good performance even with small sample sizes and overlapping force ranges for unfolding transitions.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemistry & Molecular Biology
Ettore Napolitano, Claudia Riccardi, Rosa Gaglione, Angela Arciello, Valentina Pirota, Alice Triveri, Filippo Doria, Domenica Musumeci, Daniela Montesarchio
Summary: In order to develop efficient anticancer theranostic systems, the interaction between a cyanine dye (CyOH) and two G-quadruplex-forming aptamers (V7t1 and 3R02) was studied. These aptamers recognized the Vascular Endothelial Growth Factor 165 (VEGF165), which is overexpressed in cancer cells and responsible for the rapid growth and metastases of solid tumors. Biophysical techniques, such as gel electrophoresis, circular dichroism (CD), UV-vis spectroscopy and fluorescence spectroscopy, were used to demonstrate that the cyanine interacted with both aptamers, giving a fluorescence light-up when bound to their dimeric forms. The dimeric G-quadruplexes of the aptamers showed higher affinity for VEGF165 and the fluorescence light-up was maintained when the dimeric aptamer-CyOH complexes bound to the target protein. These complexes, tested on MCF-7 cancer cells with non-tumorigenic MCF-10A cells as control, were effectively internalized in cells and colocalized with a fluorescently-labeled anti-VEGF-A antibody, enabling recognition and detection of the target. The studied systems are promising tools for anticancer theranostic strategies, combining the therapeutic potential of the G4-forming anti-VEGF aptamers with the diagnostic efficacy of the cyanine selective fluorescence light-up.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Andrew C. McShan, Kannan Natarajan, Vlad K. Kumirov, David Flores-Solis, Jiansheng Jiang, Mareike Badstubner, Jugmohit S. Toor, Clive R. Bagshaw, Evgenii L. Kovrigin, David H. Margulies, Nikolaos G. Sgourakis
NATURE CHEMICAL BIOLOGY
(2018)
Article
Chemistry, Multidisciplinary
Wu Su, Markus Schuster, Clive R. Bagshaw, Ulrich Rant, Glenn A. Burley
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2011)
Article
Biochemistry & Molecular Biology
Harriet E. Seward, Jaswir Basran, Roanne Denton, Mark Pfuhl, Frederick W. Muskett, Clive R. Bagshaw
Meeting Abstract
Biophysics
Xi Long, Joseph W. Parks, Clive R. Bagshaw, Michael D. Stone
BIOPHYSICAL JOURNAL
(2014)
Article
Biochemistry & Molecular Biology
Dmitry Cherny, Clare Gooding, Giles E. Eperon, Miguel B. Coelho, Clive R. Bagshaw, Christopher W. J. Smith, Ian C. Eperon
Article
Biochemistry & Molecular Biology
Sandip K. Badyal, Jaswir Basran, Nina Bhanji, Ju Hwan Kim, Alap P. Chavda, Hyun Suk Jung, Roger Craig, Paul R. Elliott, Andrew F. Irvine, Igor L. Barsukov, Marina Kriajevska, Clive R. Bagshaw
JOURNAL OF MOLECULAR BIOLOGY
(2011)
Biographical-Item
Cell Biology
Andrew G. Szent-Gyoergyi, Clive R. Bagshaw
JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY
(2012)
Article
Biochemistry & Molecular Biology
Paul R. Elliott, Andrew F. Irvine, Hyun Suk Jung, Kaeko Tozawa, Martyna W. Pastok, Remigio Picone, Sandip K. Badyal, Jaswir Basran, Philip S. Rudland, Roger Barraclough, Lu-Yun Lian, Clive R. Bagshaw, Marina Kriajevska, Igor L. Barsukov
Article
Multidisciplinary Sciences
Wu Su, Clive R. Bagshaw, Glenn A. Burley
SCIENTIFIC REPORTS
(2013)
Article
Multidisciplinary Sciences
Linnea I. Jansson, Jendrik Hentschel, Joseph W. Parks, Terren R. Chang, Cheng Lu, Rishika Baral, Clive R. Bagshaw, Michael D. Stone
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Chemistry, Multidisciplinary
Amelia B. Labbe, Clive R. Bagshaw, Lisa Uttal
JOURNAL OF CHEMICAL EDUCATION
(2020)
Article
Biochemistry & Molecular Biology
Clive R. Bagshaw, Jendrik Hentschel, Michael D. Stone
Summary: Telomerases are moderately processive reverse transcriptases that extend the 3' ends of linear chromosomes using an integral RNA template. The processivity values vary at different positions, with a characteristic strong band every 6th position in gel electrophoresis due to repeat nucleotides. This analysis reveals that higher product concentrations associated with a certain type of processivity arise from a stalling of nucleotide incorporation during translocation.
Article
Multidisciplinary Sciences
Archana G. Chavan, Jeffrey A. Swan, Joel Heisler, Cigdem Sancar, Dustin C. Ernst, Mingxu Fang, Joseph G. Palacios, Rebecca K. Spangler, Clive R. Bagshaw, Sarvind Tripathi, Priya Crosby, Susan S. Golden, Carrie L. Partch, Andy LiWang
Summary: The study successfully reconstructed a complete cyanobacterial circadian clock system in vitro, including the central oscillator, signal transduction pathways, downstream transcription factor, and promoter DNA. By monitoring the oscillations in real time with a fluorescence-based readout, the study revealed previously unknown mechanisms by which the circadian system of cyanobacteria maintains pace and rhythmicity under variable protein concentrations.
Meeting Abstract
Immunology
Nikolaos Sgourakis, Andrew McShan, Kannan Natarajan, Jiansheng Jiang, Jihye Park, Sarah Overall, Jugmohit S. Toor, Vlad Kumirov, David Flores-Solis, Mareike Badstubner, Evgenii L. Kovrigin, Clive R. Bagshaw, Jesper Pallesen, Erik Procko, David H. Margulies
JOURNAL OF IMMUNOLOGY
(2019)