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
Biochemistry & Molecular Biology
Poulomi Das, Khac Huy Ngo, Fernaldo Richtia Winnerdy, Arijit Maity, Blaz Bakalar, Yves Mechulam, Emmanuelle Schmitt, Anh Tuan Phan
Summary: This study investigates the adaptability of left-handed G4 structures towards the presence of bulges, presenting the structural characteristics of left-handed G4s accommodating varying numbers of bulges. Bulges in left-handed G4s exhibit distinct features compared to those in right-handed G4s, and elucidation of the intricate structural details may enhance understanding of the potential roles and limitations of these unique structures.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Anup Pandith, Yongyang Luo, Yul Jang, Jeehyeon Bae, Youngmi Kim
Summary: In this study, a fluorogenic probe CV2 was developed for the selective monitoring of G-quadruplex (G4) structures in living cells. CV2 specifically recognizes parallel G4 DNA and forms self-assembled nanoaggregates with red excimer-emitting fluorescence. The specific binding of CV2 to G4s triggers its disassembly into monomeric dyes, leading to a significant fluorescence enhancement. Moreover, CV2 can selectively stain G4s in mitochondria, making it useful for investigating the potential roles of mitochondrial DNA G4s in diseases involving mitochondrial dysfunction.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Jagannath Jana, Yoanes Maria Vianney, Nina Schroeder, Klaus Weisz
Summary: This study reveals the critical loop residue interactions in genomic and artificially designed quadruplexes through sequence mutations and thermodynamic stability analysis.
NUCLEIC ACIDS RESEARCH
(2022)
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)
Article
Biotechnology & Applied Microbiology
Vaclav Brazda, Otilia Porubiakova, Alessio Cantara, Natalia Bohalova, Jan Coufal, Martin Bartas, Miroslav Fojta, Jean-Louis Mergny
Summary: The study identified multiple potential G-quadruplex forming sequences in the G4-EA-H1N1 genomes, which could serve as potential therapeutic targets.
Article
Spectroscopy
David A. Price, Poornima Wedamulla, Tayler D. Hill, Taylor M. Loth, Sean D. Moran
Summary: Guanine-rich nucleic acid sequences can form G-quadruplex structures with different characteristics. By comparing the polarization dependences of cross-peaks in two-dimensional infrared (2D IR) spectra, parallel-stranded and antiparallel-stranded G-quadruplexes can be distinguished. This study reveals key features of a Bcl-2 proximal promoter and demonstrates the convenience of using 2D IR spectroscopy for analyzing G-quadruplex structures.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Review
Genetics & Heredity
Fangyuan Li, Jiang Zhou
Summary: Non-coding RNAs (ncRNAs), particularly lncRNAs and miRNAs, play a significant role in gene expression regulation, and their interplay with proteins and other RNAs is mediated by higher-order structures such as RNA G-quadruplexes (rG4s). The formation of rG4s, which are predicted in guanine-rich sequences, is closely associated with various human diseases. Understanding the dynamic balance between rG4s and RNA stem-loop/hairpin structures, as well as the interaction between ncRNAs and interactors, is crucial for modulating gene expression and disease progression. The folding of ncRNAs into the appropriate three-dimensional structure is of critical importance and opens up new therapeutic possibilities for diseases associated with potential-G4-containing-ncRNAs.
JOURNAL OF MOLECULAR MEDICINE-JMM
(2023)
Review
Biochemistry & Molecular Biology
Ye Teng, Ming Zhu, Zhidong Qiu
Summary: Repeat expansions are the main genetic cause of various neurodegeneration diseases. G-rich repeat sequences, such as CGG and GGGGCC, form functional G-quadruplexes and play important roles in bioprocesses. This review provides an overview of the contribution of G-quadruplex in repeat expansion disorders and summarizes the related mechanisms, including genetic instabilities, toxic RNA foci, and protein/peptide dysfunction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Jinbo Zhu, Zhiqiang Yan, Filip Boskovic, Cally J. E. Haynes, Marion Kieffer, Jake L. Greenfield, Jin Wang, Jonathan R. Nitschke, Ulrich F. Keyser
Summary: The study demonstrates the binding between DNA G4 and a self-assembled metal-organic cage, resulting in aggregate formation that protects the DNA G4 from cleavage. Experiment results show that the cage interacts with a wide range of G4s and serves as a protective barrier for DNA G4.
Article
Multidisciplinary Sciences
Ilias Georgakopoulos-Soares, Guillermo E. Parada, Hei Yuen Wong, Ragini Medhi, Giulia Furlan, Roberto Munita, Eric A. Miska, Chun Kit Kwok, Martin Hemberg
Summary: This study reveals the enrichment of G4 motifs near splice junctions, suggesting their regulatory role in RNA stability and splicing. G4 motifs play important roles in exon skipping and inclusion, and are associated with multiple RNA binding proteins. Furthermore, G4 motifs show strong enrichment at splice sites in mammals and birds, indicating the evolutionary conservation of this splice regulatory mechanism.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
So-Huei Kang, Kyung Min Lee, Seok-Kyu Cho, Ji Eun Lee, Donghoo Won, Sang-Young Lee, Sang Kyu Kwak, Changduk Yang
Summary: Inspired by guanine motifs, the G-quadruplex-forming ability of a guanine-based Y2 molecule containing bithiophene and peripheral dodecyl chain units in the presence of different cation salts was investigated. The structural characterization revealed that the radius and nature of the coordinating cations crucially affected the structural characteristics and ion migration ability of G-quadruplexes.
Article
Biochemistry & Molecular Biology
Yavuz Burak Goc, Jakub Poziemski, Weronika Smolinska, Dominik Suwala, Grzegorz Wieczorek, Dorota Niedzialek
Summary: The aim of this study was to investigate the influence of different single-stranded segments on the stability of RNA G-quadruplexes. Using a software program called NAB-GQ-builder, researchers constructed various two-tetrad G-quadruplex topologies and performed molecular dynamics simulations to study their sequence-morphology-stability relationships. The results offer insights for designing G-quadruplexes with balanced structures and programmable physicochemical properties for biomaterial applications. Additionally, the study examined the drug-targeting potential of single-stranded segments in oncogene promoter G-quadruplexes for future therapeutic strategies. The study also proposed a sequential folding mechanism for G-quadruplex folding based on a thorough quantum mechanical analysis of guanine assemblies triggered by cation coordination.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Polina Tikhonova, Iulia Pavlova, Ekaterina Isaakova, Vladimir Tsvetkov, Alexandra Bogomazova, Tatjana Vedekhina, Artem Luzhin, Rinat Sultanov, Vjacheslav Severov, Ksenia Klimina, Omar L. Kantidze, Galina Pozmogova, Maria Lagarkova, Anna Varizhuk
Summary: This study aimed to investigate the role of G-quadruplexes (G4s) in CTCF positioning, revealing both direct interactions between G4s and CTCF, as well as the facilitation of CTCF recruitment to CGIs by protecting CpG sites from methylation. Additionally, G4s were found to affect chromatin structure and thereby regulate CTCF recruitment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Marco Caterino, Katrin Paeschke
Summary: The nucleic acid structure known as G-quadruplex (G4) plays a significant role in nucleic acid-based mechanisms that impact cellular processes. DNA G4 is well-studied, while RNA G4 is gaining attention for its role in cellular homeostasis. Proper regulation of G4 structures within cells is crucial, and helicases are important in resolving them. However, only a few rG4 unwinding helicases have been identified and characterized so far.
Review
Biochemistry & Molecular Biology
Soumya Sethi, Hiroshi Sugiyama, Masayuki Endo
Summary: DNA nanotechnology is a promising toolkit for mimicking cell-cell and cell-matrix interactions, aiding in understanding and manipulating cellular functions. Future innovations in the field can be inspired by exploring the potentials of DNA-based nanostructures and addressing current challenges.
Article
Biochemistry & Molecular Biology
Yuki Hirose, Tomo Ohno, Sefan Asamitsu, Kaori Hashiya, Toshikazu Bando, Hiroshi Sugiyama
Summary: A cyclic pyrrole-imidazole polyamide (cPIP) was synthesized to bind to the abnormal expanded CAG/CTG repeat DNA sequences, showing high binding affinity and specificity for its target DNA sequence.
Article
Biochemistry & Molecular Biology
Ryu Tashiro, Ji Hye Yum, Soyoung Park, Hiroshi Sugiyama
Summary: The study showed that the photoreactivity of U-Br changes dramatically from hydrogen abstraction to cross-linking by changing the conformation of the duplex from the B-form to the A-form. Among three A-form structures, the largest amount of cross-linked products was observed when U-Br was incorporated into the RNA strand and the pyrene was conjugated to the 5 ' end of the DNA. These results indicate that the contact manner of pyrene was different between A- and B-form duplexes.
Article
Biochemistry & Molecular Biology
Kai Yu, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: Naturally occurring ribozymes with modular architecture are promising for designing and assembling three-dimensional RNA nanostructures with catalytic abilities. In this study, RNA nanostructures with polygonal-shaped ribozyme oligomers were constructed using unit RNAs from the Tetrahymena group I intron, and ribozyme trimers with a triangular shape were dimerized by introducing pillar units. The resulting double-decker nanostructures containing six ribozyme units showed higher catalytic activity than the parent ribozyme trimers.
Article
Biochemistry & Molecular Biology
Sagun Jonchhe, Shankar Pandey, Christian Beneze, Tomoko Emura, Hiroshi Sugiyama, Masayuki Endo, Hanbin Mao
Summary: Researchers found that a DNA nanobowl significantly increased the stability of a human telomeric G-quadruplex and its binding with a ligand. By minimizing the proximity effect and attributing the increased affinity to the nanoconfinement effect, they provided insights into the mechanisms of binding events in nanocavities.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Vinodh J. Sahayasheela, Zutao Yu, Yuki Hirose, Ganesh N. Pandian, Toshikazu Bando, Hiroshi Sugiyama
Summary: Research suggests that targeting Gli-mediated transcription to inhibit the proliferation of cancer stem cells may be a promising strategy.
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN
(2022)
Article
Biochemistry & Molecular Biology
Shingo Hirashima, Hiroshi Sugiyama, Soyoung Park
Summary: This study characterized 2FA-containing DNA molecules and found that they have similar structure and properties to native adenine due to their small size, but exhibit unique features due to their high electronegativity. This provides valuable information for future applications of 2FA-modified DNA.
Article
Biochemistry & Molecular Biology
Junnosuke Hatanaka, Yuki Hirose, Kaori Hashiya, Toshikazu Bando, Hiroshi Sugiyama
Summary: In this study, we synthesized linear pyrrole-imidazole polyamides (PIPs) that can selectively bind to DNA. These linear PIPs have lower molecular weights compared to commonly used hairpin PIPs. The binding affinity of the PIPs to DNA was improved by modifying the N-terminus of the linear PIPs. These findings provide insights for the design of effective linear PIPs.
Article
Cell Biology
Hamid A. Bakshi, Gerry A. Quinn, Mohamed M. Nasef, Vijay Mishra, Alaa A. A. Aljabali, Mohamed El-Tanani, Angel Serrano-Aroca, Mateus Webba Da Silva, Paul A. McCarron, Murtaza M. Tambuwala
Summary: Crocin derived from Himalayan crocus inhibits the growth of colon cancer cells by targeting NF-kB and blocking TNF-alpha/NF-kappa B/VEGF pathways, thus suppressing angiogenesis and colorectal cancer cell metastasis.
Article
Health Care Sciences & Services
Marco Zenone, Nora Kenworthy, Nason Maani
INTERNATIONAL JOURNAL OF HEALTH POLICY AND MANAGEMENT
(2023)
Article
Public, Environmental & Occupational Health
Zain Hussain, May C. I. van Schalkwyk, Sandro Galea, Mark Petticrew, Nason Maani
Summary: This study analyzed materials from the firearm industry and associated organizations to reveal the framing strategies they use when discussing firearms, firearm-related harms, and solutions to gun violence. Their strategies align with their business interests, similar to other harmful product manufacturers.
PREVENTIVE MEDICINE
(2023)
Editorial Material
Public, Environmental & Occupational Health
Jessamy Bagenal, Marco Zenone, Nason Maani, Skye Barbic
Article
Public, Environmental & Occupational Health
Nason Maani, Salma M. Abdalla, Catherine K. Ettman, Lily Parsey, Emma Rhule, Pascale Allotey, Sandro Galea
Summary: Many global health challenges are characterized by inequitable distribution of health and economic consequences, which are influenced by pre-existing inequalities in resources, power, and opportunity. This article discusses the importance of improving global equity as a prerequisite for achieving global health equity, and suggests ways to focus on foundational causes of ill health.
Article
Health Care Sciences & Services
Frank de Vocht, Cheryl McQuire, Claire Ferraro, Philippa Williams, Madeleine Henney, Colin Angus, Matt Egan, Andrea Mohan, Richard Purves, Nason Maani, Niamh Shortt, Laura Mahon, Gemma Crompton, Rachel O'Donnell, James Nicholls, Linda Bauld, Niamh Fitzgerald
Summary: This study aimed to quantify the effects of public health teams' engagement in alcohol licensing on health and crime outcomes. The results showed no clear evidence of any associations between this engagement and reductions in alcohol-related harms or crimes.
LANCET REGIONAL HEALTH-EUROPE
(2022)
Article
Substance Abuse
Ana Millot, Nason Maani, Cecile Knai, Mark Petticrew, Morgane Guillou-Landreat, Karine Gallopel-Morvan
Summary: This study analyzes the long-term lobbying strategies and arguments used by the alcohol industry to weaken the French Evin Law since its implementation. The research findings reveal that the industry employed similar tactics to other countries, but also utilized specific features unique to France.
JOURNAL OF STUDIES ON ALCOHOL AND DRUGS
(2022)
