Article
Biochemistry & Molecular Biology
Emil Laust Kristoffersen, Andrea Coletta, Line Morkholt Lund, Birgit Schiott, Victoria Birkedal
Summary: G-quadruplexes are noncanonical DNA structures that play important roles in DNA metabolic processes. We investigated the folding of consecutive G-quadruplexes in both potassium- and sodium-containing solutions and found coexistence of partially and fully folded DNA. Full consecutive G-quadruplex formation is inhibited by other DNA structures randomly nucleating on the DNA. Our study provides insights into the formation of consecutive G-quadruplexes in both equilibrium and nonequilibrium conditions.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Medicinal
Emanuela Ruggiero, Sara N. Richter
Summary: With the emergence and fast mutation rates of new viruses, there is a need for new antiviral targets and compounds. Most existing antiviral drugs target only a few specific viruses by affecting viral nucleic acid processing. However, selectively targeting nucleic acids of interest is challenging. Recently, G-quadruplexes (G4s), which are alternative structures to the classic double helix, have attracted attention due to their important biological roles. Molecules that selectively target G4s have been developed and investigated as potential antiviral drugs for various human pathologies, including viral infections.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Yu Luo, Anton Granzhan, Julien Marquevielle, Anne Cucchiarini, Laurent Lacroix, Samir Amrane, Daniela Verga, Jean-Louis Mergny
Summary: Besides the DNA double-helix, G-quadruplexes are non-canonical nucleic acid structures that regulate crucial biological activities. This article provides an overview of G-quadruplexes and a detailed description of the biophysical and biochemical methods used to study them in vitro. The aim is to establish guidelines for standardized research on G-quadruplexes.
Article
Chemistry, Analytical
Wen Lei, Jun Hu, Hong-Yuan Chen, Jing-Juan Xu
Summary: Accurate measurements of G-quadruplexes (G4s) and their interactions with metal ions and ligands under physiological conditions are crucial for understanding their biological roles and developing antitumor drugs. This study demonstrated for the first time that G4 ions can be directly released from common biochemical buffers and analyzed using mass spectrometry without non-specific adduction. The intermediate complexes of G4s with mixed di-cation coordination were successfully observed, and their structures were revealed by circular dichroism spectra.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Alexa M. Salsbury, Haley M. Michel, Justin A. Lemkul
Summary: This study used polarizable simulations to investigate telomeric DNA structures, including G-quadruplexes and G-hairpins. The presence of specific motifs, such as the G-triad, in the telomeric G-quadruplex suggests potential druggable sites. In addition, the simulations showed the unbiased formation of G-triad and G-tetrad in the G-hairpin, and the involvement of cations in their formation. Furthermore, the study demonstrated the specific interactions between K+ ions and guanine bases, providing new insights into the influence of ions on telomeric DNA structures.
Article
Chemistry, Physical
Yoann Colas, Stephane Menage, Caroline Marchi-Delapierre, Nicolas Spinelli
Summary: This study reveals the chiral control mechanism of G-quadruplexes in asymmetric sulfoxidation of thioanisole derivatives by constraining their structure. The results show that catalysis at different regions leads to the generation of different enantiomers.
Article
Biochemistry & Molecular Biology
Wei Long, Bo-Xin Zheng, Ying Li, Xuan-He Huang, Dan-Min Lin, Cui-Cui Chen, Jin-Qiang Hou, Tian-Miao Ou, Wing-Leung Wong, Kun Zhang, Yu-Jing Lu
Summary: This study reports a new approach of designing small molecules based on a non-selective thiazole orange scaffold to target G4 structures with improved selectivity. The ligands establish multi-site interactions with flanking residues and loops of the G4 motif, and demonstrate antitumor activity in cancer cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Jinbo Zhu, Filip Boskovic, Ulrich F. Keyser
Summary: This study combines DNA structures assembled based on split G-quadruplex (GQ) with a solid-state nanopore sensing platform for the rapid detection of multiple nucleic acid targets.
Article
Biochemistry & Molecular Biology
Souroprobho Chowdhury, Jiayi Wang, Sabrina Pia Nuccio, Hanbin Mao, Marco Di Antonio
Summary: This study investigates the disruption of G4s using LNA probes, finding that short LNA probes can accelerate the rate of G4 disruption and have the potential to study G4 biology.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Geng Qin, Chuanqi Zhao, Jie Yang, Zhao Wang, Jinsong Ren, Xiaogang Qu
Summary: The applicability of G-quadruplexes (G4s) as antiviral targets, therapeutic agents, and diagnostic tools for COVID-19 is being evaluated and has gained significant attention from the scientific community. There is a rapid accumulation of research in this field during the COVID-19 pandemic. This review summarizes the latest achievements and breakthroughs in using G4s, particularly G4 ligands, for the treatment, diagnosis, and prevention of COVID-19. The strengths and weaknesses of G4s in the field of anti-SARS-CoV-2 are highlighted for future projects.
CHINESE JOURNAL OF CHEMISTRY
(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)
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
Biochemistry & Molecular Biology
Alessio Cantara, Yu Luo, Michaela Dobrovolna, Natalia Bohalova, Miroslav Fojta, Daniela Verga, Lionel Guittat, Anne Cucchiarini, Solene Savrimoutou, Cecile Haberli, Jean Guillon, Jennifer Keiser, Vaclav Brazda, Jean Louis Mergny
Summary: Parasitic helminths infecting humans and cattle have significant impacts on health and livestock production. This study identified and compared G4 sequences in the genomes of various helminths and found that a Nematode species, Ascaris lumbricoides, had a high enrichment of stable G4 structures. Experimental confirmation of G4 formation and the discovery of small molecules that can selectively recognize and bind G4 motifs in a parasitic helminth demonstrate the potential for targeting G4 structures in the treatment of helminth infections.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Kevin Li, Liliya Yatsunyk, Stephen Neidle
Summary: Quadruplex DNAs can fold into distinct topologies with the help of water molecules. Different types of quadruplexes have specific hydration arrangements, playing a role in stabilizing the conformation of the structures.
NUCLEIC ACIDS RESEARCH
(2021)
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, Physical
Makoto Suzuki, Akira Tsuchiko, Yoshiyuki Tanaka, Nobuyuki Matubayasi, George Mogami, Nobuyuki Uozumi, Satoshi Takahashi
Summary: High-resolution measurements of microwave dielectric relaxation and Raman spectroscopies revealed the presence of hyper mobile water and a marked OH stretching band in ds 10-mer DNA solution. The LA band, observed at the low wavenumber tail of water's major OH stretching band, is formed by collective OH stretching vibrations of water molecules around the backbone phosphate oxygen atoms. The LA band intensity is affected by the addition of Mg(II) or Ca(II) ions, and this effect is reduced in the presence of 0.14 M KCl.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Polymer Science
Mahmoud H. Othman, Yoshihiro Ito, Jun Akimoto
Summary: In this study, water-soluble and highly antibiofouling polymers were synthesized and immobilized on polystyrene surfaces via photoirradiation. These polymers showed excellent solubility in water and suppressed nonspecific interactions between proteins and cells on the substrate, making them useful for biomaterial preparation.
Article
Materials Science, Biomaterials
Liang-Chun Wu, Seiichi Tada, Takashi Isoshima, Takeshi Serizawa, Yoshihiro Ito
Summary: Photo-reactive polymers are essential for biomaterials and have been employed for immobilizing growth factors. Different types of photo-reactive polymers were synthesized and their properties were analyzed. The study found that cell adhesion was influenced by the nature of photo-reactive polymers, while cell growth depended on the amount of immobilized growth factors and the properties of photo-reactive polymers.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)
Article
Chemistry, Analytical
Ren-Qi Wang, Ye Geng, Juan-Na Song, Huai-Dong Yu, Kai Bao, Yu-Ru Wang, Jean-Philippe Croue, Hideyuki Miyatake, Yoshihiro Ito, Yan-Ru Liu, Yong-Mei Chen
Summary: This study develops a biogenic solution map based on a 4D fingerprinting method to accurately discriminate and classify unknown species. It allows visualization of the similarities and disparities in molecular compositions of biogenic solutions, as well as the intrinsic correlations and subtle variations among them.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Fumitaka Hashiya, Hirotaka Murase, Akash Chandela, Haruka Hiraoka, Masahito Inagaki, Yuko Nakashima, Naoko Abe, Mayu Nakamura, Goro Terai, Yasuaki Kimura, Kaori Ando, Natsuhisa Oka, Kiyoshi Asai, Hiroshi Abe
Summary: Controlling PCR fidelity is crucial in molecular biology, and high-fidelity PCR is essential for gene cloning. While most studies focus on protein engineering of polymerases for fidelity control, this report explores the use of chemically modified nucleotide substrates. The modification on P-gamma of nucleotide substrates was found to affect PCR fidelity, with deoxyadenosine tetraphosphate enhancing one mutation type and deoxyguanosine tetraphosphate suppressing another. By using excess amounts of deoxyguanosine tetraphosphate, both mutations were successfully suppressed, leading to improved overall fidelity.
Article
Multidisciplinary Sciences
Masahito Inagaki, Naoko Abe, Zhenmin Li, Yuko Nakashima, Susit Acharyya, Kazuya Ogawa, Daisuke Kawaguchi, Haruka Hiraoka, Ayaka Banno, Zheyu Meng, Mizuki Tada, Tatsuma Ishida, Pingxue Lyu, Kengo Kokubo, Hirotaka Murase, Fumitaka Hashiya, Yasuaki Kimura, Satoshi Uchida, Hiroshi Abe
Summary: Starting with the clinical application of two vaccines in 2020, mRNA therapeutics are currently being investigated for various applications. Removing uncapped mRNA is important in mRNA research and clinical applications. This study developed a method to separate capped mRNA from uncapped mRNA using hydrophobic photocaged tag-modified cap analogs, achieving 100% capping efficiency. It was found that the Cap-2-type mRNA showed higher translational activity compared to the Cap-1-type mRNA prepared by the standard capping method.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Osama R. M. Metawea, Miyuki Nara, Takeharu Murakami, Satoshi Wada, Katsushi Fujii, Yoshihiro Ito, Masuki Kawamoto
Summary: A highly efficient single-walled carbon nanotube electrocatalyst, loaded with platinum nanoparticles using a newly developed suspension method, exhibits low overpotential for hydrogen evolution and shows high mass activity in a PEM electrolyzer.
ADVANCED MATERIALS INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Jyorthana Rajappa Muralidhar, Krishnachary Salikolimi, Kiyohiro Adachi, Daisuke Hashizume, Koichi Kodama, Takuji Hirose, Yoshihiro Ito, Masuki Kawamoto
Summary: We report an organic-inorganic halide perovskite compound that can chemically store ammonia through dynamic structural transformation. This compound undergoes a chemical structure change from a one-dimensional columnar structure to a two-dimensional layered structure upon NH3 uptake through addition reaction. The estimated NH3 uptake is 10.2 mmol g(-1) at 1 bar and 25℃. NH3 extraction can be performed by a condensation reaction at 50℃ under vacuum. X-ray diffraction analysis reveals that reversible NH3 uptake/extraction originates from a cation/anion exchange reaction. These findings demonstrate the potential of integrating efficient uptake and extraction in a hybrid perovskite compound through chemical reaction, paving the way for further exploration of dynamic and reversible compounds for chemical storage of NH3.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Nanoscience & Nanotechnology
Osama R. M. Metawea, Miyuki Nara, Takeharu Murakami, Hirotaka Okabe, Naoki Matsuda, Satoshi Wada, Katsushi Fujii, Yoshihiro Ito, Masuki Kawamoto
Summary: Proton exchange membrane (PEM) water electrolysis is a promising method for clean hydrogen production. A new approach using aqueous-dispersed PtNPs as a dispersant for carbon nanomaterials (CNMs) is reported, resulting in efficient PtNP/CNM composites. The PtNP/SWCNT nanocomposite exhibits a mass activity of 89,300 A g(Pt) (-1), 270 times higher than that of Pt/C.
ACS APPLIED NANO MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Avanashiappan Nandakumar, Yoshihiro Ito, Motoki Ueda
Summary: A disulfide-tethered peptide-lipid conjugate can self-assemble into a homogeneously distributed peptide-lipid hybrid vesicle. Treatment with dithiothreitol causes the homogeneous peptide-lipid membrane to spontaneously separate into lipid-rich and peptide-rich domains, while the vesicle remains unchanged in size and shape. Membrane phase separation enhances temperature-dependent cargo release.
CHEMICAL COMMUNICATIONS
(2023)
Article
Materials Science, Biomaterials
Mohamed S. S. Elafify, Toru Itagaki, Nermeen A. A. Elkasabgy, Sinar Sayed, Yoshihiro Ito, Motoki Ueda
Summary: The development of stimuli-responsive transformable biomaterials can be effectively controlled by adjusting the molecular design of their structural segments. In this study, we demonstrate a peptide assembly that exhibits morphological transformations between hydrophilic and hydrophobic morphologies. The hydrophobic α-helical unit precisely controls the packing and induces the formation of tubules in the assembly. By analyzing membrane fluidity and the surrounding environment of the assembly, we clarify that the vesicle is kinetically stable while the nanotube is thermodynamically stable.
BIOMATERIALS SCIENCE
(2023)
Article
Materials Science, Biomaterials
Kun Fang, Stefan Muller, Motoki Ueda, Yasuhiro Nakagawa, Katsuko Furukawa, Takashi Ushida, Toshiyuki Ikoma, Yoshihiro Ito
Summary: Fibroblasts confined by gelatin micropatterns and subjected to cyclic stretch showed significant changes in cell morphology. Non-patterned cells exhibited increasing length and decreasing area under the stretch. The width of the micropatterns provided different contact guidance for fibroblasts, resulting in varied cell behaviors under cyclic stretch. Vertical stretch induced a greater increase in cell area and length compared to parallel stretch. These findings provide insights into cell behaviors under geometrical confinement in a dynamic biomechanical environment and can guide biomaterial design for tissue engineering.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)
Review
Materials Science, Biomaterials
Xiaoyu Guan, Bingyuan Zhang, Zequn Wang, Qingxin Han, Meng An, Motoki Ueda, Yoshihiro Ito
Summary: Tannins, natural plant polyphenols, are widely used in various fields, especially in biomedical applications. However, their water solubility limits their use in specific applications, making separation and regeneration difficult. Tannin-immobilized composites, inspired by composite materials, combine the advantages of each component, allowing for expanded applications in different fields.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)
Article
Chemistry, Organic
Shogo Hasegawa, Masahito Inagaki, Shunichi Kato, Zhenmin Li, Yasuaki Kimura, Hiroshi Abe
Summary: We present a novel approach for synthesizing nucleoside oligophosphates by electrophilic activation of 5'-phosphorothioate nucleotides. Treatment of phosphorothioate with 2,4-dinitrochlorobenzene (DNCB) efficiently produced electrophilic thioester nucleotides (EPT-Ns), which were then coupled with various phosphate reagents to yield the desired nucleoside oligophosphates, including an mRNA cap analog.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Toshinobu Nakajo, Shinpei Kusaka, Haruka Hiraoka, Kohei Nomura, Noriaki Matsubara, Rintaro Baba, Yuki Yoshida, Kosuke Nakamoto, Masakazu Honma, Hiroaki Iguchi, Takayuki Uchihashi, Hiroshi Abe, Ryotaro Matsuda
Summary: We developed an equimolar conjugate of a metal-organic cage (MOC) and DNA (MOC-DNA). By coordinating with a template DNA, several MOC-DNA conjugates were assembled into a programmed structure. Additionally, the conjugation with MOC greatly enhanced the permeability of DNA through lipid bilayer, showing promising potential as a drug delivery system.
CHEMICAL COMMUNICATIONS
(2023)