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
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
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
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.
Review
Chemistry, Multidisciplinary
Denise Liano, Ludovica Monti, Souroprobho Chowdhury, Federica Raguseo, Marco Di Antonio
Summary: This article discusses the research on G-quadruplex structures of DNA and their biological roles. The author challenges existing beliefs by discovering a human protein with high affinity and selectivity for intermolecular G-quadruplex structures, emphasizing the need for further study on the biological significance of these DNA structures. Furthermore, the potential role of G-quadruplex structures in neurodegenerative diseases is discussed.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Anirban Ghosh, Eric Largy, Valerie Gabelica
Summary: This study focuses on using native mass spectrometry for drug screening on G-quadruplex DNA structures. By studying 28 sequences, a standardized screening method was established and recommendations for future research were provided. Furthermore, an R-based open-source application was developed to build and consult a database for further exploration.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Jiao-Na Han, Mingmin Ge, Pengfei Chen, Shi Kuang, Zhou Nie
Summary: This review provides an overview of fluorescent imaging approaches for tracking G4s and discusses the potential of G4-containing FLAPs in bioimaging. The current developments and future challenges of G4 imaging and G4-containing FLAPs are also discussed.
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
Chemistry, Multidisciplinary
Anand Lopez, Juewen Liu
Summary: K+ enhances the fluorescence of G-quadruplex DNAs, while Pb2+ quenches the fluorescence. The metals exhibit interesting quadruplex binding kinetics with various DNA sequences.
CHEMICAL COMMUNICATIONS
(2022)
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
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, Multidisciplinary
Chen Wang, Jin Shang, Li Tian, Hongwei Zhao, Peng Wang, Kai Feng, Guokang He, Jefferson Zhe Liu, Wei Zhu, Guangtao Li
Summary: This study presents a chemical probe for direct identification of HMX at ppb sensitivity based on a designed metal-organic cage (MOC). The capture of HMX inside the cage strongly modulates the emissive behavior, resulting in a highly induced fluorescence turn-on (160 folds), and the mechanism behind this phenomenon is explained through density functional theory (DFT) simulation.
CHINESE CHEMICAL LETTERS
(2021)
Article
Chemistry, Multidisciplinary
Pu Zhang, Yu Ouyang, Yang Sung Sohn, Michael Fadeev, Ola Karmi, Rachel Nechushtai, Ilan Stein, Eli Pikarsky, Itamar Willner
Summary: This article introduces an analytical platform that uses miRNA-guided imaging for selective detection of breast cancer cells and ovarian cancer cells, as well as selective photodynamic therapy to kill these cancer cells using visible light.
Review
Chemistry, Multidisciplinary
Chen Wang, Michael P. O'Hagan, Ziyuan Li, Junji Zhang, Xiang Ma, He Tian, Itamar Willner
Summary: Photoresponsive nucleic acids have significant implications in materials science, allowing for the development of light-sensitive devices and materials with applications in catalysis, sensing, and drug delivery. The integration of photoisomerizable units into DNA strands enables reversible reconfiguration of nucleic acid architectures, providing control over the composition and properties of nanostructures.
CHEMICAL SOCIETY REVIEWS
(2022)
Review
Chemistry, Multidisciplinary
Chen Wang, Michael P. O'Hagan, Bilha Willner, Itamar Willner
Summary: This article presents recent advances in developing artificial photosynthetic systems, including photobioelectrochemical cells interfacing with electrodes, light-induced electron transfer, and integration of artificial photosynthetic modules into dynamic nucleic acid networks.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Analytical
Michael Fadeev, Yu Ouyang, Gilad Davidson-Rozenfeld, Itamar Willner
Summary: Soft materials like hydrogels, polymers, or biomaterials when associated with electrodes reveal functions such as electrocatalytic, photoelectrocatalytic, and controlled release of loads. Three examples from the laboratory demonstrate these functions, involving stimuli-responsive nucleic acid-based hydrogels, pH-responsive nucleic acid-based hydrogels, and supramolecular matrices with native photosystem I interlinked with glucose oxidase.
JOURNAL OF ELECTROANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Yu Ouyang, Michael Fadeev, Pu Zhang, Raanan Carmieli, Jiang Li, Yang Sung Sohn, Ola Karmi, Rachel Nechushtai, Eli Pikarsky, Chunhai Fan, Itamar Willner
Summary: Polyadenine-stabilized Au nanoparticles (pA-AuNPs) exhibit dual nanozyme catalytic activities for the oxidation reactions of dopamine and glucose. The conjugation of a dopamine-binding aptamer (DBA) to pA-AuNPs enhances the catalytic activity. The aptananozymes can also be targeted to cancer cells and demonstrate selective cytotoxicity.
Article
Chemistry, Physical
Michael Fadeev, Michael P. O'Hagan, Yonatan Biniuri, Itamar Willner
Summary: A method combining computational and experimental approaches is introduced to identify aptamers against short peptides or amino acid clusters. The method uses in silico docking and experimental validation to demonstrate the binding affinities of miniaturized peptides to known antiprotein aptamers, as well as the specific clustering of single amino acids on the aptamers.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Polymer Science
Guokang He, Peng Wang, Ning Gao, Xianpeng Yin, Fuwei Sun, Wenyun Li, Hongwei Zhao, Chen Wang, Guangtao Li
Summary: We report a new type of brush-like triblock copolymer that can serve as a structure-directing agent for the formation of mesoporous silicates and be converted into mesostructured polymer or carbon materials. The versatile nature of this copolymer allows for the facile access to various mesostructured silica, polymer, and carbon materials. The brush-like hydrophilic segments of the copolymers can firmly anchor into the silica walls, providing a prerequisite for reliable confined chemical transformation into mesostructured materials.
Article
Nanoscience & Nanotechnology
Yu Ouyang, Michael Fadeev, Pu Zhang, Raanan Carmieli, Yang Sung Sohn, Ola Karmi, Yunlong Qin, Xinghua Chen, Rachel Nechushtai, Itamar Willner
Summary: In this study, aptamer-functionalized Ce4+-ion-modified C-dots were found to act as catalytic hybrid systems, aptananozymes, which catalyze the H2O2 oxidation of dopamine. The aptananozymes exhibited enhanced catalytic activities compared to the separated Ce4+-ion-modified C-dots and aptamer constituents. The structure and binding modes of the aptamers linked to the C-dots were shown to influence the catalytic functions of the aptananozymes. The increased catalytic functions were attributed to the concentration of reaction substrates induced by the aptamers in spatial proximity to the Ce4+-ion-modified C-dots catalytic sites. Additionally, Ce4+-ion-modified C-dots functionalized with aptamers recognizing specific biomarkers associated with cancer cells showed selective cytotoxicity towards cancer cells, suggesting their potential use for chemodynamic treatment of cancer.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Multidisciplinary
Chengcheng Liu, Wenyun Li, Wanlin Zhang, Hongwei Zhao, Guokang He, Chi Li, Chen Wang, Guangtao Li
Summary: A sensing platform using poly(ionic liquid) (PIL) photonic crystal spheres doped with aggregation-induced emission (AIE) luminogens has been developed, with the ability to identify a broad range of psychoactive substances.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Materials Science, Multidisciplinary
Fuwei Sun, Li Tian, Guokang He, Ning Gao, Hongwei Zhao, Weigang Liu, Chao Liu, Qi An, Chen Wang, Guangtao Li
Summary: Plasmonic networks have gained increasing attention due to their strong plasmon coupling effects and collective optical behavior in hotspot regions. However, engineering network architectures with flexible control over hotspot density and intensity is a challenge. This study presents a bottom-up self-assembly strategy using cage-assisted structures to construct complex plasmonic network architectures with adjustable hotspots. The integration of host-guest chemistry enables selective molecule trapping in hotspots, providing opportunities for diverse plasmon-based applications.
ADVANCED OPTICAL MATERIALS
(2023)
Article
Nanoscience & Nanotechnology
Guokang He, Ce Han, Peng Wang, Ning Gao, Fuwei Sun, Wenyun Li, Weigang Liu, Xinping Qiu, Chen Wang, Guangtao Li
Summary: In this work, a kind of bifunctional block copolymer that can serve as a structure-directing agent and a precursor for the formation of carbon materials was used to synthesize well-defined mesoporous carbon-supported TiO2 heterostructures. The generated carbon networks provide thermal stability, enabling the formation of highly crystalline TiO2 skeletons and modulating the TiO2 crystalline phase without collapsing the mesoporous structures. The nitrogen content and functional moieties in the carbon layer can be easily tuned, allowing for the facile construction of diverse heterostructures with enhanced properties. A mesoporous carbon-supported TiO2 was prepared and exhibited excellent performance in lithium battery application, indicating the potential of this synthetic concept for developing novel TiO2 nanomaterials.
ACS APPLIED NANO MATERIALS
(2023)
Review
Chemistry, Multidisciplinary
Jiadong Tang, Yibo Cheng, Muhua Ding, Chen Wang
Summary: This review presents recent progress in the development of bio-inspired supramolecular hydrogels operating out-of-equilibrium. The principle of out-of-equilibrium self-assembly for creating these hydrogels is discussed, and various design strategies are identified for achieving temporal and spatial control over their properties. The potential applications and future challenges and prospects are also addressed.
Article
Nanoscience & Nanotechnology
Yu Ouyang, Michael Fadeev, Pu Zhang, Raanan Carmieli, Yang Sung Sohn, Ola Karmi, Yunlong Qin, Xinghua Chen, Rachel Nechushtai, Itamar Willner
Summary: Aptamer-functionalized Ce4+-ion-modified C-dots show enhanced catalytic activities and can be used as targeted catalytic agents for cancer treatment.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Review
Nanoscience & Nanotechnology
Chen Wang, Junji Zhang
Summary: Stimuli-responsive DNA-based hydrogels are of growing interest due to their smart responsiveness, excellent biocompatibility, regulated biodegradability, and programmable design properties. This review highlights recent advances in the design of responsive pure DNA hydrogels, DNA-polymer hybrid hydrogels, and autonomous DNA-based hydrogels with transient behaviors, as well as their versatile applications in various fields. The challenges and future prospects of this field are also addressed.
ACS APPLIED BIO MATERIALS
(2022)
