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
Elisabeth Kallert, Malte Behrendt, Ariane Frey, Christian Kersten, Fabian Barthels
Summary: Microscale Thermophoresis (MST) is a powerful biophysical technique that investigates the interactions between biomolecules by measuring their mobility in response to temperature gradient. This study presents a novel methodology for studying RNA-containing samples using non-covalent nucleic acid-sensitive dyes in MST. The mix-and-measure protocol using non-covalent dyes has advantages over traditional covalent labelling approaches, and has been successfully applied to study ligand binding to RNA molecules and identify modifications in short RNA oligos.
Article
Chemistry, Multidisciplinary
Elisabeth Kallert, Malte Behrendt, Ariane Frey, Christian Kersten, Fabian Barthels
Summary: This study presents an innovative technique to study RNA using nucleic acid-sensitive dyes in MST. By using non-covalent dyes, this method allows for better investigation of ligand binding to RNA molecules and modifications in RNA oligos.
Article
Chemistry, Analytical
Rouba Nasreddine, Reine Nehme
Summary: Microscale thermophoresis (MST) is a sensitive biophysical tool that allows rapid and accurate determination of the dissociation constant (K-d) between enzymes and small molecules, aiding in the study of binding affinity between biomolecules. The study demonstrated that hyaluronidase maintained enzymatic activity after fluorescent labelling, but showed no affinity with flavonoid compounds under the tested conditions.
MICROCHEMICAL JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Julian A. C. Stein, Alan Ianeselli, Dieter Braun
Summary: MST is a versatile technique for measuring binding affinities, based on directional movement of molecules in a temperature gradient. We extended MST to measure binding kinetics by increasing thermal dissipation, allowing for simultaneous determination of kinetics and binding affinity. By measuring DNA hybridization rates, we observed linear dependence of on-rates on salt concentration and weak dependence on strand length and temperature.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Biochemical Research Methods
Mufarreh Asmari, Lenka Michalcova, Adel Ehab Ibrahim, Zdenek Glatz, Hermann Waetzig, Sami El Deeb
Summary: This review evaluates the applications of affinity capillary electrophoresis (ACE) and microscale thermophoresis (MST) techniques in studying molecular binding from 2016 to 2021. ACE has demonstrated high resolution efficiency for biomolecular characterization, with the potential for significant improvement compared to other analytical techniques. On the other hand, MST has shown higher sensitivity for smaller non-purified biosamples without compromising robustness and provides high throughput. The main motivation for this review is the ability of both techniques to carry out experiments without immobilizing one interacting partner, as well as the flexibility in buffering system usage. The review highlights the importance of these techniques in various areas of life sciences, and discusses recent advances in utilizing ACE and MST in other research interests.
Article
Chemistry, Physical
Wei Zhou, Yunchao Li, Louzhen Fan, Xiaohong Li
Summary: G-rich DNA sequences can transform into G-quadruplexes in the presence of metal ions, which serve as signal-transducing elements in fluorescent sensing platforms that recognize various biological molecules. The binding affinity of fluorescent small molecules with G4 is dependent on the G4 morphologies and co-existing ions.
ACTA PHYSICO-CHIMICA SINICA
(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
Chemistry, Physical
Mario Gonzalez-Jimenez, Gopakumar Ramakrishnan, Nikita V. Tukachev, Hans M. Senn, Klaas Wynne
Summary: Research indicates that low-frequency vibrations of G-quadruplexes may have an impact on the biological function of DNA, and G-quadruplexes exhibit modes at a higher frequency than B-DNA, suggesting that changes in molecular stiffness alter its vibrational profile.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biochemical Research Methods
Sila Can Osmanogullari, Mehrdad Forough, Ozgul Persil Cetinkol, Yasemin Arslan Udum, Levent Toppare
Summary: This study successfully fabricated a graphite electrode biosensor modified with gold nanoparticles (AuNPs) to investigate the interactions between OXP and the G4-forming promoter region (Pu22) of VEGF. DPV was used to monitor the decrease in guanine oxidation signal and investigate the interactions between OXP and Pu22-G4 DNA. Our findings provide new insights into the interactions between VEGF G4 and OXP.
ANALYTICAL BIOCHEMISTRY
(2023)
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)
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.
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.
Review
Biochemistry & Molecular Biology
Ai-Yu Guo, Ya-Mei Zhang, Liu Wang, Di Bai, Ya-Peng Xu, Wen-Qiang Wu
Summary: Single-molecule imaging is a revolutionary approach for studying fundamental questions in plants, but its application in plants is still underexplored compared to animals. This technique provides unprecedented quantitative details and faces challenges that require possible solutions to be addressed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Shasha Ye, Ziting Chen, Xia Zhang, Fangfang Li, Lijuan Guo, Xi-Miao Hou, Wen-Qiang Wu, Jian Wang, Cong Liu, Ke Zheng, Bo Sun
Summary: Proximal single-stranded RNA significantly impairs the stability of RG4, resulting in easier accessibility of the G-rich sequence at physiological K+ concentrations. This destabilizing effect requires a minimum of six nucleotides of ssRNA and is effective at either end of RG4. Under the influence of such proximal ssRNA, the RG4-forming sequence exhibits interconversions between at least three less stable RG4 conformers.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Multidisciplinary Sciences
Xuejie Wang, Yang Dong, Xiaocong Zhao, Jinbao Li, Jordan Lee, Zhenxin Yan, Shuangshuang Yang, Wenqiang Wu, Ximiao Hou, Guangxue Liu, Yueyue Zhang, Lun Song, Gang Cai, Qing Li, Grzegorz Ira, Xinghua Zhang, Xuefeng Chen
Summary: Rtt105 plays a critical role in high-fidelity DNA replication and recombination by regulating RPA, while also suppressing repair through deleterious pathways. Its human homolog, hRIP-alpha, displays similar functions, suggesting conservation of the Rtt105-mediated mechanism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Daichi Yamada, Junpei Yamamoto, Elizabeth D. Getzoff, Tatsuya Iwata, Hideki Kandori
Summary: In this study, conformational changes in photolyases and specific substrates upon photoactivation and photorepair processes were measured using light-induced difference Fourier transform infrared (FT-IR) spectroscopy. Different FT-IR signals were obtained in an illumination time-dependent manner for ss(6-4)PP photorepair, showing similarities in conformational changes between ss(6-4)PP and ds(6-4)PP binding to photolyases.
Article
Plant Sciences
Lin Zhang, Jinlei Liu, Jieru Cheng, Quan Sun, Yu Zhang, Jinggao Liu, Huimin Li, Zhen Zhang, Ping Wang, Chaowei Cai, Zongyan Chu, Xiao Zhang, Youlu Yuan, Yuzhen Shi, Yingfan Cai
Summary: In this study, it was found that long noncoding RNAs (lncRNAs) and their regulating genes in cotton play a role in regulating disease resistance against pathogens such as fungi. Specifically, lncRNA7 and its regulating gene GbPMEI13 were found to positively regulate disease resistance, while lncRNA2 and its regulating gene GbPG12 negatively regulated resistance. It was also discovered that fungal disease-related agents could downregulate the expression of lncRNA2 and GbPG12, resulting in pectin accumulation, while upregulating the expression of lncRNA7. Furthermore, the study revealed that a plant peptide called PSK-alpha could enhance disease resistance by regulating auxin accumulation and activating GbPMEI13 expression.
Article
Biochemistry & Molecular Biology
Jing Huang, Xiakun Chu, Yuxiang Luo, Yong Wang, Ying Zhang, Yu Zhang, Huilin Li
Summary: Allosteric regulation of glycogen phosphorylase (GP) has significant biological importance, but the structural dynamics related to this regulation remain largely unknown due to the large size of GP. In this study, multiple techniques including mass spectrometry and molecular dynamics simulations were used to investigate the structural basis and dynamics of GP allosteric regulation by phosphorylation. The results revealed differences in stability, oligomeric state, and binding interfaces between the unphosphorylated and phosphorylated forms of GP, and identified the missing link of long-range communication caused by phosphorylation.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Liu Wang, Ya-Peng Xu, Di Bai, Song-Wang Shan, Jie Xie, Yan Li, Wen-Qiang Wu
Summary: This study experimentally elucidates the folding pathway and intermediates of RNA G-quadruplexes (rG4s) and identifies and validates five rG4-specialized helicases in Arabidopsis thaliana. These findings shed light on the structural dynamics of plant rG4s.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Wen-Qiang Wu, Xin Zhang, Di Bai, Song-Wang Shan, Li-Jun Guo
Summary: This study comprehensively investigated the mechanisms of interaction between I-motifs and PCBPs, revealing how heterogeneous nuclear ribonucleoprotein K (hnRNP K) unfolds the I-motif structure in the c-MYC oncogene promoter. Furthermore, the role of KH domains in this process was also discovered. This research enhances our understanding of the interactions between I-motifs and PCBPs and may provide insights for drug development.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Plant Sciences
Liangliang Li, Linxiao Li, Shenghui Cui, Dongdong Qian, Shijie Lyu, Wencheng Liu, Jose Ramon Botella, Huilin Li, David J. Burritt, Lam-Son Phan Tran, Weiqiang Li, Yu Zhang
Summary: Seed germination in Arabidopsis is regulated by ABA through the activation of PDC1 gene, which promotes fatty acid beta-oxidation and ROS accumulation, resulting in inhibition of seed germination.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Xiao-Cong Zhao, Hai-Long Dong, Xiao-Lu Li, Hong-Yu Yang, Xue-Feng Chen, Liang Dai, Wen-Qiang Wu, Zhi-Jie Tan, Xing-Hua Zhang
Summary: 5-Methyl-cytosine (5mC) is one of the most important DNA modifications, playing versatile biological roles. This study reveals that 5mC kinetically hinders DNA hybridization due to steric effects, leading to high energy barriers.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Pharmacology & Pharmacy
Ying Zhang, Qinghua Cai, Yuxiang Luo, Yu Zhang, Huilin Li
Summary: Defects in ribosomal proteins are linked to various diseases, and comprehensive characterization of ribosomal proteoforms is important for discovering potential disease biomarkers or targets. The combination of top-down and bottom-up proteomics approaches successfully identified and analyzed the different forms and modifications of ribosomal proteins.
JOURNAL OF PHARMACEUTICAL ANALYSIS
(2023)
Article
Chemistry, Multidisciplinary
Han Liang, Liangliang Li, Houguo Fei, Yongkang Zhang, Pan Qi, Liwen Su, Yu Zhang, Cunlan Guo
Summary: Researchers have designed three improved light-oxygen-voltage (iLOV) domains, and successfully regulated the charge transport properties of iLOV self-assembled monolayers (SAMs) through pH-induced conformation changes. The current density can be controlled within an order of magnitude. This study proposes a new approach to investigate charge transport in complex molecular systems and enhances our understanding of the relationship between protein structure and charge transport.
CHEMISTRY-AN ASIAN JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Di Bai, Song-Wang Shan, Xin Zhang, Yan Li, Jie Xie, Wen-Qiang Wu
Summary: In this study, the folding, dynamics induced by environment, and protein-catalyzed unfolding of plant telomeric G4s were comprehensively studied. It was found that various plant telomeric sequences can fold into G4 structures, and the stability of G4s in dilute solution is decreased by both 5' and 3' ssDNA. Molecular crowding promotes the formation of parallel structures for three-layer G4s and increases the stability of all selected G4s. AtRecQ2 helicase can resolve the stable parallel structure of typical plant telomeric G4 in crowded solution, while ssDNA binding protein AtRPA cannot. Furthermore, AtRecQ2 unwinds the structure more efficiently in the presence of AtRPA. These results expand our understanding of the structures and dynamics of plant telomeric G4s.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Cell Biology
Jie Zhang, Er-Chi Zhou, Yan He, Ze-Lin Chai, Ben-Zhe Ji, Yi Tu, Han-Ling Wang, Wen-Qiang Wu, Yong Liu, Xing-Hua Zhang, Yu Liu
Summary: As a key dsDNA recognition receptor, cGAS plays a vital role in innate immune responses. Here, we report ZYG11B as a potent amplifier in cGAS-mediated immune responses, enhancing cGAS-DNA binding affinity, condensation, and stability. Furthermore, herpes simplex virus 1 infection induces ZYG11B degradation, dampening the innate immune response.
Article
Multidisciplinary Sciences
Yusen Zhou, Tian Zhang, Xiaocui Wang, Wenqiang Wu, Jingjing Xing, Zuliang Li, Xin Qiao, Chunrui Zhang, Xiaohang Wang, Guangshun Wang, Wenhui Li, Shenglong Bai, Zhi Li, Yuanzhen Suo, Jiajia Wang, Yanli Niu, Junli Zhang, Chen Lan, Zhubing Hu, Baozhu Li, Xuebin Zhang, Wei Wang, David W. Galbraith, Yuhang Chen, Siyi Guo, Chun-Peng Song
Summary: The researchers identified a maize gene, BZU3, that regulates the synthesis of UDP-glucose during grass guard cell wall formation and is involved in protein glycosylation. The findings shed light on the dual role of BZU3 in controlling stomatal morphogenesis and provide insights into the mechanisms of grass stomata formation.
NATURE COMMUNICATIONS
(2023)