Article
Biochemistry & Molecular Biology
Armelle Vigouroux, Thibault Meyer, Anais Naretto, Pierre Legrand, Magali Aumont-Nicaise, Aurelie Di Cicco, Sebastien Renoud, Jeanne Dore, Daniel Levy, Ludovic Vial, Celine Lavire, Solange Morera
Summary: The species-specific region SpG8-1b plays a critical role in controlling the transition between rhizospheric and pathogenic lifestyles of the plant pathogen. The transcriptional regulator Atu1419, belonging to the VanR group of GntR superfamily, represses genes in the HCAs catabolic pathway and is regulated by the effector molecule N5,N10-methylenetetrahydrofolate. The study sheds light on the allosteric mechanism of transcription employed by this GntR repressor.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Katsumasa Irie, Yoshinori Oda, Takashi Sumikama, Atsunori Oshima, Yoshinori Fujiyoshi
Summary: In this study, the authors investigated the mechanism of divalent cation block in a prokaryotic sodium channel, NavAb, by studying its mutants. They found that mutations increasing the hydrophilicity of the inner vestibule of the channel enabled a divalent cation to stack on the ion pathway. Molecular dynamics simulations showed that the stacking calcium ion repelled sodium ions at the bottom of the selectivity filter, providing insight into the primary process of divalent cation block in tetrameric cation channels.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Marc Farag, Cedric Messaoudi, Liliane Mouawad
Summary: ASC-G4 is an algorithm that calculates the advanced structural characteristics of G-quadruplexes (G4). It determines the intramolecular G4 topology and resolves the ambiguity in guanine glycosidic configuration. The algorithm shows that using C3' or C5' atoms is more appropriate than P atoms for calculating groove width in G4, and that minimum groove width is a better measure of available space. ASC-G4 was applied to 207 G4 structures, guiding the calculations. The ASC-G4 website allows users to upload their G4 structures and obtain information on topology, loop types and lengths, snapbacks and bulges, guanine distribution, glycosidic configuration, groove widths, minimum groove widths, tilt and twist angles, backbone dihedral angles, and relevant atom-atom and atom-plane distances for structure evaluation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Chao Gao, Jixin Chen, Naureen Anwar, Jieya Deng, Zhangqian Wang, Muhammad Umer, Yi He
Summary: This study compared the stability and compactness of insect monomeric and multimeric G-quadruplex structures in K+ and Na+ solutions. It was found that insect telomeric G-quadruplexes are more stable and compact in Na+ solutions. The interaction between BMPQ-1 and insect multimeric G-quadruplexes was investigated, and BMPQ-1 was found to have a significant inhibitory effect on the proliferation of pest cells.
Article
Chemistry, Analytical
Mengmeng Wu, Bing Yang, Lu Shi, Qiaorong Tang, Jing Wang, Wei Liu, Baoxin Li, Yan Jin
Summary: This study developed a label-free chemiluminescence sensor array using peroxidase-mimicking DNAzymes as receptors to discriminate various heavy metal ions in complex samples. The conformation of G-quadruplex and G-triplex affected by different metal ions resulted in a change in the activity of peroxidase-mimicking DNAzyme. Principal component analysis easily discriminated seven kinds of heavy metal ions by analyzing the unique fingerprints formed. The ability to discriminate unknown metal ions in tap water confirmed the sensor's potential. This innovative approach not only offers a label-free, rapid, environment-friendly, and cheap sensor assay for discriminating metal ions, but also provides a new way for developing sensor arrays.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Jing Liu, Taozhe Zhang, Jinyang Feng, Yue Cui, Li Zhang, Yunong Wang, Meiyu Cui, Donghao Li, Hulin Tai
Summary: It is discovered that N-acetylated microperoxidase-11 and G-quadruplex DNA can form a stable peptide-hemin/DNA hybrid-complex, and the peroxidase activity at the interface between hemin and the G-quartet planes exponentially increases with increasing K-a value.
CHEMICAL COMMUNICATIONS
(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.
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
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
Linnea I. Jansson-Fritzberg, Camila I. Sousa, Michael J. Smallegan, Jessica J. Song, Anne R. Gooding, Vignesh Kasinath, John L. Rinn, Thomas R. Cech
Summary: Aberrant DNA methylation is an early sign of cancer, and DNMT1 is responsible for methylating newly replicated DNA. In this study, we confirmed that human DNMT1 interacts with multiple RNAs, including its own nuclear mRNA. Surprisingly, DNMT1 showed a strong affinity for GU-rich RNAs that form a noncanonical G-quadruplex structure and can inhibit its activity.
Article
Biology
Osamu Hisano, Takashi Ito, Fumihito Miura
Summary: This study identified short single-stranded cfDNA fragments approximately 50 nucleotides in length in human plasma, at concentrations comparable to nucleosome-sized fragments. These fragments are derived from open chromatin regions and enriched in transcription factor-binding sites, potentially forming non-canonical DNA structures.
Article
Agriculture, Multidisciplinary
Wenming Wang, Yuan Wang, Hongfang Xi, Zidan Song, Wenlong Zhang, Leilei Xie, Danyang Ma, Nan Qin, Hongfei Wang
Summary: The extension peptide (EP) is a unique feature of mature plant ferritin and may have protease activity related to iron uptake and release. Our study on the crystal structure of ferritin-1 from Setaria italica revealed that the EP in this monocotyledon plant had a different folding pattern than other plant ferritins, suggesting a novel fold pattern for EPs in monocotyledons. Additionally, our study found additional iron atoms binding in the fourfold channels, highlighting the important role of these channels in iron diffusion.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Jesus Fernandez-Lucas, Ivan Acebron, Ruiying Y. Wu, Yohana Alfaro, Javier Acosta, Pierre A. Kaminski, Miguel Arroyo, Andrzej Joachimiak, Boguslaw P. Nocek, Isabel De la Mata, Jose M. Mancheno
Summary: The study reports the crystal structures and biochemical properties of two novel tetrameric NDTs, including the first psychrophilic NDT. Comparative analysis of the new structural and biochemical data reveals that DpNDT has unique structural motifs that likely contribute to its global stability, and its functional and structural features differ from standard psychrophilic enzymes.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Multidisciplinary Sciences
Yan Liu, Rui Wang, Zhigang Wang, Da Li, Tian Cui
Summary: In this study, the authors report the prediction of a nitrogen-rich iodine nitride compound (IN6) with an unusual twelve-fold coordination of the iodine atom under high pressure. They discovered the existence of a hypercoordinated IN6 compound composed of N-6 rings and an unusual iodine-nitrogen covalent bond network using particle swarm optimization method and first-principles calculations. The formation of twelve-fold iodine hypercoordination is facilitated by the presence of high pressure and N-6 rings. The findings also suggest that halogen elements with lower atomic numbers have weaker valence expansion propensity in halogen nitrides.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jean Chatain, Alain Blond, Anh Tuan Phan, Carole Saintome, Patrizia Alberti
Summary: Human telomeres contain GGGCTA variant motifs that show length-dependent instability, forming G4 and hairpin structures; RPA efficiently binds to G4 but poorly binds to hairpin structures of GGGCTA repeats, suggesting a potential mechanism for GGGCTA array instability.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Paul J. Paukstelis
JOURNAL OF CHEMICAL EDUCATION
(2018)
Article
Chemistry, Multidisciplinary
Diana Zhang, Paul J. Paukstelis
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2017)
Article
Biochemistry & Molecular Biology
Betty Chu, Daoning Zhang, Paul J. Paukstelis
NUCLEIC ACIDS RESEARCH
(2019)