Article
Biochemistry & Molecular Biology
Josephine Geertsen Keller, Kirstine Mejlstrup Hymoller, Maria Eriksen Thorsager, Noriko Y. Hansen, Jens Uldum Erlandsen, Cinzia Tesauro, Anne Katrine W. Simonsen, Anne Bech Andersen, Kamilla Vands-Petersen, Lise Lolle Holm, Magnus Stougaard, Brage Storstein Andresen, Peter Kristensen, Rikke Frohlich, Birgitta R. Knudsen
Summary: The function of human topoisomerase 1 (TOP1) in regulating G-quadruplex (G4) formation in the MYC P1 promoter has been investigated, revealing its involvement in the regulation of G4 formation and its potential as a regulator in gene expression.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Coralie Robert, Julien Marquevielle, Gilmar F. Salgado
Summary: This study investigated whether the promoter region of the MST1R gene contains potential G-quadruplex structures and characterized the best scored sequences using biophysical studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Fei Zhao, Hongfang Zhang, Jianbin Zheng
Summary: An ultrasensitive label-free electrochemical biosensing platform for detecting MiR-21 at a very low concentration was developed by immobilizing capture probes in nanochannels based on G-quadruplex formation. This platform was also successfully applied for MiR-21 detection in serum samples, and has the potential for the assay of other scarce tumor-related genes.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
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
Marta Cozzaglio, Silvia Ceschi, Elisabetta Groaz, Mattia Sturlese, Claudia Sissi
Summary: G-quadruplexes (G4s) are nucleic acid secondary structures detected within human chromosomes, which cluster at gene promoters and enhancers and may play specific roles in the regulation of gene expression. Vimentin, a protein highly expressed within mesenchymal cells, selectively recognizes these structures. In this study, a putative G4-repeat sequence within the promoter of the TEAD4 oncogene was selected and its folding behavior was validated, confirming its interaction with Vimentin.
FRONTIERS IN CHEMISTRY
(2022)
Article
Spectroscopy
Chenxiao Yan, Qingqing Zhang, Heng Gao, Xiong Zheng, Tong Yang, Guoxiang Zheng, Xiaoshun Zhou, Yong Shao
Summary: DNA templated dye assemblies can regulate the optical properties of molecular aggregates, with G-quadruplexes serving as versatile platforms for this purpose. The handedness of G4s can control the chirality of dye aggregates, with left-handed G4s facilitating the formation of J-aggregates and right-handed G4s favoring the growth of H-aggregates. The high sensitivity of G4s in creating chiral aggregates at low concentrations demonstrates their potential in controlling optically active dye assemblies.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Spectroscopy
Hongbo Chen, Xiaomeng Guo, Xinquan Li, Yalin Tang, Hongxia Sun
Summary: A supramolecular probe with high specificity and sensitivity to G-quadruplex structures in acute myeloid leukemia cells has been developed, potentially serving as a new indicator for AML detection.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(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
Martina Lenarcic Zivkovic, Martin Gajarsky, Katerina Bekova, Petr Stadlbauer, Lukas Vicherek, Magdalena Petrova, Radovan Fiala, Ivan Rosenberg, Jiri Sponer, Janez Plavec, Lukas Trantirek
Summary: Our recent study demonstrates the formation of an unprecedented pseudocircular G-hairpin (PGH) structure in Saccharomyces cerevisiae telomeric DNA. High-resolution NMR structure of a novel PGH family member reveals atomistic details on the junction between ssDNA and the PGH unit, providing insights into minimal sequence requirements for PGH formation. Time-resolved NMR data suggest a complex kinetic partitioning mechanism for PGH folding and the existence of K+ ion-dependent folding intermediates, explaining cation-type-dependent formation and hysteresis observed in previous studies.
NUCLEIC ACIDS RESEARCH
(2021)
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
Electrochemistry
Daniel Dobrovodsky, Ales Danhel, Emmanuelle Mothes-Martin, Genevieve Pratviel, Daniel Renciuk, Miroslav Fojta
Summary: In this study, two electrochemically active compounds, Cu-TMPy2PP and dGNPTP, were used as probes to investigate the effects of electrode potential on ODNs and their abilities to form secondary structures at the HMDE surface. The results showed that G-rich ODNs with the potential to form G-quadruplexes formed less dense adsorbed layers compared to other sequences. Additionally, the G4-forming ODNs were more easily desorbed from the HMDE surface at highly negative potentials, as confirmed by gel electrophoresis. This application of electrochemical probes provides a useful method for studying DNA conformations and transitions.
ELECTROCHIMICA ACTA
(2023)
Article
Biochemistry & Molecular Biology
Matja Zalar, Baifan Wang, Janez Plavec, Primoz Sket
Summary: The G4C2 hexanucleotide repeat expansion in the c9orf72 gene is a major genetic cause of familial ALS and FTLD, with G-quadruplexes playing a crucial role. This study investigates the impact of potassium ions on G-quadruplex structures and demonstrates the formation of stable higher-ordered species through the stacking of G-quadruplexes via their 5' end G-quartets in the presence of 15NH4+ ions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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)
Article
Nanoscience & Nanotechnology
Sohini Pal, Akshay Naik, Anjana Rao, Banani Chakraborty, Manoj M. Varma
Summary: We demonstrate the single-molecule sensing of G-quadruplex formation in target-bound aptamers using solid-state nanopores. By functionalizing the nanopores with DNA origami sheets containing the aptamer sequence, we provide a versatile configuration for nanopore-based single-molecule sensors. The DNA origami sheet also includes a pore that can modulate the translocation dynamics of the target molecule. Using this system, we successfully differentiate the formation of G-quadruplex in the well-studied thrombin aptamer.
ACS APPLIED NANO MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Yun Zhang, Junliu Huang, Kainan Yu, Xiaojie Cui
Summary: The G-quadruplex structures formed by C9orf72 gene play a crucial role in the pathogenesis of ALS and FTD. This study investigated the GQ structures formed by different lengths of C9-HRE DNA sequences and identified a natural small molecule, Fangchinoline, that can stabilize and alter the C9-HRE GQ structures in both DNA and RNA levels. The findings provide insights into therapeutic strategies targeting C9-HRE DNA and RNA in C9ALS/FTD.
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
Chemistry, Physical
Shankar Pandey, Sagun Jonchhe, Shubham Mishra, Tomoko Emura, Hiroshi Sugiyama, Masayuki Endo, Hanbin Mao
Summary: Cellular environments can alter biomolecular properties, and the effects of crowding cosolutes on macromolecules in nanoconfinement have been investigated. The study found that hexaethylene glycol (HEG) can split a telomeric G-quadruplex (GQ) into two populations with different effects, either through long-range dehydration or direct interactions. Increasing the number of HEG molecules unexpectedly decreased the stability of the GQ, indicating the dominant role of direct interactions over long-range stabilizing effects in hydrophilic nanocavities.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Mst. Ayesha Siddika, Takahiro Yamada, Risako Aoyama, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: Naturally occurring ribozymes with a modular architecture can serve as promising platforms for constructing RNA nanostructures, as their modular redesign allows for oligomerization. These resulting RNA nanostructures can retain the catalytic function of the parent ribozyme, depending on their assembly. In this study, open-form oligomers of a bimolecular form of an RNase P ribozyme were designed and constructed, and analyzed biochemically and by atomic force microscopy (AFM).
Article
Chemistry, Multidisciplinary
Soumya Sethi, Tomoko Emura, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo
Summary: Cell behavior is affected by various properties of the extracellular environment, such as ligand spacing, nanotopography, and matrix stiffness. Changes in matrix stiffness occur during biological processes like wound healing, tumorigenesis, and development. These spatio-temporal dynamic changes in stiffness can significantly impact cell morphology, signaling, migration, and cytoskeleton. In this paper, we created photocontrolled stiffness-tunable DNA nanotubes that can reversibly change their conformation upon UV and VIS irradiation. When used as a substrate for cell culture, these nanotubes can tune the cell morphology of HeLa cells. This photocontrolled nanosystem provides insights into cell-matrix interactions caused by nanoscopic changes in stiffness in the native extracellular matrix.
Article
Biochemistry & Molecular Biology
Mst. Ayesha Siddika, Hiroki Oi, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: In this study, the construction of larger RNA assemblies based on ribozyme was achieved through the use of RNA oligomerization technology. The addition of specific interacting units enabled the assembly of ribozyme dimer, open-chain oligomers, and branched oligomers.
Article
Nanoscience & Nanotechnology
Caroline Rossi-Gendron, Farah El Fakih, Laura Bourdon, Koyomi Nakazawa, Julie Finkel, Nicolas Triomphe, Lea Chocron, Masayuki Endo, Hiroshi Sugiyama, Gaetan Bellot, Mathieu Morel, Sergii Rudiuk, Damien Baigl
Summary: Using a magnesium-free buffer, DNA strands and proteins can self-assemble into user-defined nanostructures at room or physiological temperature, without the need for thermal annealing. This isothermal self-assembly is thermodynamically controlled, allows for multiple folding pathways, and results in highly reconfigurable nanostructures. This method expands the possibilities for shape and function in self-assembly and provides a foundation for adaptive nanomachines and nanostructure discovery through evolution.
NATURE NANOTECHNOLOGY
(2023)