Article
Chemistry, Multidisciplinary
Minjung Kim, Sehui Bae, Inrok Oh, Jejoong Yoo, Jun Soo Kim
Summary: This study investigates the sequence-dependent coupling between DNA bending and its helical twist, identifying specific dinucleotide steps with strong twist-bend coupling during DNA minicircle formation. This work provides new insights into the structural responses of DNA to mechanical deformation, particularly in sharply bent DNA minicircles, for nanoscale applications.
Article
Microbiology
Miriam Garcia-Lopez, Diego Megias, Maria-Jose Ferrandiz, Adela G. de la Campa
Summary: Two enzymes, gyrase and topoisomerase I, play important roles in maintaining supercoiling in Streptococcus pneumoniae. The ratio of these enzymes affects supercoiling and cell viability, suggesting a potential mechanism for the action of topoisomerase-targeting antibiotics.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Antonio A. A. de Vasconcelos Junior, Jose M. Tirado-Velez, Antonio J. Martin-Galiano, Diego Megias, Maria-Jose Ferrandiz, Pablo Hernandez, Monica Amblar, Adela G. de la Campa
Summary: In this study, a new topoisomerase I regulator protein (StaR) was characterized in Streptococcus pneumoniae. It was found that StaR directly affects novobiocin susceptibility and needs to be maintained within a narrow range.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Physics, Fluids & Plasmas
Aaron C. Meyer, Michael Karbach, Ping Lu, Gerhard Mueller
Summary: This article introduces a statistical mechanical method for analyzing polymeric chains under tension and extends it to include torque. The method can describe the response of individual bonds or groups of monomers to a combination of tension and torque, and can handle the conversion between twist chirality and plectonemic chirality in quasistatic processes. Two applications demonstrate the versatility of this method in double-stranded DNA under controlled tension and torque.
Article
Biology
Jorge Cebrian, Victor Martinez, Pablo Hernandez, Dora B. Krimer, Maria-Jose Fernandez-Nestosa, Jorge B. Schvartzman
Summary: The study utilized two-dimensional agarose gel electrophoresis to investigate the efficiency of three type II DNA topoisomerases on partially replicated bacterial plasmids. The results revealed the preferential functions and some redundancy, shedding light on their abilities to resolve supercoiling and pre-catenanes in vitro.
Review
Biochemistry & Molecular Biology
Alexandre Duprey, Eduardo A. Groisman
Summary: DNA supercoiling is a crucial factor in controlling cellular processes, with similarities and differences across different domains of life. Topoisomerases play a key role in mediating changes in DNA supercoiling.
Article
Biochemistry & Molecular Biology
Li Huang, Zhenfeng Zhang, Roger McMacken
Summary: E. coli histone-like protein HU shows a preference for binding to negatively supercoiled DNA, with affinity increasing with higher negative superhelical density. However, this binding preference becomes negligible at high HU/DNA mass ratios.
Article
Multidisciplinary Sciences
Yair A. G. Fosado, Davide Michieletto, Chris A. Brackley, Davide Marenduzzo
Summary: The study investigates the effect of transcription on DNA supercoiling kinetics, revealing the formation of writhe structures at a distance from the transcribing RNA polymerase. Additionally, it shows that positive supercoils generated by RNAP can destabilize nucleosomes long before the transcriptional machinery reaches the histone octamer. The research also analyzes the relaxation dynamics of supercoiled DNA, highlighting the significantly different timescales of twist diffusion and writhe relaxation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
G. Forte, D. Michieletto, D. Marenduzzo, E. Orlandini
Summary: In this study, it was found that the integration of short viral DNA in a DNA braid is influenced by the topology of the braid, with higher likelihood of integration in the buckled phase. The research also suggests a potential mechanistic explanation for clustered integration sites in host genomes. The experimental set-up proposed provides a novel approach to quantify integration in a supercoiled substrate in vitro and sheds light on the role of double-stranded DNA topology during this process.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2021)
Article
Biochemical Research Methods
Lisa A. Holland, Yan He, Jessica R. Guerrette, Cassandra L. Crihfield, Lloyd Bwanali
Summary: An automated and cost-effective method based on capillary gel electrophoresis laser-induced fluorescence detection was developed for quantification of trace levels of plasmid topoisomers. The method has broad applicability for laboratories requiring routine analyses of plasmid topology for the development of new plasmid-based therapies and quality control of gene therapies utilizing supercoiled DNA. The detection of topoisomers was achieved by incorporating ethidium bromide in the separation medium, with improved detector response using a specific optical filter.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Astronomy & Astrophysics
Zhenjun Zhou, Chaowei Jiang, Rui Liu, Yuming Wang, Lijuan Liu, Jun Cui
Summary: The mechanism governing the rotational motion of solar filaments during eruptions and its relationship with the initial morphology, chirality, and magnetic helicity remains unknown. A magnetohydrodynamic simulation was used to propose an alternative explanation, which found that the rotation is accompanied by a decrease in the nonlocal writhe of the magnetic flux rope's axis and an increase in the twist of the surrounding field lines.
ASTROPHYSICAL JOURNAL LETTERS
(2022)
Article
Multidisciplinary Sciences
Chen Zhang, Fujia Tian, Ying Lu, Bing Yuan, Zhi-Jie Tan, Xing-Hua Zhang, Liang Dai
Summary: DNA deformations can occur upon environmental changes, and an increase in salt concentration leads to DNA overwinding. Our magnetic tweezers experiments and simulations demonstrate that the twist change induced by salt can be quantitatively explained by the screening of electrostatic repulsion and the coupling between twist and DNA diameter. We determine the coupling constant and predict the temperature dependence of DNA twist, finding that the twist-diameter coupling is a common driving force for salt- and temperature-induced DNA twist changes.
Article
Multidisciplinary Sciences
Jonathan M. Fogg, Allison K. Judge, Erik Stricker, Hilda L. Chan, Lynn Zechiedrich
Summary: The study unveils the dynamic relationship between DNA supercoiling-induced sequence-dependent disruptions to base pairing, DNA looping, and the shape of the DNA molecule. Negative supercoiling of DNA can lead to disruptions in base pairing at superhelical apices, allowing for DNA writhe to relieve torsional strain.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Ziqi Fu, Monica S. Guo, Weiqiang Zhou, Jie Xiao
Summary: This study examines the role of positive and negative supercoiling in the organization of the bacterial genome. The findings suggest that both types of supercoiling enhance spatial contact, with positive supercoiling playing a larger role. Additionally, the majority of supercoiling sites coincide with highly active transcription units.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
George D. Watson, Elliot W. Chan, Mark C. Leake, Agnes Noy
Summary: Using molecular dynamics simulations on DNA minicircles, this study reveals the reciprocal influence between a DNA-bending protein (IHF) and DNA supercoiling. Supercoiled DNA enhances wrapping around IHF, while IHF acts as a "supercoiling relief" factor by compacting relaxed DNA loops and pinning the position of plectonemes in a unique manner. IHF also restrains DNA torsion and divides DNA into independent topological domains through bridging.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Polymer Science
Svetlana G. Karpova, Natalia A. Chumakova, Anton V. Lobanov, Anatoly A. Olkhov, Alexandre A. Vetcher, Alexey L. Iordanskii
Summary: The effect of small additions of tetraphenylporphyrin and its complexes with Fe and Sn on ultrathin fibers based on poly(3-hydroxybutyrate) has been investigated. It was found that these dopants can modify the morphology, crystallinity, and segmental dynamics of the fibers. Annealing and exposure to an aqueous medium also have an impact on the properties of the fibers.
Article
Medicine, Research & Experimental
Alexandre A. Vetcher, Kirill Zhukov, Bagrat A. Gasparuan, Alexander Y. Shishonin
Summary: Considering the functioning body as a dissipative structure implies the existence of a regulatory system to maintain homeostasis. Interference with correct information input can lead to dysfunction. Arterial hypertension may be caused by the obstruction of information flow to the cerebellum due to damaged cervical cartilage. The correlation between blood flow through cervical vertebral arteries and arterial blood pressure can provide additional support for this hypothesis.
MEDICAL HYPOTHESES
(2022)
Review
Biochemistry & Molecular Biology
Alexandre A. Vetcher, Yaroslav M. Stanishevskiy
Summary: The paper discusses the revival of the term DNA microcircles and its redefined as topologically closed DNA circles with a length less than 1 Kbp from the entire population of circular DNA known as minicircles. It also explores the potential applications of this tool for in vivo studies of non-canonical DNA and demonstrates the prospects for in vivo and in vitro studies of non-canonical DNA cloned into microcircles. Additionally, a method of stepwise elongation or shortening of plasmids is discussed.
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Valentina V. Sinitsyna, Alexandre A. Vetcher
Summary: This review focuses on the characteristics and applications of nucleic acid aptamers, specifically DNA and RNA aptamers, and discusses the recent advances in their application in nanotechnology.
Letter
Medicine, General & Internal
Alexandre A. Vetcher, Kirill V. Zhukov, Bagrat A. Gasparyan, Alexander Y. Shishonin
EUROPEAN JOURNAL OF INTERNAL MEDICINE
(2023)
Article
Polymer Science
Alexandr V. Shchegolkov, Aleksei V. Shchegolkov, Natalia V. Zemtsova, Yaroslav M. Stanishevskiy, Alexandre A. Vetcher
Summary: The development of reliable and effective functional materials for various technological fields and environmental conditions is a goal of modern nanotechnology. By studying elastomers based on silicon-organic compounds and polyurethane modified with multi-walled carbon nanotubes, it has been found that using a polyurethane matrix can reduce the power degradation caused by voltage surges and make heaters safer to use at higher voltages.
Review
Polymer Science
Incherah Bekkouche, Alexander Y. Y. Shishonin, Alexandre A. A. Vetcher
Summary: The structure of triple-stranded DNA, consisting of three oligonucleotide chains, is explored. Hoogsteen base pairing is described as a mechanism for forming triple-stranded DNA. The involvement of these structures in various diseases is discussed. The focus of the review is on the development of biomedical oligonucleotides with triple-stranded DNA.
Article
Polymer Science
Kristina G. Gasparyan, Polina M. Tyubaeva, Ivetta A. Varyan, Alexandre A. Vetcher, Anatoly A. Popov
Summary: As a response to the current environmental situation, biopolymers, especially poly-3-hydroxybutyrate (PHB), have gained attention as biodegradable polymer alternatives to synthetic polymers. This study compared the biodegradation rate of films and fibers based on PHB, evaluating the influence of soil exposure on their structure and properties using mechanical analysis, DSC method, and FTIR spectroscopy. Results showed rapid decomposition of fibrous material and indicated the impact of material surface on the biodegradation rate and mechanical properties. Understanding the biodegradation mechanisms of PHB is of great importance for the development of medical devices, packaging materials, and short-lived consumer products.
Article
Environmental Sciences
Tutuk Djoko Kusworo, Andri Cahyo Kumoro, Nita Aryanti, Fadhilah Fatma Lingga, Ade Widiastuti, Alexandre A. Vetcher, Febio Dalanta
Summary: This study investigates the use of UV irradiation and PVA cross-linked modified PSf membrane to improve fouling issues and applies it to industrial rubber wastewater treatment. The results show that the modified membrane effectively increases the permeate flux and removes a significant amount of dissolved solids, chemical oxygen demand, and ammonia compound. The study also finds that UV irradiation and PVA cross-linked coating can enhance the fouling resistance of the membrane and further improve its performance.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2023)
Review
Materials Science, Composites
Mourad Nachtane, Mostapha Tarfaoui, Mohamed Amine Abichou, Alexandre Vetcher, Marwane Rouway, Abdeouhaed Aamir, Habib Mouadili, Houda Laaouidi, Hassan Naanani
Summary: The environmental impact of CO2 emissions is widely recognized, leading to the necessity of developing alternative propulsion systems. Hydrogen is a potential candidate for replacing fossil fuels in transportation, and three technologies for onboard hydrogen storage have been considered: compressed gas, cryogenic liquid, and solid storage. This paper reviews the technological advancements in Hydrogen Storage Vessel (HSV) designs, including their performance, costs, safety, and environmental impact. The utilization of fiber-reinforced polymer composites and numerical models, including artificial intelligence techniques, are explored to achieve more sustainable HSV designs.
JOURNAL OF COMPOSITES SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Vladimir B. B. Markeev, Evgenia V. V. Blynskaya, Sergey V. V. Tishkov, Konstantin V. V. Alekseev, Anna I. I. Marakhova, Alexandre A. A. Vetcher, Alexander Y. Y. Shishonin
Summary: This study aimed to develop a water-soluble, high-release active pharmaceutical ingredient (API) composite based on the practically water-insoluble API N-butyl-N-methyl-1-phenylpyrrolo[1,2-a]pyrazine-3-carboxamide (GML-3), which has antidepressant and anxiolytic action, to ensure the bioavailability of the medicinal product. Composites obtained by creating amorphous solid dispersions using polyvinylpyrrolidone (PVP) or Soluplus® as a polymer were studied for crystallinity, stability, and API release into purified water. The results showed that the composites achieved amorphous state at 1:15 API:PVP ratio and 1:5 Soluplus® ratio, ensuring the solubility of GML-3 in purified water and maintaining the supercritical state in solution.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Polymer Science
Vladimir B. Markeev, Sergey V. Tishkov, Anton M. Vorobei, Olga O. Parenago, Evgenia V. Blynskaya, Konstantin V. Alekseev, Anna I. Marakhova, Alexandre A. Vetcher
Summary: N-butyl-N-methyl-1-phenylpyrrole[1,2-a] pyrazine-3-carboxamide (GML-3) is a potential candidate for combination drug therapy due to its anxiolytic and antidepressant activity. This study explored the effects of dry grinding, the rapid expansion of a supercritical solution (RESS), and the composite of GML-3 with polyvinylpyrrolidone (PVP) on the particle size and dissolution rate of GML-3. It was found that the formation of a composite with PVP significantly improved the solubility of GML-3.
Review
Chemistry, Multidisciplinary
Incherah Bekkouche, Maria N. Kuznetsova, Dovlet T. Rejepov, Alexandre A. Vetcher, Alexander Y. Shishonin
Summary: The applications of DNA-containing nanomaterials (DNA-NMs) in various fields such as medicine, environment, and engineering are gaining increasing attention. These materials have become important due to their small size, high controllability, clustering actions, and strong permeability. However, there are still challenges in precise cluster control, targeted drug distribution, and cellular micro-nano operation. This review summarizes the recent progress in DNA-NMs and their integration into multiple disciplines, aiming to inspire new research perspectives and advancements in nanomanipulation.
Article
Biochemistry & Molecular Biology
Alexandre A. Vetcher, Kirill V. Zhukov, Bagrat A. Gasparyan, Pavel I. Borovikov, Arfenia S. Karamian, Dovlet T. Rejepov, Maria N. Kuznetsova, Alexander Y. Shishonin
Summary: It has been found that restoring cervical vertebral arterial blood flow access can lead to the recovery of HbA1c level in patients with pre-Diabetes Mellitus. The theory of centralized aerobic-anaerobic energy balance compensation provides a successful explanation for this observation. This study presents a model that fits the experimental data obtained and discusses the differences in the pathways and consequences of onset and recovery from pre-DM.
Review
Plant Sciences
Selvaraj Barathi, Jintae Lee, Raja Venkatesan, Alexandre A. Vetcher, Karthik Chinnannan, Padma Nimmakayala
Summary: Rising waste construction, agricultural actions, and manufacturing sewages contribute to heavy metal accumulation in water resources. Phytoremediation, using hyper-accumulator plants, is a promising method for eliminating heavy metals from contaminated environments. Conventional phytoremediation methods have limitations, thus researchers are exploring biotechnological advancements for improved plant effectiveness and wider application.
Article
Biochemistry & Molecular Biology
Hsiao-Chieh Tsai, Ching-Hong Huang, Ling-Hsien Tu
Summary: Islet amyloid polypeptide (IAPP) is a polypeptide hormone co-secreted with insulin by pancreatic beta-cells. It tends to aggregate into soluble oligomers, which are considered one of the hallmarks of type II diabetes. This study successfully grafted the aggregation-induced emission molecule TPE onto IAPP, allowing real-time monitoring of IAPP oligomer formation and potential application in the diagnosis of T2D.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Aristeidis Papagiannopoulos, Aggeliki Sklapani, Nikolaos Spiliopoulos
Summary: This study presents a method for preparing Hb-based nanoparticles (NPs) using a fully biocompatible approach. These NPs have a spherical structure with a diameter ranging from 50 to 100 nm, and can form electrostatic complexes with CS at pH 4. The NPs can be pH-tunable and stable in solutions with high salt content, making them suitable for nanodelivery of nutrients and drugs.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Andrey V. Struts, Alexander V. Barmasov, Steven D. E. Fried, Kushani S. K. Hewage, Suchithranga M. D. C. Perera, Michael F. Brown
Summary: This article summarizes and reviews the osmotic stress studies of G-protein-coupled receptor rhodopsin. It is found that water plays an important role in the activation of the receptor, with at least 80 water molecules entering the receptor in the transition to the active state. If water influx is prevented, the functional transition of the receptor is reversed. These findings reveal the phenomenon of solvent swelling in the activation mechanism of rhodopsin, with water acting as an allosteric modulator of function for rhodopsin-like receptors in lipid membranes.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Maria Chiara Saija, Adela Melcrova, Wojciech Pajerski, Itay Schachter, Matti Javanainen, Marek Cebecauer, Lukasz Cwiklik
Summary: We used molecular dynamics simulations to investigate the effects of palmitoylation on a transmembrane peptide in different lipid environments. The study found that palmitoylation reduces the peptide's impact on membrane thickness, particularly in lipid-ordered and boundary environments. The hydrophobic palmitoyl chains on the peptide did not significantly affect membrane hydration. Interestingly, the boundary membrane environment was found to be highly compatible with the palmitoylated peptide. These findings have important implications for understanding cell signaling, membrane organization, and optimizing lipid membrane-based drug delivery systems.
BIOPHYSICAL CHEMISTRY
(2024)
Article
Biochemistry & Molecular Biology
Achanta Rishisree, Brayer Mallory, Karnaukhova Elena, Jankovic Teodora, Zdunic Gordana, Savikin Katarina, Jeremic Aleksandar
Summary: Pomegranate peel, ironwort, and chokeberry leaf extracts exhibit anti-aggregative and antitoxic properties against human amylin. They can prevent amyloidosis and cell loss in patients with Type 2 Diabetes Mellitus.
BIOPHYSICAL CHEMISTRY
(2024)