Article
Biochemistry & Molecular Biology
Klaudia Jomova, Marcel Cvik, Peter Lauro, Marian Valko, Erik Cizmar, Suliman Y. Alomar, Saleh H. Alwasel, Patrik Oleksak, Zofia Chrienova, Eugenie Nepovimova, Kamil Kuca, Christopher J. Rhodes
Summary: The antioxidant properties of flavonoids with hydroxyl groups allow them to chelate redox active metals and scavenge free radicals. This paper studies the antioxidant and prooxidant properties of baicalein and its complexes with Cu(II) under different conditions. The results show that baicalein and Cu(II)-baicalein complexes have moderate ROS scavenging efficiency and can protect DNA from damage caused by ROS. These findings suggest that baicalein could be a therapeutic agent for diseases involving disrupted metabolism of copper, while low concentrations of baicalein may not inhibit the pro-oxidant effect of copper ions and ascorbate in cancer cells, leading to effective DNA damage.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Miriama Simunkova, Zuzana Barbierikova, Klaudia Jomova, Lenka Hudecova, Peter Lauro, Saleh H. Alwasel, Ibrahim Alhazza, Christopher J. Rhodes, Marian Valko
Summary: Kaempferol, a flavonoid found in tea, vegetables, and fruits, has demonstrated efficacy in treating various cancers and leukemia. Studies have focused on its prooxidant properties and activation of pro-apoptotic pathways. Research investigated the antioxidant vs. prooxidant properties of flavonoids in the presence of redox-active copper (II) ions during the Fenton reaction. The results suggest that Cu-kaempferol complexes may provide anticancer activity and suggest potential therapeutic use in oxidative stress-related medical conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Nobuyuki Futai, Yuto Fukazawa, Tomohiro Kashiwagi, Shogo Tamaki, Riho Sakai, Catherine A. Hogan, Kanagavel Murugesan, Ashwin Ramachandran, Niaz Banaei, Juan G. Santiago
Summary: This study presents a method for the high-efficiency separation and extraction of short cfDNA fragments, using a millimeter-scale fluidic device to extract the fragments into solid agarose gel slabs from liquid human plasma samples. The method demonstrates high sensitivity in cfDNA detection.
ANALYTICA CHIMICA ACTA
(2022)
Article
Biochemistry & Molecular Biology
Atsuya Matsui, Jean-Pierre Bellier, Takeshi Kanai, Hiroki Satooka, Akio Nakanishi, Tsukasa Terada, Takafumi Ishibe, Yoshiaki Nakamura, Hiroyasu Taguchi, Nobuyasu Naruse, Yutaka Mera
Summary: This study investigated the effect of ethanol on A beta pentameric assemblies and found that ethanol can be used as a solvent without affecting the stability of A beta pentamers within a certain concentration range. Higher concentrations of ethanol led to the disassembly of A beta pentamers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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.
Article
Infectious Diseases
Hung-Jen Tang, Yi-Tsung Lin, Chi-Chung Chen, Chih-Wei Chen, Ying-Chen Lu, Wen-Chien Ko, Hung-Jui Chen, Bo-An Su, Ping-Chin Chang, Yin-Ching Chuang, Chih-Cheng Lai
Summary: The study revealed that E. anophelis isolates were susceptible to certain antibiotics, with the combination of minocycline and cefoperazone/sulbactam showing the best synergistic effects in combating biofilm formation of clinical isolates. Additionally, novel mutations were identified, indicating antibiotic resistance mechanisms.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2021)
Article
Chemistry, Inorganic & Nuclear
Fadime Aydin, Esra Bagda, Efkan Bagda, Mahmut Durmus
Summary: G-quadruplex DNAs are secondary DNA structures formed in guanine-rich genome sequences, such as telomeres, and their stability and interactions with ligands are important for anticancer drug development.
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Chemistry, Physical
Bruna B. S. Souza, Thiago C. Lourenco, Barbara B. Gerbelli, Pedro L. Oseliero Filho, Cristiano L. P. Oliveira, Antonio Miranda, Emerson R. da Silva
Summary: The compaction of long DNA strands into confined spaces is essential for the emergence of complex life forms. This study investigated the structure of complexes formed between DNA and histones or protamines using a range of biophysical methods. The results showed that protamines form highly compact structures that hinder access to the spaces between bases, while histone-based complexes have larger separations between strands and allow access to guest molecules. These findings enhance our understanding of DNA condensation mediated by these nucleoproteins and have implications for optimizing gene vehicles based on these nano assemblies.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Ji Ma, Guoxia Huang, Changxin Mo, Junsheng Li, Liujuan Yan, Qian Zhang
Summary: In this study, the relationship between Benzo[b]fluorathene (BbF) and herring sperm DNA (hs-DNA) under simulated physiological conditions was investigated using multiple spectroscopic approaches. The results showed that BbF formed complexes with DNA through intercalative binding. The study also explored the potential use of DNA and magnetic beads to selectively capture and remove BbF. These findings provide insights into the toxicity of BbF and offer a novel approach for BbF clearance based on BbF-DNA intercalation.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Analytical
Behnaz Abbasgholi N. Asbaghi, Ahmed Alsadig, Loredana Casalis, Pietro Parisse, Joseph Niemela, Stefano Bellucci, Humberto Cabrera
Summary: A novel approach using a miniaturized gel electrophoresis chip integrated with online thermal lens detection was reported for monitoring the amount of DNA on the surface of gold nanoparticles, enabling the detection of small differences in DNA surface density and high sensitivity biorecognition. The system demonstrated a low detection limit and potential as an advanced instrumental platform for designing biosensors in nanotechnology.
MICROCHEMICAL JOURNAL
(2022)
Article
Chemistry, Physical
Banabithi Koley Seth, Shuvankar Dey, Pooja Trivedi, Gaurang Sindhav, Vinod K. Jain
Summary: In this study, a systematic and comparative investigation of the biological activities of different oxacalix[4]arene systems was conducted. The results revealed the diverse capabilities of oxacalix[4]arene in DNA protection, DNA damage, and antioxidant activity. Among them, the oxacalix[4]arene functionalized with phenolic OH displayed the best DNA protection ability and the strongest antioxidant activity.
JOURNAL OF MOLECULAR STRUCTURE
(2024)
Article
Multidisciplinary Sciences
Heng Liu, He Cheng, Jun Xu, Jiayi Hu, Chenchen Zhao, Lihua Xing, Mengjin Wang, Zhendong Wu, Daiyin Peng, Nianjun Yu, Junling Liu
Summary: Polygonatum cyrtonema Hua is a traditional medicinal and edible herb in China with significant value, but overharvesting and chaotic cultivation have led to depletion of wild resources and genetic erosion. This study assessed the genetic diversity and population structure of Polygonatum cyrtonema Hua using SSR markers and found genetic differentiation between populations. The findings support the conservation of germplasm resources and provide new parental material for genetic improvement and breeding programs.
Article
Biochemistry & Molecular Biology
U. M. S. Andrade, A. S. B. Castro, P. H. F. Oliveira, L. H. M. da Silva, M. S. Rocha
Summary: We conducted a comprehensive characterization of the molecular interactions between DNA and two imidazolium-based ionic liquids (ILs), and identified DNA compaction at high IL concentrations as a result. By using various techniques, we obtained the changes in mechanical properties of DNA complexes formed with ILs and determined the thermodynamic characteristics and driving forces of the interactions. Our findings provide important insights into the interaction between DNA and imidazolium-based ionic liquids.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biophysics
Adam A. Jabak, Nicholas Bryden, Fredrik Westerlund, Per Lincoln, Micah J. McCauley, Ioulia Rouzina, Mark C. Williams, Thayaparan Paramanathan
Summary: The study reveals that the left-handed enantiomer requires more DNA lengthening for threading and extends the DNA more than the right-handed enantiomer at equilibrium. Additionally, the left-handed complex unthreads three times faster than the right-handed complex. These results suggest a preference in DNA binding to the chiral enantiomer having the same chirality as the DNA molecule.
BIOPHYSICAL JOURNAL
(2022)
Article
Chemistry, Physical
P. S. Alves, O. N. Mesquita, M. S. Rocha
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Optics
T. A. Moura, U. M. S. Andrade, J. B. S. Mendes, M. S. Rocha
Article
Biochemistry & Molecular Biology
J. A. D. Batista, L. Oliveira, T. A. Moura, V. C. dos Anjos, M. J. Bell, M. S. Rocha
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2020)
Article
Optics
U. M. S. Andrade, A. M. Garcia, M. S. Rocha
Summary: The study introduces a Bessel beam optical tweezers setup that can stably trap superparamagnetic beads, with trap stiffness practically independent of beam radius and bead height. Despite the absorption coefficient of the beads, trap stiffness linearly increases with laser power. A geometric optics model accurately predicts optical forces and trap stiffness, advancing the field of optical trapping of absorbing magnetic particles.
Article
Chemistry, Physical
Rayane M. de Oliveira, Tiago A. Moura, Marcio S. Rocha
Summary: This study demonstrates that caffeine enhances the anticancer effects of cisplatin and other platinum-based drugs not only at the cellular level, but also at the molecular level. It acts as an allosteric catalyst, increasing the binding constant between DNA and platinum drugs and interfering with the binding reactions' cooperativity. This research provides new insights into the use of caffeine for chemotherapeutic applications.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Ethe A. Costa, Amanda P. Goncalves, Josiane A. D. Batista, Raniella F. Bazoni, Anesia A. Santos, Marcio S. Rocha
Summary: This study investigates the molecular mechanism of action of the drug chloroquine (CLQ) in its interaction with double-stranded DNA at the single-molecule level, and reveals that the ionic strength of the surrounding medium strongly influences this interaction. Furthermore, the cytotoxicity of CLQ against different cell lines is evaluated and compared to the closely related compound hydroxychloroquine (HCLQ).
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
U. M. S. Andrade, A. S. B. Castro, P. H. F. Oliveira, L. H. M. da Silva, M. S. Rocha
Summary: We conducted a comprehensive characterization of the molecular interactions between DNA and two imidazolium-based ionic liquids (ILs), and identified DNA compaction at high IL concentrations as a result. By using various techniques, we obtained the changes in mechanical properties of DNA complexes formed with ILs and determined the thermodynamic characteristics and driving forces of the interactions. Our findings provide important insights into the interaction between DNA and imidazolium-based ionic liquids.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Microbiology
Lorena Souza Castro Altoe, Ethe de Araujo Costa, Gabriella Peterlini Tavares, Marcio Santos Rocha, Jose Humberto de Queiroz, Juliana Barbosa Coitinho Goncalves, Suely Gomes de Figueiredo, Jackson Victor de Araujo
Summary: The use of force spectroscopy with optical tweezers is valuable in studying the physical chemistry of DNA interactions with ligands. This study focuses on the poorly understood interactions between helminthophagous fungi enzymes and nucleic acids. The experimental assays show that the fungal protease strongly binds to dsDNA, forming aggregates and altering the DNA's properties. The findings provide molecular-level insights into the pathogenicity of these proteins when applied to target specimens.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Materials Science, Multidisciplinary
Kairon M. Oliveira, Tiago A. Moura, Janaisa L. C. Lucas, Alvaro V. N. C. Teixeira, Marcio S. Rocha, Joaquim B. S. Mendes
Summary: This paper proposes the use of PANI as handles in optical tweezers experiments. The stable trapping and manipulation of PANI beads using optical tweezers are demonstrated for the first time. The results suggest the potential of using semiconductor polymeric materials in optical manipulation and open up new possibilities for related applications.
ACS APPLIED POLYMER MATERIALS
(2023)
Article
Optics
T. A. Moura, U. M. S. Andrade, J. B. S. Mendes, M. S. Rocha
Summary: We demonstrate that optical trapping and manipulation of spherical-shaped semiconductor (germanium) particles can be effectively controlled using optical tweezers based on a highly focused Bessel beam. The behavior of the trapped germanium beads, including stable trapping, oscillatory dynamics, and repulsion, can be modulated by adjusting laser power, beam radius, and trap focal height. The versatility of Bessel beam optical tweezers opens up new possibilities for applications in various fields.
OPTICS AND LASERS IN ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Jefferson V. P. B. Baeta, Ulisses M. S. Andrade, Rayane M. Oliveira, Leandro Oliveira, Anesia A. Santos, Gaspar Diaz-Munoz, Marcio S. Rocha, Marisa A. N. Diaz
Summary: The study found that DPAP has cytotoxic effects on B16F10 melanoma cells and interacts with DNA, causing a bending deformation of the polymer chain and reducing its persistence length. Each DPAP molecule likely occupies a single base pair upon binding to the double helix.
JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
R. F. Bazoni, T. A. Moura, M. S. Rocha
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2020)
Article
Physics, Fluids & Plasmas
E. F. Silva, U. M. S. Andrade, K. M. de Oliveira, A. V. N. C. Teixeira, M. S. Rocha
Article
Physics, Fluids & Plasmas
L. Oliveira, J. M. Caquito Jr, M. S. Rocha
Article
Physics, Multidisciplinary
W. H. Campos, T. A. Moura, O. J. B. J. Marques, J. M. Fonseca, W. A. Moura-Melo, M. S. Rocha, J. B. S. Mendes
PHYSICAL REVIEW RESEARCH
(2019)