Article
Chemistry, Analytical
Ryo Iwao, Hiroki Yamaguchi, Makoto Obata, Yu Matsuda
Summary: Polymer chains in solutions of different concentrations exhibit stretching and compression under shear flow conditions, which is different from classical theory. FRET measurement is a promising diagnostic method for understanding the dynamics of polymer chains.
Article
Physics, Multidisciplinary
Jesus Sambrano, Felicia Rodriguez, John Martin, Jessica P. Houston
Summary: Conventional flow cytometry is a valuable quantitative tool that provides users with multiparametric data and high-throughput cell information. Time-resolved flow cytometry plays an important role in fluorescence decay kinetics, Forster Resonance Energy Transfer studies, but faces challenges in handling high flow rates. The innovative approach of combining time-resolved hardware with microfluidics and acoustics in an acoustofluidic time-resolved flow cytometer shows promise in balancing throughput with necessary optical signals for lifetime data.
FRONTIERS IN PHYSICS
(2021)
Article
Agriculture, Multidisciplinary
Jun-Ling Deng, Meng-Jie Tang, Xiao-Xia Su, Yu-Tong Ye, Jie-Ying Wei, Zhong-Xiu Chen, Yu-Mei Qin
Summary: This study investigated the rapid interactions of sugars and sugar alcohols with sweet taste receptors using fluorescence spectroscopy, revealing that sweeteners can be divided into two groups based on their effects on the hydrogen bond network structure of water. Additionally, the cell response kinetics parameters were found to be negatively correlated with the apparent specific volume of sweeteners.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Chemistry, Physical
Xing-Long Li, Ying Wang, Ao Song, Ming-Hui Zhang, Man Jiang, Hui Liu, Rongzhou Wang, Shengsheng Yu, Ling-Bao Xing
Summary: An artificial light-harvesting system was constructed using PPTA and BSC4 supramolecular polymers, achieving efficient two-step energy transfer processes and promoting the dehalogenation reaction of alpha-bromoacetophenone with a high yield in aqueous solution.
Article
Biochemistry & Molecular Biology
Lyubov Yu Kanazhevskaya, Denis A. Smyshliaev, Nadezhda A. Timofeyeva, Alexander A. Ishchenko, Murat Saparbaev, Nikita A. Kuznetsov, Olga S. Fedorova
Summary: This study investigated the conformational transformations during the removal of alkylated bases from DNA by ALKBH2 using fluorescence spectroscopy and stopped-flow kinetic analysis. The results provide insights into the overall conformational dynamics of ALKBH2 and damaged DNA during the catalytic cycle.
Article
Chemistry, Analytical
Yanke Shan, Yufan Feng, Jiahao Li, Weijie Yi, Meng Ge, Huachuan Huang, Keding Yan, Shouyu Wang, Fei Liu
Summary: A portable fluorescence resonance energy transfer (FRET)-based enzyme-linked immunosorbent assay (ELISA) was designed for on-site detection of the porcine epidemic diarrhea virus (PEDV). The FRET immunoassay achieved high sensitivity and accuracy, and could detect PEDV in a 96-well plate in just 35 minutes.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Chemistry, Multidisciplinary
Ryusuke Hagihara, Tomohiro Umeno, Shoji Ueki, Daisuke Yoshihara, Yasufumi Fuchi, Kazuteru Usui, Masaomi Sakuma, Ken-ichi Yamada, Satoru Karasawa
Summary: Emissive push-pull-type bisnaphthyridylamine derivatives aggregate in aqueous methanol, with the emission and aggregation process controllable by varying the methanol-to-water ratio. The NPs of BNA-BuTEMPO exhibit slow rotational correlation time, suggesting potential applications as magnetic resonance imaging contrast agents.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
A. San Martin, R. Arce-Molina, C. Aburto, F. Baeza-Lehnert, L. F. Barros, Y. Contreras-Baeza, A. Pinilla, I Ruminot, D. Rauseo, P. Y. Sandoval
Summary: Metabolism research is undergoing a renaissance with the introduction of over 50 genetically-encoded fluorescent indicators (GEFIs) capable of monitoring metabolites with high resolution. These indicators allow monitoring of relative levels, concentrations, and fluxes in living systems, providing important tools for confirmation, rebuttal, and exploration.
FREE RADICAL BIOLOGY AND MEDICINE
(2022)
Article
Chemistry, Multidisciplinary
Claudio Avila, Carlo Cassani, Thierry Kogej, Javier Mazuela, Sunil Sarda, Adam D. Clayton, Michael Kossenjans, Clive P. Green, Richard A. Bourne
Summary: This work proposes a stopped-flow synthesis as an alternative method for small molecule pharmaceutical discovery. By integrating a stopped-flow reactor into a high-throughput continuous platform, the success rate of synthesizing smaller libraries is significantly improved. The experimental datasets are used to train a neural network model, which shows good predictive performance when tested against external data.
Article
Chemistry, Applied
Xinyao Wang, Shiqi Liuye, Xinhuan Ma, Shiqiang Cui, Shouzhi Pu
Summary: A novel photo-controlled solid-state fluorescence switching based on carbon dots (CDs) and diarylethene was designed and constructed. The fluorescence switching not only had excellent modulation efficiency, but also exhibited good photochromic properties. The mechanism of the reversible fluorescence modulation was attributed to the FRET between the CDs (energy donor) and the closed-ring diarylethene (energy acceptor). This work suggests the strategy of constructing solid-state fluorescence switching is feasible, and will provide new ways for the potential application of CDs and diarylethene.
Article
Chemistry, Multidisciplinary
Sung Hyun Kim, Hyunwoo Kim, Hawoong Jeong, Tae-Young Yoon
Summary: The study demonstrates the use of single-molecule FRET technology to encode virtual signals in DNA barcodes, allowing for precise measurement of FRET efficiency for each binding event and differentiation of six DNA barcodes.
Article
Chemistry, Multidisciplinary
Fung-Kit Tang, Yanyan Chen, Daniel Nnaemaka Tritton, Zongwei Cai, Ken Cham-Fai Leung
Summary: A class of rhodamine-based fluorescent sensors that can selectively and sensitively detect Pd2+ metal ions in aqueous media have been developed. These sensors, PMS and PRS, exhibit colorimetric and fluorescent changes when exposed to Pd2+, due to the opening and restoring of their spirolactam rings. PRS has high selectivity for Pd2+ over 22 other metal ions, with a 0.6-fold ratiometric difference at I-600nm/I-515nm. The closed form of the lactam ring in PRS-Pd can be switched back in the presence of various thiols, providing a red-green traffic light detection mechanism. PRS also shows excellent cell viability and can be used to image Pd2+ and detect biothiols in cancer cells.
CHEMISTRY-AN ASIAN JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Quinn A. Besford, Huaisong Yong, Holger Merlitz, Andrew J. Christofferson, Jens-Uwe Sommer, Petra Uhlmann, Andreas Fery
Summary: Polymer brush surfaces that can alter their physical properties in response to chemical stimuli have potential as new surface-based sensing materials. This study reports on ultrathin polymer brush surfaces integrated with FRET technology for optical sensing of changes in liquid mixture compositions, with high spatial resolution. The sensitivity and real-time sensing capabilities of these brush surfaces make them promising for enhanced surface-based sensing at complex interfaces.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Analytical
Khaow Tonsomboon, Prae Noppakuadrittidej, Sarochapat Sutikulsombat, Anuwut Petdum, Waraporn Panchan, Nantanit Wanichacheva, Thanasat Sooksimuang, Nitsara Karoonuthaisiri
Summary: This study developed a fluorescent electrospun fibrous membrane that can detect mercury contamination at sub-ppb levels in less than a minute. By designing a novel mercury-favored organic dye and utilizing the mechanism of fluorescence resonance energy transfer, the sensitivity of the test strip was significantly enhanced. With a detection limit of 0.309 ppb, this low-cost test strip could be used for safety evaluation and large-scale screening of commercial products.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Nanoscience & Nanotechnology
Jyoti, Jose Munoz, Martin Pumera
Summary: Graphene quantum dot-based microrobots demonstrate potential for optical real-time monitoring of DNA, offering high sensitivity and selectivity.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Microbiology
Elena M. Maksimova, Daria S. Vinogradova, Ilya A. Osterman, Pavel S. Kasatsky, Oleg S. Nikonov, Pohl Milon, Olga A. Dontsova, Petr V. Sergiev, Alena Paleskava, Andrey L. Konevega
Summary: The research reveals that Amicoumacin A inhibits bacterial growth by halting ribosomal translation, impacting steps in polypeptide synthesis such as initiation complex formation and inducing the formation of erroneous ICs.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Eva Absmeier, Karen Vester, Tahereh Ghane, Dmitry Burakovskiy, Pohl Milon, Petra Imhof, Marina Rodnina, Karine F. Santos, Markus C. Wahl
Summary: Brr2 is an essential RNA helicase with a unique structure in the spliceosome, containing catalytically active N-terminal helicase cassette and structurally similar but enzymatically inactive C-terminal helicase cassette. The study reveals that both cassettes exhibit high specificity for adenine nucleotides, with the C-terminal cassette showing significantly higher affinity than the N-terminal cassette. Additionally, mutations and abrogation of nucleotide binding at one cassette can affect nucleotide binding at the other cassette through long-range allosteric effects.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Evan Mercier, Xiaolin Wang, Manisankar Maiti, Wolfgang Wintermeyer, Marina Rodnina
Summary: The study reveals that during the synthesis of membrane proteins, the lateral gate fluctuations are highly dynamic, continuously sampling between open and closed states even without ligands. Ribosome binding and transmembrane segment insertion do not stop the gate fluctuations but tend to increase sampling of the open state. Binding of YidC facilitates substantial opening of the gate, aiding in the folding of YidC-dependent polytopic membrane proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Alicia Arica-Sosa, Roberto Alcantara, Gabriel Jimenez-Avalos, Mirko Zimic, Pohl Milon, Miguel Quiliano
Summary: In this study, the compound RO9021 was identified as a PknG inhibitor using virtual screening and biochemical assays, suggesting its potential as a drug for tuberculosis treatment.
Article
Microbiology
Eva Duenas, Jose A. Nakamoto, Luis Cabrera-Sosa, Percy Huaihua, Maria Cruz, Jorge Arevalo, Pohl Milon, Vanessa Adaui
Summary: This study developed CRISPR-based assays for molecular detection of Leishmania spp., with high specificity and sensitivity. These assays show potential applicability for first-line diagnosis of Leishmania infections at the genus and L. (Viannia) subgenus levels.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
George A. Saratov, Vasiliy I. Vladimirov, Alexey L. Novoselov, Rustam H. Ziganshin, Guo Chen, Timur N. Baymukhametov, Andrey L. Konevega, Alexey A. Belogurov, Anna A. Kudriaeva
Summary: In this study, the researchers characterized human constitutive and immune 20S and 26S/30S proteasomes using engineered versions fused with different subunits. They found that immunoproteasomes produced peptides that can be directly loaded onto HLA class I molecules, based on their hydrolysis of the multiple sclerosis autoantigen MBP. They identified five immunodominant core regions of MBP, and found that all peptides, except one, were associated with HLA I alleles known to increase MS risk. They also observed that certain HLA-A*44 molecules showed high affinity binding to a specific MBP peptide, potentially linking their protective phenotype to the depletion of autoreactive cytotoxic T cells or induction of CD8+ regulatory T cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Madhura N. Paranjpe, Valeria Marina, Aleksandr A. Grachev, Tinashe P. Maviza, Olga A. Tolicheva, Alena Paleskava, Ilya A. Osterman, Petr Sergiev, Andrey L. Konevega, Yury S. Polikanov, Matthieu G. Gagnon
Summary: Thermorubin (THR) is an antibiotic that can inhibit translation initiation and disrupt tRNA accommodation in the ribosomal A site, causing ribosome stalling at internal and termination codons. Our findings reveal that THR affects multiple steps of translation elongation and can coexist with P- and A-site tRNAs, allowing ribosomes to continue elongation in the presence of the drug.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Infectious Diseases
Julia A. Pavlova, Andrey G. Tereshchenkov, Pavel A. Nazarov, Dmitrii A. Lukianov, Dmitry A. Skvortsov, Vladimir I. Polshakov, Byasilya F. Vasilieva, Olga V. Efremenkova, Mikhail Y. Kaiumov, Alena Paleskava, Andrey L. Konevega, Olga A. Dontsova, Ilya A. Osterman, Alexey A. Bogdanov, Natalia V. Sumbatyan
Summary: To improve the properties of antimicrobial compounds, new conjugates were synthesized and studied, which consisted of two different biologically active agents in a single chimeric molecule based on chloramphenicol and a hydrophobic cation. These conjugates, named CAM-Cn-BER, effectively bound to the bacterial ribosome and inhibited protein synthesis, similar to chloramphenicol. CAM-C8-BER displayed selective inhibition of Gram-positive bacteria and acted on both the ribosome and the cell membrane. Moreover, CAM-Cn-BERs did not inhibit eukaryotic translation and were non-toxic to eukaryotic cells.
Article
Biochemistry & Molecular Biology
Evgeniia A. Diatlova, Grigory V. Mechetin, Anna V. Yudkina, Vasily D. Zharkov, Natalia A. Torgasheva, Anton V. Endutkin, Olga V. Shulenina, Andrey L. Konevega, Irina P. Gileva, Sergei N. Shchelkunov, Dmitry O. Zharkov
Summary: The protein encoded by the D4R gene in vaccinia virus has both base excision repair uracil-DNA N-glycosylase (vvUNG) activity and acts as a processivity factor in the viral replication complex. The processivity of vvUNG has been characterized using the correlated cleavage assay, which suggests that it plays a role in lesion search through one-dimensional diffusion. Inhibitors carrying a tetrahydro-2,4,6-trioxopyrimidinylidene moiety can suppress the processivity of vvUNG.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Nhan Hau Tran, Vyacheslav Ryzhov, Andrey Volnitskiy, Dmitry Amerkanov, Fedor Pack, Aleksander M. Golubev, Alexandr Arutyunyan, Anastasiia Spitsyna, Vladimir Burdakov, Dmitry Lebedev, Andrey L. Konevega, Tatiana Shtam, Yaroslav Marchenko
Summary: In this study, the potential of iron oxide nanoparticles as radiosensitizers in glioblastoma cells was evaluated. The results showed that the nanoparticles can significantly enhance the effect of X-ray irradiation, while having a weaker or no effect on gamma and proton irradiation. The findings suggest that the nanoparticles may enhance radiation therapy by generating secondary electrons.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Alicia Arica-Sosa, Roberto Alcantara, Gabriel Jimenez-Avalos, Mirko Zimic, Pohl Milon, Miguel Quiliano
Summary: This study identifies compound RO9021 as a potential inhibitor of the mycobacterial serine/threonine protein kinase G (PknG) through pharmacophore-based virtual screening and biochemical assays. In vitro experiments demonstrate the inhibitory effect of RO9021 on PknG activity, making it a promising candidate for the development of new anti-tuberculosis drugs. Molecular dynamics simulations also predict the stability of the PknG-RO9021 complex.
Article
Biochemical Research Methods
Roberto Alcantara, Katherin Penaranda, Gabriel Mendoza-Rojas, Jose A. Nakamoto, Eva Duenas, Daniela Alvarez, Vanessa Adaui, Pohl Milon
Summary: The protocol provides a detailed step-by-step guide for detecting SARS-CoV-2 RNA using RT-PCR amplification and CRISPR/Cas visualization, with options for qualitative and quantitative measurements, as well as including a human control sample. It is designed for remote regions and uses a portable molecular workstation from BentoLab.
Article
Biochemical Research Methods
Gabriel Mendoza-Rojas, Vanessa Sarabia-Vega, Ana Sanchez-Castro, Lesia Tello, Luis Cabrera-Sosa, Jose A. Nakamoto, Katherin Penaranda, Vanessa Adaui, Roberto Alcantara, Pohl Milon
Summary: This detailed protocol outlines the steps for the expression, purification, quantification, and activity determination of key enzymes used for molecular detection of pathogens. It has been optimized for use with minimal laboratory equipment in low- and middle-income countries, and the enzymes produced using this protocol have been successfully utilized for molecular detection applications. For full details on the protocol's use and implementation, please refer to Alcantara et al. (2021a, 2021b).
Article
Biochemical Research Methods
Roberto Alcantara, Katherin Penaranda, Gabriel Mendoza-Rojas, Jose A. Nakamoto, Johanna Martins-Luna, Juana Del Valle-Mendoza, Vanessa Adaui, Pohl Milon
Summary: The study presents a molecular toolkit for batch production and detection of SARS-CoV-2 in low- and middle-income countries, with high sensitivity and specificity. Validation results show that the toolkit can be used in a mobile laboratory, potentially assisting LMICs in implementing detection services in remote regions.
CELL REPORTS METHODS
(2021)
Meeting Abstract
Biochemistry & Molecular Biology
A. E. Sanchez-Castro, K. Penaranda, J. A. Nakamoto, P. Milon
