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
Multidisciplinary Sciences
Steve L. Bonilla, Quentin Vicens, Jeffrey S. Kieft
Summary: This study used cryo-EM to visualize a long-lived misfolded state in the folding pathway of Tetrahymena thermophila group I intron, revealing its structure and providing insights into RNA folding. The misfolded state contains incorrectly crossed strands, causing mispositioning of a critical catalytic domain that requires extensive refolding. The findings of this study have important implications for understanding RNA folding pathways.
Article
Multidisciplinary Sciences
Shanshan Li, Michael Z. Palo, Grigore Pintilie, Xiaojing Zhang, Zhaoming Su, Kalli Kappel, Wah Chiu, Kaiming Zhang, Rhiju Das
Summary: The Tetrahymena group I intron has provided valuable insights into the folding and misfolding of RNA. In this study, cryo-EM was used to visualize the misfolded structures of the Tetrahymena L-21 ScaI ribozyme. Multiple misfolded substates were identified and compared to the native state, revealing topological differences that explain the failure of substrate docking and suggest pathways for refolding.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Karolina Maleckaite, Jelena Dodonova, Stepas Toliautas, Rugile Zilenaite, Dziugas Jurgutis, Vitalijus Karabanovas, Sigitas Tumkevicius, Aurimas Vysniauskas
Summary: Viscosity imaging at a microscopic scale is important for studying biosystems, and developing red-emitting, viscosity-sensitive fluorophores is a challenging task. Successful prediction of the viscosity sensitivity of fluorophores through DFT calculations aided in the design of a new red viscosity probe.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Jingye Zhang, Lu Wang, Andres Jaeschke, Murat Sunbul
Summary: FLAPs have become a promising tool for visualizing RNAs in living cells by dramatic fluorescence increase upon specific binding. In this study, a color-shifting aptamer-fluorophore system was presented, allowing ratiometric RNA imaging unlike other FLAPs reported. This system was used as a light-up RNA marker to image mRNAs in the NIR region and demonstrated its utility in ratiometric analysis of target RNAs expressed at different levels in single cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Carolin P. M. Scheitl, Takumi Okuda, Juliane Adelmann, Claudia Hoebartner
Summary: This article reports a method for synthesizing aldehyde-functionalized RNA by directly converting a purine nucleobase using a ribozyme-based approach. The modified nucleotide can react with aldehyde-reactive probes, allowing for the conjugation of biotin or fluorescent dyes to short synthetic RNAs and tRNA transcripts. The condensation of a 2,3,3-trimethylindole with the modified RNA generates a novel hemicyanine chromophore directly on the RNA. This work expands the application of the MTR1 ribozyme from a methyltransferase to a tool for site-specific late-stage functionalization of RNA.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Inga Jarmoskaite, Pilar Tijerina, Rick Russell
Summary: The research reveals that several hundred ATP molecules are hydrolyzed during the refolding of each ribozyme molecule, specifically due to interactions with the misfolded ribozyme. This process is insensitive to changes in ATP and CYT-19 concentration, but decreases as ribozyme stability decreases.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Miroslav Kuba, Radek Pohl, Tomas Kraus, Michal Hocek
Summary: Nucleosides and 2'-deoxyribonucleoside triphosphates (dNTPs) containing a bodipy fluorophore attached to position S of 2'-deoxycytidine were synthesized. They exhibited strong fluorescence and sensitivity to viscosity. The modified dNTPs served as substrates for DNA polymerases and were used for enzymatic synthesis of labeled DNA. The modified DNA probes acted as viscosity sensors, responding to protein binding. The dNTP with a longer linker was successfully transported into live cells and incorporated into genomic DNA, enabling DNA staining and imaging of DNA synthesis.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Xing Li, Jiahui Wu, Samie R. Jaffrey
Summary: Fluorogenic aptamers can potentially show minimal photobleaching during continuous irradiation due to exchanges with fluorescent dyes, but designing fluorophores for optimized recycling can enhance fluorescence.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biology
Suvam Roy, Supratim Sengupta
Summary: The encapsulation of genetic material and formation of functionally diverse components inside compartments played a crucial role in the development of replicating protocells in an RNA world. Experimental evidence suggests that RNA replication inside lipid vesicles can lead to vesicular growth and division. The impact of such replication on the emergence of ribozymes inside protocells and their subsequent evolution remains uncertain.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Anja Henning-Knechtel, D. Thirumalai, Serdal Kirmizialtin
Summary: The stability of RNA is influenced by the charge density of alkali metal cations, with sodium showing stronger stability than potassium due to their different binding modes with RNA.
Article
Biochemistry & Molecular Biology
Tak Ian Chio, Akiva J. Grimaldi, Thomas Radford, Susan L. Bane
Summary: Given the popular usage of BODIPY fluorophores in biological research, it is necessary to pay more attention to their tendency to aggregate in aqueous solution and its impact on their spectroscopic properties. This study focuses on a particular probe and reveals that it exhibits a much-reduced fluorescence in aqueous solution due to aggregation-caused quenching (ACQ). However, it is capable of responding to complementary reactive substrates and generates a substantial turn-on signal. The probe assumes a disaggregated form and unleashes a significant fluorescence enhancement through disaggregation-induced emission (DIE). The results suggest that the probe functions via a target-mediated inhibition of probe aggregation instead of dispersing from preformed aggregates to react with the target.
Article
Biology
Xavier Portillo, Yu-Ting Huang, Ronald R. Breaker, David P. Horning, Gerald F. Joyce
Summary: A study has shown that through evolution, an RNA polymerase ribozyme underwent significant structural changes to develop a new tertiary structural element that improved catalytic activity. The evolving population stabilized the new structure, leading to the discovery of a new fitness locale and the potential for further enhancement of polymerase activity.
Article
Biochemistry & Molecular Biology
Irina S. Trukhan, Denis N. Tomilin, Nataliya N. Dremina, Lyubov N. Sobenina, Michael G. Shurygin, Konstantin B. Petrushenko, Igor K. Petrushenko, Boris A. Trofimov, Irina A. Shurygina
Summary: A bright far-red emitting unsymmetrical meso-CF3-BODIPY fluorescent dye was synthesized and studied as a lysosome-specific fluorescent dye in Ehrlich carcinoma cells.
Article
Biology
Dominique Bourgeois
Summary: Single Molecule Imaging Simulator (SMIS) is a simulation software that models the photophysical behavior of fluorophores in single-molecule localization experiments. It can simulate a widefield microscope and incorporate fluorophores with their spectral and photophysical properties. SMIS allows the evaluation of advanced fluorophore characteristics, imaging conditions, and environmental parameters, facilitating the design of real experiments and their interpretation.
COMMUNICATIONS BIOLOGY
(2023)
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
Chemistry, Inorganic & Nuclear
Misaki Kamioka, Yitong Wang, Shigeki Mori, Hiroyuki Furuta, Soji Shimizu
Summary: A sigma-bonded platinum(II) diketopyrrolopyrrole (Pt-DPP) complex with high fluorescence properties in both solution and solid state was synthesized. The intense emission of the Pt-DPP complex is attributed to the DPP-centered fluorescence. In the solid state, aggregation-caused quenching is mitigated by the well-segregated molecular packing due to the bulky triphenylphosphine ligands. The easy synthesis and unique fluorescence properties of the Pt-DPP complex are beneficial for the development of DPP-based functional chromophores.
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY
(2022)
Editorial Material
Chemistry, Multidisciplinary
Calvin Chau, Sajal Sen, Adam C. Sedgwick, Philip A. Gale, G. Dan Pantos, Sung Kuk Kim, Jung Su Park, Elisa Tomat, Jonathan F. Arambula, Anne E. Gorden, Hiroyuki Furuta
Summary: This article celebrates Professor Jonathan Sessler's 65th birthday by tracing his life and career path. It highlights his early days as an independent researcher and his contributions to the field of chemistry. The article aims to inspire readers to pursue their academic endeavors and emphasizes Jonathan's guiding motto.
Article
Biotechnology & Applied Microbiology
Md Dobirul Islam, Kumi Hidaka, Yuki Suzuki, Hiroshi Sugiyama, Masayuki Endo, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: In this study, a hexameric ribozyme nanostructure was constructed by dimerizing a pair of triangular ribozyme trimers, while the dimerization strategy was expanded to a square-shaped ribozyme tetramer with four pillar units. The resulting box-shaped nanostructures contain eight ribozyme units and can be assembled from different numbers of unit RNAs.
JOURNAL OF BIOSCIENCE AND BIOENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Keito Shimomura, Yuma Nakamura, Hiroto Kai, Kyosuke Saito, Ko Furukawa, Shigeki Mori, Masatoshi Ishida, Hiroyuki Furuta
Summary: Novel site-selective hetero-copper/zinc complexes were synthesized and characterized, showing unique NIR absorption features and easy redox properties. The differences in structural parameters and Lewis acidity between the copper and zinc centers in different complexes highlight their potential applications as pi-materials responding to NIR light.
JOURNAL OF PORPHYRINS AND PHTHALOCYANINES
(2022)
Article
Chemistry, Multidisciplinary
Qizhao Li, Masatoshi Ishida, Yunyun Wang, Chengjie Li, Glib Baryshnikov, Bin Zhu, Feng Sha, Xinyan Wu, Hans agren, Hiroyuki Furuta, Yongshu Xie
Summary: In this study, we report the synthesis of a 20 pi antiaromatic sapphyrin isomer, which exhibits a reactivity for further oxidation due to its distinct antiaromatic electronic structure. The resulting compound possesses a unique spiro-carbon-containing [5.6.5.6]-tetracyclic structure and can be easily transformed to novel porphyrinoids with variable aromaticity. This research highlights the synthesis of porphyrinoid compounds with different aromatic properties.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Applied
Ru Feng, Tatsuya Mori, Takuma Yasuda, Hiroyuki Furuta, Soji Shimizu
Summary: The authors present two new pyrrolopyrrole aza-BODIPY (PPAB) based panchromatic chromophores, TT-2PPAB and DFBT-2PPAB, with an acceptor-donor-acceptor configuration. Among them, TT-2PPAB exhibits a moderate power conversion efficiency (PCE) of 3.11% when combined with [6,6]-phenyl-C71 butyric acid methyl ester (PC71BM) acceptor, with an energy loss of 0.48 eV, smaller than the empirical limit of 0.6 eV. The efficient photovoltaic performance of the TT-2PPAB-based device is attributed to the sufficiently deep LUMO level of TT-2PPAB for charge transfer to PC71BM, as revealed by electrochemistry and theoretical calculations.
Article
Chemistry, Multidisciplinary
Jiping Hao, Akihide Nishiyama, Shigeki Mori, Hiroyuki Furuta, Soji Shimizu
Summary: A ring-opening reaction of nickel 10,20-dimesityl-5,15-dioxaporphyrin (NiDOP) with aryl Grignard reagents resulted in the formation of 1,9-diaryldipyrrins instead of the expected demetallation reaction. Reactions with less-sterically hindered aryl Grignard reagents yielded the dipyrrin products, while no reaction occurred with alkyl, ethynyl, and 2-thienylmagnesium bromides as well as sterically hindered mesitylmagnesium bromide. The unique ring-opening reactivity of NiDOP and the characterization of the 1,9-diaryldipyrrin products are reported.
JOURNAL OF PORPHYRINS AND PHTHALOCYANINES
(2023)
Article
Chemistry, Multidisciplinary
Osamu Iwanaga, Naoya Yoshida, Takaaki Miyazaki, Fumito Tani, Shigeki Mori, Soji Shimizu, Masatoshi Ishida, Hiroyuki Furuta
Summary: Novel cobalt(III) complexes of N-confused porphyrin and its dimer were synthesized and their structures were elucidated. The redox properties of the complexes were examined using electrochemical approaches, spectroelectrochemistry, and DFT calculations. The results indicate the unique multi-electron reservoir capability of the metal complexes of the N-confused porphyrin dimer.
JOURNAL OF PORPHYRINS AND PHTHALOCYANINES
(2023)
Article
Chemistry, Multidisciplinary
Yuma Sato, Takahide Shimada, Shigeki Mori, Yuhsuke Yasutake, Susumu Fukatsu, Hiroyuki Furuta, Masatoshi Ishida
Summary: Researchers have synthesized a previously unknown butadiyne-linked BODIPY dimer, using the ethynyl-substituted pyrrolyl-BODIPY precursor prepared by gold-catalyzed C-H alkynylation. The dimer showed a characteristic broad absorption band in the near-infrared (NIR) region due to the pi-extended structure of the BODIPY chromophore. Upon photoexcitation, varied fluorescent responses were observed, which originated from the conformational changes in the rigid dimer. Therefore, the BODIPY dimer could be a potential NIR fluorescence material for probing distinct viscous environments in biological tissues.
JOURNAL OF PORPHYRINS AND PHTHALOCYANINES
(2023)
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
Biochemistry & Molecular Biology
Tomoki Ueda, Kei-ichiro Nishimura, Yuka Nishiyama, Yuto Tominaga, Katsushi Miyazaki, Hiroyuki Furuta, Shigeyoshi Matsumura, Yoshiya Ikawa
Summary: Alternative splicing is an important mechanism in eukaryotic cells that allows multiple proteins to be produced from a single gene. Although it is usually associated with group I self-splicing introns, limited examples of alternative splicing have been reported. This study focuses on exon-skipping splicing in genes containing two group I introns and reveals the key structural elements important for this type of splicing through pairwise engineering and biochemical characterization.
Article
Chemistry, Multidisciplinary
Qizhao Li, Masatoshi Ishida, Chengjie Li, Glib Baryshnikov, Feng Sha, Bin Zhu, Xinyan Wu, Hans Agren, Hiroyuki Furuta, Yongshu Xie
Summary: This study reports the synthesis of novel dimeric porphyrin analogs through a one-pot oxidation reaction. These compounds exhibit tunable conformations and unique properties, making them potential candidates for organic optoelectronic materials.
Review
Chemistry, Multidisciplinary
Michal J. Bialek, Karolina Hurej, Hiroyuki Furuta, Lechoslaw Latos-Grazynski
Summary: The world of modified porphyrins was revolutionized when an N-confused porphyrin (NCP), a porphyrin isomer, was first published in 1994. By replacing one inner nitrogen with a carbon atom, the chemistry that can be performed within the coordination cavity underwent a revolutionary change. The introduction of a carbon fragment from the ring or an inner substituent close to an inserted metal ion allowed exploration of new pathways in the organometallic chemistry of porphyrins. Since the discovery of NCP, various modifications have been available to tune the coordination properties of the cavity, introducing a fascinating realm of carbaporphyrins. This review surveys all possible carbatetraphyrins(1.1.1.1) and their spectacular coordination and organometallic chemistry.
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
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
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)
