Article
Biochemistry & Molecular Biology
Laura Fabre, Corentin Rousset, Karine Monier, Fernande Da Cruz-Boisson, Philippe Bouvet, Marie-Therese Charreyre, Thierry Delair, Etienne Fleury, Arnaud Favier
Summary: In this study, we developed a novel fluorescent polymer-aptamer probe for precise localization and recognition of nucleolin using super-resolution techniques. The probe exhibited brightness and small size, making it an appealing alternative to immunofluorescence.
Article
Chemistry, Analytical
Li Guan, Yanyan Zhou, Xiao Li, Yongbao Mao, Anyang Li, Yile Fu, Wen Liu, Sheying Dong, Zhen Liang, Yukui Zhang, Qun Zhao, Lihua Zhang
Summary: A universal strategy has been developed to synthesize pentamethine cyanines with different aromatic heterocycle substituents on the meso-polymethine chain, leading to the development of specific fluorescent probes with high sensitivity and robust OFF/ON switching for targeting G4s. These probes exhibit self-quenching in aqueous solution due to H-aggregation, but can be triggered to emit fluorescence upon recognition of G-quadruplexes.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Karolina Maleckaite, Domantas Narkevicius, Rugile Zilenaite, Jelena Dodonova-Vaitkuniene, Stepas Toliautas, Sigitas Tumkevicius, Aurimas Vysniauskas
Summary: Mapping microviscosity, temperature, and polarity in biosystems is important for disease detection. This study investigates how different electron-withdrawing and electron-donating groups can alter the spectral and sensory properties of BODIPY compounds, providing insights for the development of fluorescent sensors. The research utilizes experimental results and quantum chemical calculations to understand the effects of non-radiative relaxation on the probe's sensitivity to temperature and viscosity.
Article
Spectroscopy
Jian Yang, Ran Zhang, Yue Zhao, Jiangwei Tian, Shifa Wang, Claude P. Gros, Haijun Xu
Summary: Two mitochondrial-targeted fluorescent probes based on a BODIPY scaffold and piperidinyl groups were easily synthesized and displayed excellent imaging ability in live cells, showing promise for mitochondrial visualization.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Chemistry, Multidisciplinary
Yu Zhou, Silvia P. Centeno, Kuan Zhang, Lifei Zheng, Robert Goestl, Andreas Herrmann
Summary: This study reports the development of a series of ratiometric optical force probes (OFPs) based on fluorescent-protein-dye and protein-protein conjugates, and their incorporation into genetically engineered bio-glues. The OFPs efficiently modulate Forster resonance energy transfer upon force application, reporting on force-induced molecular alterations independent of concentration and fluorescence intensity. By fluorescence spectroscopy in solution and in the solid state, as well as fluorescence lifetime imaging microscopy, stress concentrations are visualized and adhesive and cohesive failure in the fracture zone is differentiated.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Simon Ludwanowski, Avik Samanta, Sebastian Loescher, Christopher Barner-Kowollik, Andreas Walther
Summary: The study presents a modular fluorescent probe called StyPy with a large tunable Stokes shift and diverse applicability. Through thorough characterization, StyPy is demonstrated to report viscosity changes in DNA microspheres and characterize hydrophilic and hydrophobic regions in hybrid DNA-based mesostructures.
Article
Chemistry, Analytical
Dmytro Dziuba
Summary: Fluorescent nucleoside analogues (FNAs) are important tools in studying the interactions of nucleic acids with nucleic acid-binding proteins. They enable real-time monitoring of binding interactions in solutions, with high sensitivity. FNAs are also used to study the conformational dynamics of biomolecular complexes. Therefore, FNAs have potential applications in fundamental biological research and molecular diagnostics drug discovery.
METHODS AND APPLICATIONS IN FLUORESCENCE
(2022)
Article
Chemistry, Analytical
Yun Wen, Xue-Wei Zhang, Yuan-Yuan Li, Shuai Chen, Yong-Liang Yu, Jian-Hua Wang
Summary: The combination of nanosatellites, CHA, and ICP-MS enables simultaneous and sensitive detection of multiple exosomal miRNAs, achieving accurate cancer diagnosis and classification through machine learning analysis.
ANALYTICAL CHEMISTRY
(2022)
Article
Materials Science, Multidisciplinary
Masayasu Taki, Keiji Kajiwara, Eriko Yamaguchi, Yoshikatsu Sato, Shigehiro Yamaguchi
Summary: Researchers have developed a dye, LAQ1, based on the BTBT scaffold that meets the requirements of LD staining, high photostability, and biocompatibility. With LAQ1, they were able to capture ultrasmall LDs using STED microscopy with super-resolution imaging, and perform long-term trajectory analysis.
ACS MATERIALS LETTERS
(2021)
Article
Chemistry, Analytical
Xinran Dong, Yuchen Huang, Dechen Jiang
Summary: A fluorescent polymerase chain reaction (PCR) nanokit was established for detecting specific DNA sequences in single living cells. This strategy involves sorting the DNA sequence in a cellular nucleus into a nanopipette, where it reacts with PCR kit components to complete a PCR amplification reaction. The presence of the target DNA sequence is validated through an increase in fluorescence, and the nanokit offers a general and highly sensitive approach for single cell analysis.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Benjamin W. Lewis, Niels Bisballe, Marco Santella, Peter A. Summers, Jean-Baptiste Vannier, Marina K. Kuimova, Bo W. Laursen, Ramon Vilar
Summary: This study expanded the library of triangulenium probes and investigated the interactions of two new molecules featuring ethyl-morpholino substituents with DNA topologies. However, despite modifications to the core structure, these two probes were unable to distinguish between DNA topologies based on fluorescence lifetime.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Analytical
Dongliu Xiang, Hui Wen, Hongmei Fang, Yuan Zhou, Lei Luo, Qing Wang, Xueting Yan, Jin Huang, Jianbo Liu, Xiaohai Yang, Kemin Wang
Summary: A versatile detection technique was developed using magnetic beads, barcoded DNA strands released from gold nanoparticles, and exonuclease III cyclic cleavage-assisted signal amplification. This technique was integrated into a microfluidic chip with multiple chambers and the mixing was achieved by acoustic vibration from a portable sonic toothbrush. The detection limits of three different targets were successfully demonstrated, and this platform is expected to be developed into an automatic sample-to-answer device.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Yurie Tehee Kim, Hyesoo Oh, Myung Jun Seo, Dong Hyeun Lee, Jieun Shin, Serang Bong, Sujeong Heo, Natalia Diyah Hapsari, Kyubong Jo
Summary: This study constructed 21 FP-DBPs to stain and visualize DNA molecules, with the choice of FP and DBP affecting the brightness and stretching of DNA staining, providing guidance for the development of novel DNA-binding fluorescent proteins.
Review
Biochemical Research Methods
Lulu Winer, Leila Motiei, David Margulies
Summary: The development of fluorescent labels, sensors, and analytical techniques for detecting and imaging proteins in the life sciences has been driven by the crucial role of fluorescence detection. Many research groups have utilized oligodeoxynucleotides (ODNs) to develop simple-to-produce, modular, and versatile fluorescent tools for studying proteins. The important properties of DNA probes include tight control over protein binders and fluorescent dyes, as well as the ability to predict molecular architectures through self-assembly, inherent solubility, and stability.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Eiji Nakata, Hisaaki Hirose, Khongorzul Gerelbaatar, Jan Vincent V. Arafiles, Zhengxiao Zhang, Shiroh Futaki, Takashi Morii
Summary: Real-time monitoring of cellular environment, such as intracellular pH, in a defined cellular space provides a comprehensive understanding of dynamic processes in living cells. By assembling multiple fluorophores within a space smaller than the spatial resolution of conventional microscopy, a flexible combinatorial design strategy for developing fluorescent probes is enabled. Assembling fluorescein (CF) and tetramethylrhodamine (CR) on a DNA nanostructure with controlled numbers of each fluorophore type allows for controlled fluorescence emission intensity and ratiometric pH monitoring within the defined space.
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
Vaclav Houska, Egor Ukraintsev, Jaroslav Vacek, Jiri Rybacek, Lucie Bednarova, Radek Pohl, Irena G. Stara, Bohuslav Rezek, Ivo Stary
Summary: The synthesis of helically chiral macrocycles composed of dibenzo[5]helicene units and trans-stilbene-4,4'-diyl linkers is reported. Different stereoisomers of these macrocycles were obtained through chiral resolution. The self-assembly of these macrocycles into long 1D molecular stripes in ordered 2D nanocrystals was studied using AFM.
Article
Biochemical Research Methods
Ambra Spampinato, Erika Kuzmova, Radek Pohl, Veronika Sykorova, Milan Vrabel, Tomas Kraus, Michal Hocek
Summary: A series of modified dNTPs with different linkers were designed and synthesized as substrates for DNA polymerase. The reactivity of these modified nucleotides and DNA was systematically tested and compared in click reactions. The longer linker was found to be crucial for efficient labeling. These modified dNTPs were transported into live cells and successfully used for staining DNA and imaging DNA synthesis within short time periods. This method provides a new approach for in cellulo metabolic labeling and imaging of DNA synthesis that overcomes previous limitations.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Catherine Mulholland, Ivana Jestrabova, Arghya Sett, Marek Ondrus, Veronika Sykorova, C. Lorena Manzanares, Oliver Simoncik, Petr Muller, Michal Hocek
Summary: The authors describe the selection of hydrophobic 7-phenylbutyl-7-deazaadenine-modified DNA aptamers against Heat Shock Protein 70 using PEX and magnetic bead-based SELEX. The modified aptamers showed higher binding affinity to Hsp70 than their natural counterparts and have potential for diagnostic or therapeutic applications.
COMMUNICATIONS CHEMISTRY
(2023)
Article
Chemistry, Analytical
David Kodr, Mayreli Ortiz, Veronika Sykorova, Cansu Pinar Yenice, Zbigniew J. Lesnikowski, Ciara K. O'Sullivan, Michal Hocek
Summary: The previous approach of orthogonal multipotential redox coding only allowed analysis of relative nucleotide composition of short DNA stretches. In this study, two methods for normalization of electrochemical readout were presented, enabling determination of total nucleotide composition. The first method involved the presence or absence of an internal standard in the DNA primer, while the second method utilized a viologen-modified primer acting as a reference label for signal normalization. Both methods accurately analyzed DNA sequences and demonstrated potential for targeted DNA sequence analysis.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Miroslav Kuba, Petro Khoroshyy, Martin Lepsik, Erika Kuzmova, David Kodr, Tomas Kraus, Michal Hocek
Summary: A modified dC(TO)TP was designed and synthesized with a thiazole orange moiety tethered via an oligoethylene glycol linker. It could be incorporated into DNA by DNA polymerases in vitro and live cells. The fluorescence lifetime of the thiazole orange moiety differed significantly when dC(TO)TP was incorporated into DNA compared to its non-incorporated forms. By delivering dC(TO)TP into live U-2 OS cells using a synthetic nucleoside triphosphate transporter, it enabled real-time detection and monitoring of cells actively synthesizing DNA from the beginning.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Organic
Chao Yang, Michal Tichy, Lenka Postova Slavetinska, Enzo Vaiedelich, Sona Gurska, Petr Dzubak, Marian Hajduch, Michal Hocek
Summary: This study reports the design and synthesis of a series of benzofuro-fused 7-deazapurine nucleosides and ribonucleosides. The target compounds were successfully synthesized through multiple reactions, and showed moderate to weak cytostatic activity and interesting fluorescence properties.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Natalia Kuprikova, Marek Ondrus, Lucie Bednarova, Miguel Riopedre-Fernandez, Lenka Postova Slavetinska, Veronika Sykorova, Michal Hocek
Summary: Researchers designed and synthesized a set of new DNA nucleotide derivatives, which were successfully used for DNA modification and hypermodification. The study found that one to two modified nucleotides could achieve exponential amplification in PCR, while three to four modified nucleotides only achieved linear amplification. In addition, hypermodified DNA exhibited a different secondary structure.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Mayreli Ortiz, Miriam Jauset-Rubio, Olivia Trummer, Ines Foessl, David Kodr, Josep Lluis Acero, Mary Luz Botero, Phil Biggs, Daniel Lenartowicz, Katerina Trajanoska, Fernando Rivadeneira, Michal Hocek, Barbara Obermayer-Pietsch, Ciara K. O'Sullivan
Summary: A generic platform was developed for cost-effective and rapid electrochemical SNP genotyping from fingerprick blood samples, enabling early diagnosis of osteoporosis. The platform utilizes isothermal solid-phase primer elongation with ferrocene-labeled nucleoside triphosphates, allowing for targeted genotyping of SNPs associated with osteoporosis. The system was validated using real blood samples, with results matching those from Taqman SNP genotyping assays and Sanger sequencing. The platform is highly versatile and has the potential to be deployed in an automated device for targeted SNP genotyping.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Ivana Jestrabova, Lenka Postova Slavetinska, Michal Hocek
Summary: We designed and synthesized a series of novel nucleoside phosphoramidites for the solid-phase synthesis of modified oligonucleotides. The hybridization properties of these modified oligonucleotides were studied, and they have potential for the synthesis of highly modified functional nucleic acid-based polymers.
Article
Chemistry, Multidisciplinary
Vladimir Motornov, Radek Pohl, Blanka Klepetarova, Petr Beier
Summary: Elusive N-acyl-1,2,3-triazoles formed by direct acylation of NH-1,2,3-triazoles were isolated and characterized. Thermodynamic N2 isomers were found to be preferred. Direct evidence of interconversion between N1- and N2-acyltriazoles confirmed their usefulness in denitrogenative transformations. An efficient synthesis of enamido triflates from NH-triazoles via N2-acyl-1,2,3-triazole intermediates was developed.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
David Kodr, Erika Kuzmova, Radek Pohl, Tomas Kraus, Michal Hocek
Summary: We designed and synthesized lipid-modified dNTPs, which served as substrates for DNA polymerase and could be incorporated simultaneously into the DNA strand. These lipid-ON probes showed enhanced membrane anchoring efficiency and better stability in the cell membrane compared to commonly studied ON analogues. The probes were detected at the cell surface even after 24 hours, indicating their long-lasting effect.
Article
Chemistry, Multidisciplinary
Anna Kovalova, Vit Prouza, Martin Zavrel, Miroslav Hajek, Rastislav Dzijak, Alzbeta Magdolenova, Radek Pohl, Zdenek Voburka, Kamil Parkan, Milan Vrabel
Summary: This study presents a method for identifying lectin-binding ligands with low micromolar affinity by screening synthetic click glycopeptide libraries. The selected glycopeptides showed enhanced binding potency to the target lectins compared to the starting sugar moieties. This approach offers a promising alternative means of discovering ligands for galectins and other carbohydrate-binding proteins.
Review
Biology
Walter Wolfsberger, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova, Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, Dmytro Dziuba, Andrii Parkhomenko, Volodymyr Smolanka, Zeynep H. Guemues, Efe Sezgin, Alondra Diaz-Lameiro, Viktor R. Toth, Megi Maci, Eric Bortz, Fyodor Kondrashov, Patricia M. Morton, Pawel P. Labaj, Veronika Romero, Jakub Hlavka, Serghei Mangul, Taras K. Oleksyk
Summary: Conflicts and natural disasters not only cause destruction to lives, but also have a significant negative impact on the scientific advancements of the affected countries. These events result in infrastructure collapse, destruction of educational and research institutions, and hinder the progress of scientists. In our interconnected world, conflicts and disasters have far-reaching effects on the global community.
Review
Chemistry, Multidisciplinary
Dan He, Yawen Li, Fuwen Zhao, Yuze Lin
Summary: High trap density in organic solar cells leads to localized charge carriers and reduced carrier lifetime, limiting device efficiency. This feature article summarizes the recent advances of trap suppression by material design and device engineering.
CHEMICAL COMMUNICATIONS
(2024)
Review
Chemistry, Multidisciplinary
Olivier Monfort, Arshitha Madhusudhan, Martin Motola
Summary: This article presents the advantages of coupling photocatalysis and Fenton-based processes for environmental remediation and discusses their synergy. It critically examines the simultaneous triggering of these two processes and provides insights into research approaches. The study aims to enhance understanding of this complex process and highlight the potential integration of new catalysts in current wastewater treatment technology.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Manideepa Dhar, Chittaranjan Mishra, Avijit Das, Uttam Manna
Summary: An approach of 'polymerization of monomers in its aggregated form' has been introduced to tailor the water wettability of fibrous and porous substrates, achieving hydrophobicity to superhydrophobicity transition, as well as patterned wettability. This facile chemical method provides a durable coating with adjustable and patterned wettability for various potential applications.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Saswat Ranjan Bhoi, Chhanda Debnath, Shikha Gandhi
Summary: In this article, a novel catalytic reaction using Pd(0) and Bronsted acid is reported for the synthesis of biologically important imidazolidinone-fused N-heterocycles through redox-neutral intramolecular N-allylation of indoles and pyrroles with alkynes. This atom-economical method is applicable to a wide range of substrates and eliminates the need for leaving groups or oxidizing agents commonly used in traditional allylation reactions.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Longkun Chen, Mingshuai Zhang, Meichen Liu, Zhuoyuan Liu, Yuetong Qiu, Zhilai Zhang, Fuchao Yu, Jiuzhong Huang
Summary: In this study, an efficient Rh(III)-catalyzed selective mono- and dual-C-H bond functionalization/cyclization with iodonium ylide as the sole coupling partner was demonstrated. Fused benzodiazepine skeletons were obtained in excellent yields, providing an improved approach to dual C-H unsymmetrical functionalization.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Alice Kennett, Sven Epple, Gabriella van der Valk, Irene Georgiou, Evelyne Gout, Romain R. Vives, Angela J. Russell
Summary: This study presents the design and synthesis of sulfated disaccharide inhibitors based on IdoA(2S)-GlcNS(6S), which showed potent inhibition of Sulf-2. The results suggest that IdoA(2S)-GlcNS(6S) is the shortest fragment size required for effective inhibition of Sulfs, and a trisulfated disaccharide is identified as the minimal fragment size of heparan sulfate for effective endosulfatase inhibition.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Mauro Garbini, Andrea Brunetti, Riccardo Pedrazzani, Magda Monari, Massimo Marcaccio, Giulio Bertuzzi, Marco Bandini
Summary: The self-adaptability of galvanostatic electrolysis was found to be helpful in a multistage chemo- and diastereoselective electrochemically promoted cyclodimerization of chalcones. Through a series of reductive events, densely functionalized cyclopentanes with five contiguous stereocenters were obtained (25 examples, yields up to 95%, dr values up to >20:1). Further experimental and electrochemical investigations indicated the crucial role of dynamic kinetic resolution of the aldol intermediate in the reaction mechanism.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Dhananjay S. Nipate, Neha Meena, Prakash N. Swami, Krishnan Rangan, Anil Kumar
Summary: In this study, the synthesis of functionalized benzo[a]phenazines and indazolo[2,3-a]quinolines was achieved through Rh(III)-catalyzed oxidative annulation of 2-arylquinoxalines and 2-aryl-2H-indazoles with allyl alcohols. The method showed a wide substrate scope, excellent functional group tolerance, good to high yields of annulated products, and the capability for scaled-up synthesis. A tentative mechanism of the annulation reaction was proposed based on a preliminary mechanistic investigation.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Ruonan Zhang, Abudukadi Tudi, Xia Yang, Xuping Wang, Zhihua Yang, Shujuan Han, Shilie Pan
Summary: A new lead tellurium borate material with a unique fundamental building block [B4O10] was synthesized and found to exhibit high birefringence. The structure-property relationship was discussed using first-principles calculations.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Amresh Kumar Singh, Baishali Thakurta, Anupam Giri, Monalisa Pal
Summary: This study introduces three key concepts for the quick synthesis of large-scale high-quality 2D materials films and their utilization in device fabrication.
CHEMICAL COMMUNICATIONS
(2024)
Article
Chemistry, Multidisciplinary
Reina Hagiwara, Shun Nishimura, Kosuke Okeyoshi
Summary: A copolymer-conjugated nanocatalytic system has been developed to improve electron transfer and enhance photoinduced H2 generation.
CHEMICAL COMMUNICATIONS
(2024)
