Article
Biotechnology & Applied Microbiology
Vaclav Brazda, Otilia Porubiakova, Alessio Cantara, Natalia Bohalova, Jan Coufal, Martin Bartas, Miroslav Fojta, Jean-Louis Mergny
Summary: The study identified multiple potential G-quadruplex forming sequences in the G4-EA-H1N1 genomes, which could serve as potential therapeutic targets.
Article
Biochemistry & Molecular Biology
Masataka Mizunuma, Mirai Suzuki, Tamaki Kobayashi, Yuki Hara, Atsushi Kaneko, Kazuhiro Furukawa, Yoshiro Chuman
Summary: The development of new molecules for monitoring metal ion concentrations with high sensitivity and selectivity is important. DNA, especially guanine-rich DNA, can be used in metal ion-detection sensors and functional materials.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Kathleen L. Morrissey, Dylan DeWitt, Nikhil Shah, William Fall, Hari Shah, Linda B. McGown
Summary: The study investigates a genome-inspired approach for aptamer discovery in cancer-related DNA-protein interactions, focusing on G-rich sequences that can form G-quadruplex structures. By using naturally occurring DNA sequences, the research aims to increase the chances of uncovering protein-DNA affinity binding interactions with biological significance and analytical utility, especially in oncogene promoters. The presence of a large diversity of G4-forming sequences throughout the human genome provides promising candidates for aptamers to regulatory proteins in cancer.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Ji Hong Kim, Chae Hwan Cho, Jae Hwan Shin, Moon Seop Hyun, Eunha Hwang, Tae Jung Park, Jong Pil Park
Summary: An electrochemical biosensor was developed to detect the HA protein in the envelope of the influenza virus, using high-affinity peptide-displaying phage particles identified through phage display technology. The sensor showed good performance characteristics, including low limit of detection, high reproducibility, and compatibility with human plasma samples. The sensor system demonstrated advantages such as low cost, rapid analysis, and minimal sample volume requirement, making it suitable for rapid and effective detection of the influenza virus antigen.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
Article
Nanoscience & Nanotechnology
Sohini Pal, Akshay Naik, Anjana Rao, Banani Chakraborty, Manoj M. Varma
Summary: We demonstrate the single-molecule sensing of G-quadruplex formation in target-bound aptamers using solid-state nanopores. By functionalizing the nanopores with DNA origami sheets containing the aptamer sequence, we provide a versatile configuration for nanopore-based single-molecule sensors. The DNA origami sheet also includes a pore that can modulate the translocation dynamics of the target molecule. Using this system, we successfully differentiate the formation of G-quadruplex in the well-studied thrombin aptamer.
ACS APPLIED NANO MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Min Zou, Jing-Yan Li, Meng-Jia Zhang, Jun-Hui Li, Jun-Tao Huang, Pei-Dan You, Shu-Wen Liu, Chun-Qiong Zhou
Summary: The study indicates that the G-quadruplex binder PDS can serve as a multi-target ZIKV inhibitor with high antiviral activity, effectively suppressing ZIKV replication and protein expression, and reducing ZIKV catalytic activity.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
David Moreira, Daniela Leitao, Jessica Lopes-Nunes, Tiago Santos, Joana Figueiredo, Andre Miranda, Daniela Alexandre, Candida Tomaz, Jean-Louis Mergny, Carla Cruz
Summary: In this study, the formation and stability of G-quadruplex structure of a G-rich DNA aptamer AT11-L2 were explored under different experimental conditions, along with its interactions with various G4 ligands and nucleolin (NCL). The results showed that AT11-L2 adopted different topologies depending on the KCl concentration, and the addition of ligands significantly stabilized the G-quadruplex structure. Furthermore, a specific interaction between AT11-L2 G-quadruplex and NCL was identified, and co-localization of these two molecules was observed in certain cell lines.
Review
Chemistry, Physical
Jerome Dejeu, Angeline Van der Heyden, Nicolas Spinelli, Eric Defrancq, Liliane Coche-Guerente
Summary: Aptamer-based electrochemical sensors have been developed for detecting a wide variety of analytes with high selectivity, sensitivity, and stability, using specific G-quadruplex (G4) conformations for molecular recognition. These sensors can be miniaturized, have low production costs, and offer great flexibility in design assemblies.
CURRENT OPINION IN ELECTROCHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Weronika Kotkowiak, Anna Pasternak
Summary: G-quadruplexes play a crucial role in nucleic acid structures and can be utilized as regulatory elements in cells. Extending quadruplexes with additional structural elements enhances stability and biological activity, and the specific interaction of G-quadruplexes with target molecules is pivotal. Future applications of G-quadruplex junctions hold promise, and there is still room for development in emerging research areas.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Ji Zheng, Dayong Li, Jin Jiao, Chengjie Duan, Zhongyun Wang, Yang Xiang
Summary: In this study, a dual-aptamer recognition strategy based on G-quadruplex nanowires was developed for selective analysis of exosomes, allowing sensitive and specific analysis of target exosomes. This method is simple and universal for different types of exosomes, showing great significance for clinical cancer diagnosis.
Article
Biochemistry & Molecular Biology
Yaqin Li, Yance Zhu, Yue Wang, Yi Feng, Dongliang Li, Shuai Li, Panpan Qin, Xia Yang, Lu Chen, Jun Zhao, Chao Zhang, Yongtao Li
Summary: Porcine epidemic diarrhea virus (PEDV) is a significant threat to the global pig industry, but there is a lack of accurate targets for anti-PEDV drugs. This study identified G-quadruplex structures in the PEDV genome and showed that G4-specific compounds can inhibit the virus at the replication and protein expression stages. These findings provide new insights into developing antiviral drugs targeting PEDV RNA G-quadruplexes.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Pharmacology & Pharmacy
Andrea P. Falanga, Monica Terracciano, Giorgia Oliviero, Giovanni N. Roviello, Nicola Borbone
Summary: G-quadruplex (G4) structures in plants have significant implications in biological processes and pathological states. The exploration of plant compounds and G4 ligands can lead to potential anticancer treatments and biomedical applications.
Article
Biochemistry & Molecular Biology
Maria Tomaszewska, Marta Szabat, Karolina Zielinska, Ryszard Kierzek
Summary: Influenza A virus (IAV) is a significant research subject due to its ability to cause seasonal epidemics and pandemics. This study focused on the presence of G-rich sequences in the IAV genome and their potential to form RNA G-quadruplex structures. The researchers identified 12 potential quadruplex-forming sequences (PQS), with three confirmed to adopt G4 structures by various biophysical methods, potentially indicating their role in virus biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Materials Science, Multidisciplinary
Rana Bagheri, Fathallah Karimzadeh, Ahmad Kermanpur, Mahshid Kharaziha
Summary: A simple and novel method for immobilization of AS1411 aptamer on Cu nanoparticles electrode was presented and validated by experiments. The study found that choosing 0.03 M Cu concentration, 10 μM aptamer concentration, and 20 minutes incubation time achieved the optimized performance, which was confirmed by quartz crystal microbalance.
Article
Chemistry, Multidisciplinary
Aitor Patino Diaz, Sara Bracaglia, Simona Ranallo, Tania Patino, Alessandro Porchetta, Francesco Ricci
Summary: This study developed a cell-free in vitro transcription system for the detection of specific target antibodies. The system uses programmable antigen-conjugated DNA-based conformational switches that can trigger cell-free transcription upon binding to a target antibody, resulting in the production of a light-up fluorescence-activating RNA aptamer. The system combines the programmability and responsiveness of DNA-based systems with the specificity and sensitivity offered by in vitro genetic circuitries and commercially available transcription kits. The study demonstrates that cell-free transcriptional switches can efficiently measure antibody levels directly in blood serum and can be adapted to different antibodies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Dmitry Gribanyov, Gleb Zhdanov, Andrei Olenin, Georgii Lisichkin, Alexandra Gambaryan, Vladimir Kukushkin, Elena Zavyalova
Summary: The development of sensitive techniques, such as Surface-enhanced Raman spectroscopy (SERS) and DNA aptamers, shows promise for combining rapid specific detection and quantitative determination of viruses, addressing the limitations of existing SERS-based aptasensors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Fedor Grabovenko, Liudmila Nikiforova, Bogdan Yanenko, Andrey Ulitin, Eugene Loktyushov, Timofei Zatsepin, Elena Zavyalova, Maria Zvereva
Summary: Study on nucleic acid aptamers specific to S-protein and its receptor binding domain reveals their sensitivity to glycosylation patterns and biotinylation sites, highlighting the importance of careful testing for new viral variants in the development of specific therapy and biosensors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Dmitry A. Bunin, Nobuhle Ndebele, Alexander G. Martynov, John Mack, Yulia G. Gorbunova, Tebello Nyokong
Summary: The synthesis and characterization of A(3)B-type phthalocyanines, ZnPc1-4, with bulky substituents on isoindoline units A and carboxylic anchors on isoindoline unit B are reported. The simplified sTD-DFT approximation accurately reproduces the key trends in the spectral properties, providing a valuable tool for guiding the rational design of new phthalocyanines.
Article
Nanoscience & Nanotechnology
Elena Yu Poimanova, Polina A. Shaposhnik, Daniil S. Anisimov, Elena G. Zavyalova, Askold A. Trul, Maxim S. Skorotetcky, Oleg Borshchev, Dmitry Z. Vinnitskiy, Marina S. Polinskaya, Vadim B. Krylov, Nikolay E. Nifantiev, Elena Agina, Sergey A. Ponomarenko
Summary: EGOFETs show great potential in the field of bioelectronic sensing. This article proposes a simple and fast technique for functionalizing the semiconducting surface and demonstrates the specific response of a BTBT-based biorecognition layer to influenza A virus. The method can be used for different receptor molecules and enables the fabrication of various biosensors.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Analytical
Elena Zavyalova, Daria Tikhonova, Gleb Zhdanov, Elena Rudakova, Vera Alferova, Andrey Moiseenko, Polina Kamzeeva, Alexei Khrulev, Arthur Zalevsky, Alexander Arutyunyan, Roman Novikov, Vladimir Kukushkin, Andrey Aralov
Summary: Phosphorylated adenosine derivatives play important roles in the energetic balance of the cell, biosynthesis of cell components, and regulation of protein activity. Surface-enhanced Raman spectroscopy (SERS) is an optical method that can provide a unique spectrum of a substance at low concentrations. By using nucleic acid aptamers and Raman-active dyes, the specificity and limit of detection of SERS-based sensors can be significantly increased. In this study, a biosensor based on the AMP-dependent interaction between a DNA aptamer and a novel Raman-active dye was described, showing a low limit of detection and a wide dynamic range.
ANALYTICA CHIMICA ACTA
(2022)
Article
Chemistry, Multidisciplinary
Gleb Zhdanov, Ekaterina Nyhrikova, Nadezda Meshcheryakova, Olga Kristavchuk, Assel Akhmetova, Evgeny Andreev, Elena Rudakova, Alexandra Gambaryan, Igor Yaminsky, Andrey Aralov, Vladimir Kukushkin, Elena Zavyalova
Summary: Biosensors combining the ultrahigh sensitivity of surface-enhanced Raman scattering (SERS) and the specificity of nucleic acid aptamers have recently drawn attention in the detection of respiratory viruses. Here, a novel design of SERS-based aptasensor with a detection limit close to RT-PCR sensitivity is proposed. The sensor utilizes silver nanoparticles and a unique Raman-active dye to detect influenza viruses.
FRONTIERS IN CHEMISTRY
(2022)
Article
Chemistry, Applied
Dmitry A. Bunin, Alexander G. Martynov, Evgeniya A. Safonova, Aslan Yu. Tsivadze, Yulia G. Gorbunova
Summary: A new synthetic pathway has been developed for water-soluble phthalocyanines with cationic groups. These compounds exhibit strong absorption in the phototherapeutical spectral range and high quantum yields of singlet oxygen generation. Some complexes exist in monomeric forms in water.
Article
Chemistry, Analytical
Mariia Samodelova, Olesya O. Kapitanova, Nadezda F. Meshcheryakova, Sergey M. Novikov, Nikita R. Yarenkov, Oleg A. Streletskii, Dmitry Yakubovsky, Fedor Grabovenko, Gleb A. Zhdanov, Aleksey Arsenin, Valentyn S. Volkov, Elena G. Zavyalova, Irina A. Veselova, Maria Zvereva
Summary: The recent SARS-CoV-2 infection has presented a challenge for the development of fast virus identification methods based on sensor principles. Researchers have created a novel aptasensor using a sandwich mode with a structure modeling surface and size of the virus. The results show high stability and potential for detecting coronaviruses.
Article
Biotechnology & Applied Microbiology
Vladimir Kukushkin, Olga Kristavchuk, Evgeny Andreev, Nadezda Meshcheryakova, Olga Zaborova, Alexandra Gambaryan, Alexander Nechaev, Elena Zavyalova
Summary: Aptasensors based on surface-enhanced Raman spectroscopy (SERS) are highly desirable due to their superior specificity and low limit of detection. In this study, we developed a method that combines membrane filtration and SERS-active substrates for efficient adsorption of viruses. The specific determination of viruses was achieved using aptamers labeled with Raman-active probes.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Vladimir Kukushkin, Oganes Ambartsumyan, Alexei Subekin, Anna Astrakhantseva, Vladimir Gushchin, Alexandra Nikonova, Anastasia Dorofeeva, Vitaly Zverev, Anna Keshek, Nadezda Meshcheryakova, Olga Zaborova, Alexandra Gambaryan, Elena Zavyalova
Summary: In light of recurring epidemics and pandemics, rapid and reliable virus identification techniques are needed. Polymerase chain reaction with reverse transcription is a reliable and sensitive, though not rapid, tool. The antibody-based strip is a rapid, though not reliable, and sensitive tool. Alternative tools are being developed to meet all the customer's needs, such as surface-enhanced Raman spectroscopy (SERS) which allows single molecule detection in minutes. A multiplex lithographic SERS aptasensor was developed to detect several respiratory viruses in one pot within 17 min by using labeled aptamers anchored onto metal surfaces.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Azat F. Akbulatov, Anna Y. Akyeva, Pavel G. Shangin, Nikita A. Emelianov, Irina V. Krylova, Mariya O. Markova, Liliya D. Labutskaya, Alexander V. Mumyatov, Egor I. Tuzharov, Dmitry A. Bunin, Lyubov A. Frolova, Mikhail P. Egorov, Mikhail A. Syroeshkin, Pavel A. Troshin
Summary: Inverted perovskite solar cells with p-i-n configuration have gained attention in research due to their simple design, lack of hysteresis, improved stability, and low-temperature fabrication. However, they still have lower power conversion efficiency compared to classical n-i-p perovskite solar cells. This study addresses this issue by designing tin and germanium coordination complexes as interlayers for perovskite solar cells. These interlayers improve the efficiency from 16.4% to 18.0-18.6% by forming uniform coatings on the electron transport layer. This research shows the potential of tin and germanium complexes in improving the performance of perovskite solar cells.
Article
Chemistry, Applied
Alexey V. Yagodin, Ilya A. Mikheev, Dmitry A. Bunin, Anna A. Sinelshchikova, Alexander G. Martynov, Yulia G. Gorbunova, Aslan Yu Tsivadze
Summary: A novel ionogenic water-soluble zinc complex, ZnQPz(COONa)8, was synthesized by template condensation and alkaline hydrolysis. It exhibited a significant bathochromic shift and higher photostability compared to similar NIR-absorbing derivatives, making it a promising candidate for photodynamic therapy.
Article
Chemistry, Multidisciplinary
Alexei Subekin, Rugiya Alieva, Vladimir Kukushkin, Ilya Oleynikov, Elena Zavyalova
Summary: Surface-enhanced Raman scattering (SERS) is a powerful technique for the detection of analytes. In this paper, a SERS-based sensor was proposed for the rapid and sensitive detection of botulinum toxin type A using a functionalized silver nanoisland substrate. The proposed sensor architecture allows for one-stage detection without additional staining, with a limit of detection of 2.4 ng/mL.
Article
Chemistry, Analytical
Elena Y. Poimanova, Elena G. Zavyalova, Elena A. Kretova, Anton A. Abramov, Askold A. Trul, Oleg V. Borshchev, Anna K. Keshek, Sergey A. Ponomarenko, Elena V. Agina
Summary: In this paper, the possibility of fast quantitative specific determination of virus particles using EGOFET-based aptasensors in an aqueous environment was demonstrated. The sensitivity and selectivity of the devices were examined using various analytes including influenza A and B viruses, Newcastle disease viruses, and allantoic fluid. The effects of the thickness of the semiconducting layer on the sensory properties of EGOFETs were discussed, and the fabrication of a multi-flow cell and a multi-sensor flow device were reported. The responses obtained with the portable multi-flow mode were well correlated with those obtained in the laboratory stationary mode.
Article
Chemistry, Multidisciplinary
Oskar I. Koifman, Tatyana A. Ageeva, Natalia S. Kuzmina, Vasilii F. Otvagin, Alexander V. Nyuchev, Alexey Yu. Fedorov, Dmitriy V. Belykh, Nataliya Sh. Lebedeva, Elena S. Yurina, Sergey A. Syrbu, Mikhail O. Koifman, Yury A. Gubarev, Dmitry A. Bunin, Yulia G. Gorbunova, Alexander G. Martynov, Aslan Yu. Tsivadze, Semyon V. Dudkin, Alexey V. Lyubimtsev, Larissa A. Maiorova, Maria V. Kishalova, Maria V. Petrova, Vladimir B. Sheinin, Vladimir S. Tyurin, Ilya A. Zamilatskov, Eduard I. Zenkevich, Philipp K. Morshnev, Dmitry B. Berezin, Eduard A. Drondel, Andrey V. Kustov, Viktor A. Pogorilyy, Alexey N. Noev, Elizaveta A. Eshtukova-Shcheglova, Ekaterina A. Plotnikova, Anna D. Plyutinskaya, Natalia B. Morozova, Andrei A. Pankratov, Mikhail A. Grin, Olga B. Abramova, Ekaterina A. Kozlovtseva, Valentina V. Drozhzhina, Elena V. Filonenko, Andrey D. Kaprin, Anastasiya V. Ryabova, Daria V. Pominova, Igor D. Romanishkin, Vladimir I. Makarov, Victor B. Loschenov, Kseniya A. Zhdanova, Anastasia V. Ivantsova, Yulia S. Bortnevskaya, Natal'ya A. Bragina, Anna B. Solovieva, Anastasya S. Kuryanova, Petr S. Timashev
Summary: This review provides an overview of the wide application of tetrapyrrole photosensitizers in photodynamic therapy, antimicrobial photodynamic therapy, and photoinactivation of pathogens. The synthesis methods and design of new photosensitizers to enhance their selectivity in tumor tissue and their photoinduced antitumor activity are discussed. The review also examines the properties of new photosensitizers, their photoactivity, the generation of singlet oxygen, and the potential use of targeted photodynamic therapy in clinical practice.