Article
Biochemistry & Molecular Biology
Shokoufeh Hassani, Armin Salek Maghsoudi, Milad Rezaei Akmal, Shahram Shoeibi, Fatemeh Ghadipasha, Taraneh Mousavi, Mohammad Reza Ganjali, Rohollah Hosseini, Mohammad Abdollahi
Summary: In this study, an aptamer-based electrochemical biosensor was developed for evaluating low levels of zearalenone in foodstuffs and agricultural products. The biosensor exhibited a wide linear dynamic range, high specificity, and a simple, quick, precise, and cost-effective design.
CURRENT MEDICINAL CHEMISTRY
(2022)
Article
Biophysics
Qianying Cao, Ding Jiang, Meihua Dong, Xiaomei An, Fangmin Xu, Wenchang Wang, Zhidong Chen
Summary: Recently, the development of up-conversion luminescent (UCL) materials with improved optical signal has gained attention. This research focuses on using organic dye-sensitized UCL materials to enhance the electrochemiluminescence (ECL) performance for the determination of enrofloxacin (ENR) by utilizing antenna effects. The specific recognition function of an aptamer was incorporated to eliminate interference and improve the sensitivity of the sensor. In the presence of ENR, the aptamer-detachment from the electrode surface resulted in a significant enhancement of the signal, enabling a wide detection range, low limit of detection, and high recoveries during water sample analysis.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Chemistry, Multidisciplinary
Amani A. Hariri, Alyssa P. Cartwright, Constantin Dory, Yasser Gidi, Steven Yee, Ian A. P. Thompson, Kaiyu X. Fu, Kiyoul Yang, Diana Wu, Nicolo Maganzini, Trevor Feagin, Brian E. Young, Behrad Habib Afshar, Michael Eisenstein, Michel J. F. Digonnet, Jelena Vuckovic, H. Tom Soh
Summary: This study presents a design architecture that can convert existing aptamers into reversible aptamer switches, allowing for tuning of their kinetic and thermodynamic properties without prior knowledge of the ligand binding domain. By combining these switches with evanescent-field-based optical detection hardware, the study demonstrates a biosensor system that can continuously measure multiple biomarkers in complex samples with rapid time responses.
ADVANCED MATERIALS
(2023)
Article
Marine & Freshwater Biology
Ruth Cooper, Arthur David, Tetsuhiro Kudoh, Charles R. Tyler
Summary: Effluents from wastewater treatment works have varying estrogenic activity and health effects on fish, with the use of ERE-GFP transgenic zebrafish proving to be an effective model for monitoring these effects.
AQUATIC TOXICOLOGY
(2021)
Review
Chemistry, Analytical
Reza Eivazzadeh-Keihan, Zahra Saadatidizaji, Ali Maleki, Miguel de la Guardia, Mohammad Mahdavi, Sajjad Barzegar, Samad Ahadian
Summary: Thrombin is a serine protease that plays a crucial role in blood clotting and homeostasis. Detecting thrombin quickly and accurately is important for biological analysis and clinical diagnosis. Various biosensors have been developed to achieve highly selective and specific detection of thrombin. Aptasensors, which use DNA or RNA aptamers as biological recognition elements, have shown great sensitivity and affinity in identifying thrombin.
Article
Environmental Sciences
Daqing Jia, Qinzhi Li, Khalil Hanna, Gilles Mailhot, Marcello Brigante
Summary: This study investigated the degradation of three endocrine-disrupting chemicals by gamma-MnOOH activated peroxymonosulfate, showing that 40% of the degradation can be attributed to heterogeneous electron transfer reaction with freshly generated Mn(IV) and 60% to sulfate radical degradation pathway. The system showed complete degradation of EDCs after 30mM of reaction with specific conditions. The application of this system in real sewage treatment plant water showed decreased degradation rate constants of EDCs, providing new insights into the reactivity of combined gamma-MnOOH and PMS.
ENVIRONMENTAL POLLUTION
(2021)
Article
Chemistry, Multidisciplinary
Chan Ho Park, Ian A. P. Thompson, Sharon S. Newman, Linus A. Hein, Xizhen Lian, Kaiyu X. Fu, Jing Pan, Michael Eisenstein, H. Tom Soh
Summary: Cells rely on secreted signaling molecules to coordinate essential biological functions, but direct measurement of these signals is challenging. This study presents an aptamer-conjugated hydrogel matrix that enables real-time measurement of specific secreted analytes. By monitoring inter-cellular cAMP signals in amoeba cells, the researchers achieved direct measurements of oscillatory cAMP signaling. This approach can be generalized to visualize diverse extracellular signaling processes and their effects on recipient cells.
ADVANCED MATERIALS
(2023)
Review
Chemistry, Analytical
Gona K. Ali, Khalid M. Omer
Summary: This review highlights the development and advantages of diagnostic devices based on memetic molecular recognitions, particularly focusing on the hybrid recognition element of MIP-aptamer and its enhanced properties for target molecule detection in various matrices.
Article
Chemistry, Analytical
Yong-Qiang He, Ying Chen, Xian-Zhu Meng, Hong -Chao Yi, Hui-Wen Gu, Xiao-Li Yin
Summary: A visual and smartphone-integrated aptasensor for rapid Staphylococcus aureus determination was developed using Exo III-assisted recycling and hemin/G-quadruplex DNAzymes for signal amplification. The assay quantified the released DNAzymes via Exo III-assisted recycling reaction and analyzed them with a smartphone and UV-Vis spectrophotometer. This method exhibited good analytical performance, low cost, and portability, making it a rapid point-of-care test method with great potential in food safety control.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Chemistry, Analytical
Bassam Bachour Junior, Marina Ribeiro Batistuti, Aline Sanches Pereira, Elisa Maria de Sousa Russo, Marcelo Mulato
Summary: An electrochemical biosensor for NS1 detection was developed in this study by optimizing the molar ratio between aptamers and MCH, achieving high sensitivity and low detection limits for NS1 detection in the early stages of disease. By adding bovine serum albumin to stabilize NS1, the sensor accurately detected NS1 from different Dengue serotypes.
Article
Agriculture, Multidisciplinary
Xiaoze Dong, Qianqian Cheng, Shuo Qi, Mingwei Qin, Ning Ding, Yuhan Sun, Yu Xia, Yin Zhang, Zhouping Wang
Summary: We present a method using a riboswitch sensor to detect tetracycline content in foods. The sensor is based on a lyophilized cell-free expression system, allowing for long-term storage. The riboswitch, constructed with artificially screened tetracycline RNA aptamers, can be used to detect tetracyclines in various samples, with a detection limit as low as 0.47 μM. Additionally, this method enables qualitative detection of tetracyclines in milk samples by the naked eye.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Chemistry, Analytical
Kexin Sun, Junlong Li
Summary: CEA is a widely used tumor marker, especially for gastrointestinal cancers like colorectal malignancy. The current methods for CEA detection are limited by high costs and long waiting times. By altering the secondary structure of fluorescent modified DNA, a new method for CEA detection was established, providing a simple, fast, and cheap sensing platform for biomarkers detection. This method shows great potential in tumor screening among populations and may have prospective effects on tumor treatment.
Article
Chemistry, Analytical
Bin Zhou, Runlin Yang, Muhammad Sohail, Xiaoxue Kong, Xing Zhang, Ninghua Fu, Bingzhi Li
Summary: CRISPR is revolutionizing biosensing technology with its programmability, sensitivity, and specificity. While most CRISPR-based biosensors are developed using Cas12 and Cas13, the biosensing potential of the newly discovered Cas14 is not yet fully understood. This study introduces HARRY, a fluorometric biosensor that utilizes the specificity of Cas14a for versatile aptasensing. HARRY shows improved sensitivity and versatility compared to Cas12a-based aptasensors, detecting various targets at low-nanomolar levels. The study suggests that the detection limit of HARRY is correlated to the binding affinities of aptamers. These findings unlock the potential of Cas14a in CRISPR-based biosensing and inspire further development in this field.
Article
Biochemistry & Molecular Biology
Hu Xing, Yiting Zhang, Markus Kraemer, Ann-Kathrin Kissmann, Marius Henkel, Tanja Weil, Uwe Knippschild, Frank Rosenau
Summary: Changes in the abundance of intestinal bacterium Blautia producta are closely associated with various diseases. A high-affinity nucleic acid aptamer library was obtained to efficiently discriminate Blautia producta from other gut bacteria.
Article
Biochemical Research Methods
Dawei Li, Shen Ling, Xinru Cheng, Zhaoqi Yang, Bei Lv
Summary: A colorimetric biosensor assay has been developed for the detection of Cd2+ and Hg2+ based on Cd2+-dependent DNAzyme cleavage and Hg2+-binding-induced conformational switching of the G-quadruplex fragment. The assay exhibits excellent selectivity and high sensitivity, making it suitable for environmental water sample testing and further environmental monitoring.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Taku Ohtomi, Sayuri L. Higashi, Daisuke Mori, Aya Shibata, Yoshiaki Kitamura, Masato Ikeda
Summary: By adjusting the position of the side chain phenyl group, the dimensions and morphology of self-assembled nanostructures of dipeptide hydrazides can be changed, highlighting the significance of systematic investigations in exploring functional soft nanomaterials.
Article
Biochemistry & Molecular Biology
Naoki Tsutsumi, Akitaka Ito, Azumi Ishigamori, Masato Ikeda, Masayuki Izumi, Rika Ochi
Summary: In this study, a novel bola-amphiphilic glycosylated lipopeptide-type supramolecular hydrogelator is presented, exhibiting reversible thermochromism and gel-sol transition. The investigation focused on the effects of different numbers of F residues on gelation ability and morphology of self-assembled nanostructures.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Polymer Science
Nanami Shirakami, Sayuri L. Higashi, Yugo Kawaki, Yoshiaki Kitamura, Aya Shibata, Masato Ikeda
Summary: In this study, a reduction-responsive oligonucleotide was constructed by post-modifying an oligonucleotide with a diazo compound bearing a 4-nitrobenzyl group. The introduction of the 4-nitrobenzyl group and the subsequent reduction-triggered recovery of the original oligonucleotide were confirmed using HPLC and mass spectrometry. The protocol for preparing this reduction-responsive oligonucleotide is simple and it holds promise for various applications in the fields of chemical and synthetic biology.
Article
Chemistry, Multidisciplinary
Nanami Shirakami, Yugo Kawaki, Sayuri L. Higashi, Aya Shibata, Yoshiaki Kitamura, Sharina Abu Hanifah, Lim Lee Wah, Masato Ikeda
Summary: Oxidation-responsive oligonucleotides can exhibit controlled functions by sensing dysregulated oxidation conditions in living systems. The postmodification approach described here involves introducing a 4-boronobenzyl group to a phosphate group at the 5'-terminal of an ON using the reactivity of diazo compounds.
Article
Chemistry, Multidisciplinary
Yuki Shintani, Taku Ohtomi, Aya Shibata, Yoshiaki Kitamura, Koichiro M. Hirosawa, Kenichi G. N. Suzuki, Masato Ikeda
Summary: In this study, we demonstrated the construction of thermally stable supramolecular hydrogels through thermolysin-assisted biocatalysis, as well as the post-assembly modification of these structures using fluorescence imaging.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Sayuri L. Higashi, Yuki Shintani, Masato Ikeda
Summary: Artificially synthesized stimuli-responsive biomolecules are attractive molecular tools for monitoring and modulating biological systems. This Concept article reviews the molecular design of reduction-responsive biomolecules, such as peptides, nucleic acids, and saccharides, produced by introducing nitroaryl groups into them, with a special emphasis on simple 4-nitrobenzene-based motifs.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Sayuri L. Higashi, Ayaka Isogami, Junko Takahashi, Aya Shibata, Koichiro M. Hirosawa, Kenichi G. N. Suzuki, Shunsuke Sawada, Shinya Tsukiji, Kazunori Matsuura, Masato Ikeda
Summary: In this study, a new reduction-cleavable spacer (RCS) based on a nitrobenzene scaffold was designed and synthesized for constructing reduction-responsive oligonucleotides using standard phosphoramidite chemistry. Furthermore, it was demonstrated that the introduction of the RCS in the middle of an oligonucleotide (30 nt) allowed for the construction of a self-assembled microsphere capable of exhibiting a reduction-responsive disassembly.
CHEMISTRY-AN ASIAN JOURNAL
(2022)
Editorial Material
Polymer Science
Takeshi Serizawa, Masato Ikeda, Keiji Tanaka
Review
Polymer Science
Aya Shibata, Sayuri L. Higashi, Masato Ikeda
Summary: In this review, the application of nucleic acid-based fluorescent sensors in exploring intracellular phenomena is discussed. Different types of sensing systems and their characteristics are introduced, with a focus on recent examples of signal amplification systems for detecting small amounts of target analytes under isothermal conditions.
Article
Chemistry, Multidisciplinary
Shintaro Sugiura, Yuki Shintani, Daisuke Mori, Sayuri L. Higashi, Aya Shibata, Yoshiaki Kitamura, Shin-ichiro Kawano, Koichiro M. Hirosawa, Kenichi G. N. Suzuki, Masato Ikeda
Summary: The artificial construction of multicomponent supramolecular materials has attracted attention due to their orthogonally assembled architectures. In this study, we combined peptide-based self-assembled fibrous nanostructures with globular DNA nanoflowers to develop unique hybrid materials. Fluorescence imaging was used to dissect the orthogonally constructed architectures. By utilizing the distinct functions of peptides and DNA, these materials show promising opportunities for bioapplications as a soft matrix.
Article
Chemistry, Multidisciplinary
Naoki Tsutsumi, Akitaka Ito, Yosuke Niko, Yui Bando, Kiyonori Takahashi, Masato Ikeda, Kaori Yoneyama, Takayoshi Nakamura, Masayuki Izumi, Rika Ochi
Summary: In this study, we developed glycolipid-type amphiphiles with aggregation-induced emission (AIE) features and found that the design of molecular packing plays a crucial role in controlling the AIE properties.
Article
Chemistry, Analytical
Normazida Rozi, Sharina Abu Hanifah, Nurul Huda Abd Karim, Lee Yook Heng, Sayuri L. L. Higashi, Masato Ikeda
Summary: This study successfully developed an electrochemical biosensor for rapid detection of E2 in water samples. The biosensor uses split DNA aptamers and differential pulse voltammetry to detect E2 even at low concentrations, with good selectivity and repeatability.
Article
Polymer Science
Ayaka Isogami, Sayuri L. Higashi, Bioru Okumura, Aya Shibata, Koichiro M. Hirosawa, Kenichi G. N. Suzuki, Shinya Tsukiji, Kazunori Matsuura, Masato Ikeda
Summary: The article describes the construction of a hierarchical supramolecular structure composed of reduction-responsive DNA microspheres and semi-artificial glycopeptide-based micro-asters, which are obtained through the (self-)assembly of oligonucleotides and a semi-artificial glycopeptide in a single thermal annealing process under aqueous conditions in the presence of Mg2+.
Article
Chemistry, Multidisciplinary
Sayuri L. Higashi, Masato Ikeda
Summary: Stimuli-responsive supramolecular hydrogels are a newly emerging class of aqueous soft materials developed based on modular molecular design. Glucosamine-based derivatives were found to be the only molecules capable of forming hydrogels, compared to galactosamine-based molecules.
