Article
Chemistry, Analytical
Yunyun Ning, Cuiling Zhang, Chunyan Wang, Chuqing Zhou, Nana Gong, Qiang Wang, Ye Zhu
Summary: In this study, a highly sensitive and specific electrochemical strategy was proposed for accurate detection of miRNA-21. The strategy utilized DSN-assisted target recycling and DNA self-assembled FeNxC nanocatalytic network, and achieved ultrasensitive detection of miRNA-21.
ANALYTICA CHIMICA ACTA
(2022)
Article
Chemistry, Multidisciplinary
Anuj Nehra, Anil Kumar, Sweeti Ahlawat, Vinay Kumar, Krishna Pal Singh
Summary: A simple and ultrasensitive electrochemical biosensor was developed for rapid detection of miR393a. The streptavidin-coated carbon electrode served as an excellent platform for biorecognition due to its 2D structure and chemical functionality. The biosensor exhibited good linear response and high sensitivity to miR393a, making it a feasible option for detecting miRNA in plant disease samples.
Article
Chemistry, Analytical
Wei-Wei Liu, Xiao-Long Zhang, Xin Wang, Ya-Qin Chai, Ruo Yuan
Summary: Herein, we developed a novel three-dimensional self-accelerated DNA walker (SADW) that can construct an electrochemical biosensor for ultrasensitive detection of microRNA. By introducing a target analogue sequence in the walker's double-loop hairpin, the SADW can achieve a continuous self-acceleration and expedite the reaction rate, surpassing traditional 3D self-circulating DNA walkers. This approach shows promising applications in clinic diagnosis, biosensing assay, and DNA nanobiotechnology.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemistry & Molecular Biology
Ya Zhang, Ning Li, Wenhao Ma, Mei Yang, Changjun Hou, Xiaogang Luo, Danqun Huo
Summary: This study developed a novel electrochemical microRNA biosensor based on antimonene nano-flakes and carbon quantum dots for specific detection of breast cancer-related biomarker microRNA-21. The sensor exhibited a lower detection limit and stronger interaction force with the target, showing promise for early diagnosis and monitoring of breast cancer.
BIOELECTROCHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Liang Zhu, Xiaolong Zhang, Yuanyuan Chang, Sai Xu, Ruo Yuan, Yaqin Chai
Summary: A novel co-catalytic nanocomposite Fc/HGQs/Fe3O4 was synthesized to significantly amplify the electrochemical signal of ferrocene, enabling ultrasensitive detection of miRNA-155. This approach opens a new avenue for exploring efficient signal labels for signal amplification and developing biosensors for biological detection and early clinical diagnosis.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Lingqi Kong, Hao Li, Xiaolong Zhang, Ying Zhuo, Yaqin Chai, Ruo Yuan
Summary: A novel ratiometric electrochemical biosensor with methylene blue (MB) as the only signal tag was developed for highly reliable and ultrasensitive detection of microRNA-21 (miRNA-21). The strategy utilized an intelligent target-induced dual signal amplification (T-DSA) to controllably load and release MB, avoiding false positive responses. With the aid of innovative T-DSA recycle and rolling circle amplification (RCA)-produced functional DNA nanospheres, the detection sensitivity of this biosensor was significantly improved.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Lingqi Kong, Hao Li, Xiaolong Zhang, Ying Zhuo, Yaqin Chai, Ruo Yuan
Summary: In this study, a novel ratiometric electrochemical biosensor with methylene blue (MB) as the only signal tag was developed for highly reliable and ultrasensitive detection of microRNA-21 (miRNA-21). The biosensor utilized an intelligent target-induced dual signal amplification (T-DSA) strategy to control the loading and release of MB, thereby avoiding false positive responses. The detection sensitivity was significantly improved through the use of innovative T-DSA recycle and rolling circle amplification (RCA) to generate functional DNA nanospheres (DSP). The biosensor successfully achieved highly reliable and ultrasensitive detection of miRNA-21 with a detection limit of 26.7 aM.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Yong-ping Gao, Ke-jing Huang, Fu-ting Wang, Yang-yang Hou, Lu-di Zhao, Bo-ya Wang, Jing Xu, Honglei Shuai, Guoqiang Li
Summary: A self-powered biosensor (SPB) utilizing a capacitor/enzymatic biofuel cell (EBFC), rolling circle amplification (RCA), and a digital multimeter (DMM) was developed for ultra-sensitive detection of miR-155. The EBFC-SPB exhibited a sensitivity of 15.85 mu A/pM with the matching capacitor, which is 513% higher than without capacitor (3.09 mu A/pM), achieving the first signal amplification. RCA triggered by miR-155 generated continuous electrons that flowed to the biocathode, catalyzing oxygen reduction and achieving the second signal amplification. DMM was used for signal conversion and real-time amplification, resulting in a LOD of 0.17 fM and a linear range of 0.5 fM to 10,000 fM, indicating the broad application prospects of EBFC-SPB for ultra-sensitive detection of miR-155.
ANALYTICA CHIMICA ACTA
(2023)
Article
Chemistry, Multidisciplinary
Zhenming Zhang, Xin Ma, Jinwen Zhu, Ruhong Yan, Peng Miao
Summary: The study introduces a roll-to-roll DNA nanomachine for highly sensitive electrochemical detection of miRNA, offering a wide detection range with a limit of detection as low as 10 aM. The practicality is demonstrated by satisfactory results in human serum samples.
Article
Immunology
Javad Mohammadnejad, Niki Basirhaghighi, Fatemeh Yazdian, Mehrab Pourmadadi, Javad Shabani Shayeh, Meisam Omidi, Mojdeh Mirshafiei, Abbas Rahdar, Ana M. Diez-Pascual
Summary: In this study, a novel electrochemical nanobiosensor based on reduced graphene oxide (RGO) and gold nanoparticles (AuNPs) was developed to detect miRNA-128, which is a useful biomarker for both diagnosis of ALL and discrimination of ALL from AML. The nanobiosensor exhibited excellent selectivity and sensitivity to miR-128, with a limit of detection of 0.08761 fM in label-free assay and 0.00956 fM in labeling assay. Furthermore, the nanobiosensor showed potential to detect and discriminate ALL and AML samples from control cases.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Article
Chemistry, Analytical
Xiankang Niu, Changtong Lu, Dan Su, Fang Wang, Weihong Tan, Fengli Qu
Summary: In this study, a photoelectrochemical biosensing platform was developed for ultrasensitive miRNA-141 detection using CdS quantum dots and Tph-2H coated GCE. By combining an enzyme-assisted recycle amplification reaction and a magnetic bead-based separation strategy, the detection sensitivity of miRNA-141 could be significantly enhanced. The proposed biosensor demonstrated efficient elimination of false-positive or false-negative signals and a wide linear response range with a low detection limit for miRNA-141.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Xuejun Dong, Ziyun Tang, Hua Zhang, Yong Hu, Zhiyi Yao, Ruiyun Huang, Jie Bai, Yang Yang, Wenjing Hong
Summary: In this study, a highly sensitive acetylcholinesterase sensor based on 3,3',5,5'-tetramethylbenzidine(TMB) and scanning tunneling microscopy break junction (STM-BJ) was developed for the detection of organophosphorus pesticides (OPs) in environmental samples. By utilizing the enzyme inhibition kinetics of OPs and a customized spectral clustering analysis method, the sensor achieved the detection of methamidophos (MTMP) with a limit of 10 aM (10(-17) mol/L) and improved selectivity for mixed OPs. The sensor also demonstrated high reproducibility, stability, and recovery when applied to natural lake waters. This work opens up a new avenue for the application of single-molecule conductance characterizations in biochemical analysis and environmental monitoring.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Xiao-Long Zhang, Sha-Sha Li, Yi-Jia Liu, Wei-Wei Liu, Ling-Qi Kong, Ya-Qin Chai, Xi-Liang Luo, Ruo Yuan
Summary: An ingenious three-dimensional DNA walker with high walking efficiency is developed by limiting the reaction space, providing a rapid and sensitive detection method for miRNA. Compared to traditional DNA walkers, this immobilized DNA walker shows improved kinetic and thermodynamic favorability, resulting in faster reaction speed and higher walking efficiency. By utilizing this walker, a sensitive sensing platform for rapid miRNA-21 detection is constructed with a limit of detection of 19.8 aM, allowing for highly sensitive biomarker detection in cancer cell lysates.
ANALYTICAL CHEMISTRY
(2023)
Article
Biophysics
Ruiying Yang, Guihua Jiang, Huimin Liu, Leiliang He, Fei Yu, Li'e Liu, Lingbo Qu, Yongjun Wu
Summary: The dual-model biosensor utilizing a 3D DNA walker strategy achieved highly sensitive detection of miRNA-224, avoiding interference and significantly increasing sensitivity through distance-controllable signal enhancing and quenching strategies.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Nanoscience & Nanotechnology
Fujia Zhao, Shan Zhou, Yingjie Zhang
Summary: A novel electrochemical sensor based on the topological insulator Bi2Te3 was reported, showing superior performance in hydrogen peroxide sensing with high sensitivity and low detection limit, surpassing traditional noble metal-based electrochemical sensors.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Chemistry, Multidisciplinary
Vladimir Mironov, Irina A. Shchugoreva, Polina Artyushenko, Dmitry Morozov, Nicola Borbone, Giorgia Oliviero, Tatiana N. Zamay, Roman Moryachkov, Olga S. Kolovskaya, Kirill A. Lukyanenko, Yanling Song, Iuliia A. Merkuleva, Vladimir N. Zabluda, Georgy Peters, Lyudmila S. Koroleva, Dmitry V. Veprintsev, Yury E. Glazyrin, Ekaterina A. Volosnikova, Svetlana Belenkaya, Tatiana Esina, Anastasiya A. Isaeva, Valentina S. Nesmeyanova, Daniil Shanshin, Anna N. Berlina, Nadezhda S. Komova, Valery A. Svetlichnyi, Vladimir N. Silnikov, Dmitriy N. Shcherbakov, Galina S. Zamay, Sergey S. Zamay, Tatyana Smolyarova, Elena P. Tikhonova, Kelvin H-C Chen, U-Ser Jeng, Gerolama Condorelli, Vittorio Franciscis, Gerrit Groenhof, Chaoyong Yang, Alexander A. Moskovsky, Dmitri G. Fedorov, Felix N. Tomilin, Weihong Tan, Yuri Alexeev, Maxim Berezovski, Anna S. Kichkailo
Summary: This study developed a new approach for designing high-affinity aptamers, which can accelerate the development process. It can also be used to improve existing aptamers and provide a blueprint for designing targeting molecules against new pathogens.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Zoran Minic, Nico Huettmann, Suttinee Poolsup, Yingxi Li, Vanessa Susevski, Emil Zaripov, Maxim V. Berezovski
Summary: In this study, the phosphoproteomic analysis of breast cancer-derived small extracellular vesicles (sEVs) provided insights into the molecular and cellular regulatory mechanisms important for breast cancer tumor progression and metastasis. Functional metabolic enzymes were found in sEVs, which could potentially be used for early breast cancer diagnosis and therapy.
Article
Biology
Abdolamir Allameh, Nico Huettmann, Edouard Charlebois, Angeliki Katsarou, Wen Gu, Konstantinos Gkouvatsos, Elisa Pasini, Mamatha Bhat, Zoran Minic, Maxim Berezovski, Maria Guido, Carine Fillebeen, Kostas Pantopoulos
Summary: HJV has a hepatoprotective function and its deficiency in mice leads to mitochondrial dysfunction and hepatocarcinogenesis.
COMMUNICATIONS BIOLOGY
(2022)
Article
Nanoscience & Nanotechnology
Mutalifu Abulikemu, Bita E. A. Tabrizi, Shahrokh M. Ghobadloo, Hamed M. Mofarah, Ghassan E. Jabbour
Summary: The ongoing COVID-19 outbreak highlights the crucial need for effective disinfectants to reduce the spread of the virus. Research has shown that assembling antiviral metal nanoparticles on face masks can significantly improve efficacy against the SARS-CoV-2 virus, potentially reaching a 99.99% virus inactivation rate. This approach can be easily scaled up for mass production to help combat the rapid spread of the virus.
ACS APPLIED NANO MATERIALS
(2022)
Article
Biochemistry & Molecular Biology
Katia Pane, Cristina Quintavalle, Silvia Nuzzo, Francesco Ingenito, Giuseppina Roscigno, Alessandra Affinito, Iolanda Scognamiglio, Birlipta Pattanayak, Enrico Gallo, Antonella Accardo, Guglielmo Thomas, Zoran Minic, Maxim Berezovski, Monica Franzese, Gerolama Condorelli
Summary: Extracellular vesicles (EVs) play a crucial role in cell-to-cell communication by shuttling proteins, RNA, DNA, and lipids. Recent studies have shown that EVs may also contribute to breast cancer growth and metastasis. This pilot study evaluated the physicochemical composition and proteomic profiles of EVs from benign and malignant breast cells, providing potential implications for precision medicine in breast cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Ana Medic, Nico Huttmann, Marija Ljesevic, Yousef Risha, Maxim V. Berezovski, Zoran Minic, Ivanka Karadzic
Summary: This study examined the carbon metabolic pathways and aromatic degradation potential of the polyextremophilic Pseudomonas aeruginosa san ai under different carbon sources. It was found that P. aeruginosa san ai efficiently degrades sodium benzoate and undergoes metabolic reconfiguration when grown on benzoate compared to glucose. Additionally, this strain exhibits extremophilic characteristics and can survive in harsh conditions.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Zachary Provost, Ella Olivia Hansen, Morgan Viola Lynds, Barry S. Flinn, Zoran Minic, Maxim Berezovski, Illimar Altosaar
Summary: Starch is the primary reserve carbohydrate storage in plants, with rice being a monocot where starch is organized into compounded structures within the amyloplast. Different methods of starch granule preparation were utilized to characterize the proteome associated with these compounded structures, revealing known and novel proteins as well as septum-like structure proteins in the mature rice starch granules. The proteomic analysis showed differential impacts on observed cytoplasmic and plastid proteins, emphasizing the importance of methodology in extracting proteomic information from compound starch granules.
Article
Biochemistry & Molecular Biology
Yulia I. Maltzeva, Daria A. Gorbenko, Ekaterina V. Nikitina, Maria S. Rubel, Dmitry M. Kolpashchikov
Summary: Rapid, inexpensive, and accurate determination of nucleic acids is crucial in evaluating population's health and monitoring treatment at point-of-care settings. Visual testing systems with instrument-free signal detection are preferred. Isothermal amplification technologies, such as SPA, can replace PCR testing for point-of-care diagnostics. The combination of DNA nanomachines with peroxidase-like activity (PxDM) and SPA amplification shows promise as a valid platform with no false positive signals.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Muhannad Ateiah, Erik R. Gandalipov, Aleksandr A. Rubel, Maria S. Rubel, Dmitry M. Kolpashchikov
Summary: A simple and straightforward assay based on DNA nanomachines (DNMs) is described for the detection of unamplified bacterial 16S rRNA. The DNM binds to 16S rRNA and forms a catalytic core that cleaves a fluorescent reporter, producing an amplified signal over time. This biplex assay enables the detection of specific 16S rRNA sequences with high selectivity and has potential applications in environmental monitoring and nucleic acid analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Zongjie Wang, Hansen Wang, Sichun Lin, Mahmoud Labib, Sharif Ahmed, Jagotamoy Das, Stephane Angers, Edward H. Sargent, Shana O. Kelley
Summary: Nanoneedles are effective in delivering biomolecules to cells, but the mechanisms underlying cell-nanoneedle interactions are not well understood. In this study, we developed a new method to generate nanoneedles, confirmed their cargo delivery capability, and investigated the genetic factors involved in the process. Our results showed that the nanoneedles disrupted cell membranes, increased the expression of cell-cell junction proteins, and downregulated transcriptional factors of the NF kappa B pathway. This disturbance caused most cells to be trapped in the G2 phase, where endocytosis activities are highest. This system provides a new model for studying cell interactions with high-aspect-ratio materials.
Article
Chemistry, Multidisciplinary
Dingran Chang, Zongjie Wang, Connor D. Flynn, Alam Mahmud, Mahmoud Labib, Hansen Wang, Armin Geraili, Xiangling Li, Jiaqi Zhang, Edward H. Sargent, Shana O. Kelley
Summary: Pro-SELEX is an approach for the rapid discovery of aptamers with precisely defined binding affinities. It combines efficient particle display, high-performance microfluidic sorting, and high-content bioinformatics. Using Pro-SELEX, aptamers with a 20-fold range of affinities can be identified within one round of selection, as demonstrated with human myeloperoxidase as the target.
Article
Medicine, Research & Experimental
Suttinee Poolsup, Emil Zaripov, Nico Huttmann, Zoran Minic, Polina V. Artyushenko, Irina A. Shchugoreva, Felix N. Tomilin, Anna S. Kichkailo, Maxim V. Berezovski
Summary: This study aimed to develop a label-free optical aptasensor using a novel single-stranded DNA aptamer to detect the SARS-CoV-2 nucleocapsid (N) protein. The tNSP3 aptamer was identified to bind the N protein of different variants with high affinity. Utilizing tNSP3, the N protein could be detected in human saliva with a limit of detection of 4.5 nM. Mass spectrometry analysis and molecular dynamics simulation provided insights into the binding mechanism of tNSP3 with the N protein. Overall, this aptamer demonstrated potential as an analytical tool for COVID-19 diagnosis.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Engineering, Biomedical
Zongjie Wang, Sharif Ahmed, Mahmoud Labib, Hansen Wang, Licun Wu, Fatemeh Bavaghar-Zaeimi, Nastaran Shokri, Soraly Blanco, Saraf Karim, Kasia Czarnecka-Kujawa, Edward H. Sargent, A. J. Robert McGray, Marc de Perrot, Shana O. Kelley
Summary: Potent circulating tumour-reactive lymphocytes (cTRLs) can be isolated from peripheral blood at high yield and purity via microfluidic immunomagnetic cell sorting, allowing for comprehensive downstream analyses of these rare cells. This method provides a solution to the clinical challenge of obtaining large and fresh tumour fractions for the use of tumour-infiltrating lymphocytes in solid tumour treatment.
NATURE BIOMEDICAL ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Daria D. Nedorezova, Mikhail V. Dubovichenko, Arseniy J. Kalnin, Moustapha A. Y. Nour, Ahmed A. Eldeeb, Anna I. Ashmarova, Gabdulla F. Kurbanov, Dmitry M. Kolpashchikov
Summary: This study optimized DNAzymes for the cleavage of RNA targets with different folding energies. It was found that one optimized DNAzyme had high-affinity RNA-binding arms without suffering from product inhibition or low selectivity, which could be explained by the formation of stable secondary structures in the cleavage products. This suggests that DNAzymes with long RNA-binding arms should be considered in the optimization workflow and the folding of cleavage products should be analyzed.
Article
Chemistry, Multidisciplinary
Brittany L. Mueller, Mark J. Liberman, Dmitry M. Kolpashchikov
Summary: Hybridization probes have been widely used in nucleic acid detection for the past 50 years. However, commonly used probes face challenges such as low selectivity for single nucleotide variations at low temperatures, low affinity for binding folded nucleic acids, and high cost of fluorescent probes. To address these issues, a multicomponent hybridization probe called OWL2 sensor is introduced, which uses analyte binding arms and sequence-specific strands to tightly bind and unwind folded analytes, and a universal molecular beacon (UMB) probe to form a fluorescent 'OWL' structure. The OWL2 sensor is able to differentiate single base mismatches in folded analytes within a temperature range of 5-38 degrees C, and is cost-efficient due to the use of the same UMB probe for detecting any analyte sequence.
