Article
Biochemical Research Methods
Julian Gebhard, Lara Hirsch, Christian Schwechheimer, Hans-Achim Wagenknecht
Summary: Fluorescent DNA probes were prepared using a modular approach and a click post-synthetic modification strategy. The probes showed high fluorescence light-up effect and brightness. Additionally, electron transfer and energy transfer processes were utilized to further enhance the fluorescence readout.
BIOCONJUGATE CHEMISTRY
(2022)
Article
Chemistry, Analytical
Dinghui Xiong, Jie Cheng, Fengxiang Ai, Xinyu Wang, Jiaxuan Xiao, Fang Zhu, Kun Zeng, Kun Wang, Zhen Zhang
Summary: Adsorption of DNA probes onto nanomaterials has great potential for bioassay establishment. However, there is a lack of systematic understanding of the sensing behaviors based on nanomaterial-DNA interactions, limiting design and applications. In this study, metal-organic frameworks (MOFs) were used to investigate the issue. The results revealed the quenching of fluorescently labeled DNA adsorbed onto MOFs and provided insights into the interaction mechanisms.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Xiang Xiong, Wenya Dang, Ruxin Luo, Ying Long, Chunyi Tong, Liqin Yuan, Bin Liu
Summary: This study developed a versatile nanoprobe based on rGO and DNA probe for simultaneous visualization of miR451a and miR-214-3p in living cells, showing excellent selectivity and sensitivity. In vitro experiments demonstrated good linearity of detection signals for miR-451a and miR-214-3p, and successful dual-color imaging in human breast cancer cells was achieved using the nanoprobe.
Article
Food Science & Technology
Caroline Puente-Lelievre, Anne C. Eischeid
Summary: The study developed a novel real-time PCR assay targeting two chloroplast regions using LNA probes to specifically detect walnut in foods. By spiking food matrices with walnut at different concentrations and achieving high reaction efficiencies, the assay proved to be an effective tool for allergenic walnut detection.
Review
Chemistry, Multidisciplinary
Agnieszka Tomaszewska-Antczak, Piotr Guga
Summary: This review summarizes the synthetic efforts on acyclic analogs of nucleic acids and evaluates their synthetic methods, thermal stability, and applications in biological and biochemical research as well as nanotechnology.
APPLIED SCIENCES-BASEL
(2021)
Article
Multidisciplinary Sciences
Renan B. Ferreira, Ling Fu, Youngeun Jung, Jing Yang, Kate S. Carroll
Summary: The authors have developed a fluorogenic probe for detecting cysteine sulfenic acid, a redox modification closely related to H2O2 signaling and oxidative stress. They also found that kinase inhibitors can modulate the cysteine sulfenome, which has important implications for the field of redox medicine.
NATURE COMMUNICATIONS
(2022)
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)
Review
Immunology
Zongwei Liu, Ting Meng, Xiaofang Tang, Ran Tian, Weijiang Guan
Summary: The long-term pandemic of COVID-19 calls for accurate diagnostic assays. Aggregation-induced emission (AIE) luminogens show potential in enhancing detection sensitivity in both nucleic acid and immunological assays.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Chemistry, Analytical
Jia-Jen Tsai, Yan-Cen Zhan, Yi-Ying Wu, Yu-Chie Chen
Summary: The authors developed a convenient fluorescence sensing method for the detection of phosphates. The method utilizes the binding of the probe Gd3+ and riboflavin-5'-phosphate (RFMP) to switch on the fluorescence signal. In the presence of phosphates, the competitive binding with Gd3+ releases RFMP, restoring the fluorescence signal. The method can be used for the determination of phosphates in real samples such as drinking water and fetal bovine serum.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Chemistry, Analytical
Agustin Robles-Remacho, M. Angelica Luque-Gonzalez, Roberto A. Gonzalez-Casin, M. Victoria Cano-Cortes, F. Javier Lopez-Delgado, Juan J. Guardia-Monteagudo, Mario Antonio Fara, Rosario M. Sanchez-Martin, Juan Jose Diaz-Mochon
Summary: Nucleic acid-based molecular diagnosis is crucial for genetic disease detection and infectious disease control, and a system combining nanotechnology and dynamic chemical labeling technology can achieve single-base resolution reading of nucleic acids, offering a potentially easy-to-implement detection method.
Article
Biochemical Research Methods
Rebecca P. Chen, Wilfred Chen
Summary: The programmability of nucleic acids allows the design of detection devices with complex behaviors. However, these high-order circuits are often sequence constrained, limiting their adaptability towards biological targets. In this study, a new strategy called indirect associative strand displacement is proposed to overcome the sequence constraints between miRNA inputs and de novo strand displacement circuits.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Chemistry, Analytical
Gangpei Cai, Yuxin Huang, Bailiang Chen, Yuemin Shen, Xiaolu Shi, Bo Peng, Shengli Mi, Jiajun Huang
Summary: Modular integration of functional components on the chip and real-time alteration in the force direction of droplets optimizes centrifugal microfluidic systems and allows for passive components, compact modules, and high-throughput control. A novel centrifugal microfluidic system is introduced to improve chip control freedom and accuracy while facilitating the design and addition of passive functional components. The system is modularized to shorten design and optimization cycles and achieve chip reusability and multi-threaded control. Testing the nucleic acid purification and detection reactions on the modular chip verifies its feasibility for high-throughput nucleic acid screening.
Article
Oncology
Luiza I. Hernandez, Marcos J. Arauzo-Bravo, Daniela Gerovska, Ricardo Rezola Solaun, Isabel Machado, Alien Balian, Juliana Botero, Tania Jimenez, Olaia Zuriarrain Bergara, Lide Larburu Gurruchaga, Ander Urruticoechea, Frank J. Hernandez
Summary: A study has identified nuclease activity as a potential new biomarker for breast cancer diagnosis, with a panel of three nucleic acid probes showing high accuracy, sensitivity, and specificity in biopsy samples. This breakthrough suggests a promising future for utilizing nuclease activity as a biomarker in clinical settings for diagnosing breast malignancy.
Review
Chemistry, Analytical
Siyu Chen, Bo Gong, Cong Zhu, Chunyang Lei, Zhou Nie
Summary: Nucleic acid molecules possess attractive properties for biosensing and bioimaging due to their high designability and structural predictability. CRISPR-Cas systems, with high programmability and flexibility, recognize and cleave nucleic acid targets and have been engineered as multifunctional tools. Integration of nucleic acids with CRISPR-Cas systems has advanced biosensing and bioimaging methodologies, holding great promise in biochemical research and clinical diagnosis.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Cell Biology
Ying Li, Xiangjun Wang, Minghui Wang, Moyi Liu, Helin Wang, Wei Xia, Limei Liu
Summary: Gene mutation detection is a research hotspot, and ligase-related nucleic acid amplification technology has become widely used. This review analyzes and compares several techniques, including the ligase detection reaction, ligase chain reaction, rolling circle amplification reaction, enzyme-assisted polymerase chain reaction, and loop-mediated isothermal amplification reaction, and summarizes their advantages, disadvantages, sensitivity, specificity, cost, detection time, and applications.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Juexiao Sherry Wang, David Yu Zhang
Article
Multidisciplinary Sciences
Chunyan Wang, Jin H. Bae, David Yu Zhang
NATURE COMMUNICATIONS
(2016)
Article
Engineering, Biomedical
Lucia R. Wu, Sherry X. Chen, Yalei Wu, Abhijit A. Patel, David Yu Zhang
NATURE BIOMEDICAL ENGINEERING
(2017)
Article
Multidisciplinary Sciences
Alessandro Pinto, Sherry X. Chen, David Yu Zhang
NATURE COMMUNICATIONS
(2018)
Article
Biochemistry & Molecular Biology
Yan Helen Yan, David Yu Zhang, Lucia R. Wu
NUCLEIC ACIDS RESEARCH
(2020)
Article
Chemistry, Multidisciplinary
Lucia R. Wu, John Z. Fang, Dmitriy Khodakov, David Yu Zhang
Article
Biochemistry & Molecular Biology
Jin H. Bae, John Z. Fang, David Yu Zhang
NUCLEIC ACIDS RESEARCH
(2020)
Article
Engineering, Biomedical
Ping Song, Sherry X. Chen, Yan Helen Yan, Alessandro Pinto, Lauren Y. Cheng, Peng Dai, Abhijit A. Patel, David Yu Zhang
Summary: Low-frequency DNA variants can be detected via low-depth multiplexed sequencing after their amplification using polymerase chain reaction and rationally designed 'blocker' oligonucleotides. This method has been shown to be effective in analyzing human cell lines and tumor samples.
NATURE BIOMEDICAL ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
Jin H. Bae, David Yu Zhang
Summary: A model predicting the thermodynamics of sliding bulges within microsatellites was constructed in this paper, helping to explain the critical role of these bulges in cancer genomics and neurological disease studies. The model accurately predicts the stability penalty of sliding bulges with a median prediction error of 0.22 kcal/mol, providing insights into the mutation patterns observed in microsatellites.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Engineering, Biomedical
Dmitriy Khodakov, Jiaming Li, Jinny X. Zhang, David Yu Zhang
Summary: The study demonstrates that portable and battery-powered PCR assay conducted in a toroidal convection chamber enables rapid and sensitive quantification of multiple DNA targets with single-nucleotide discrimination, which can be used for detecting human genomic DNA samples and clinical isolates.
NATURE BIOMEDICAL ENGINEERING
(2021)
Article
Chemistry, Analytical
Kerou Zhang, Luis Rodriguez, Lauren Yuxuan Cheng, Michael Wang, David Yu Zhang
Summary: The study introduces a method, As-BDA, combining BDA with allele-specific TaqMan probes, which can effectively enrich and identify multiple rare variants with a detection limit of 0.01% VAF. The method demonstrates high clinical sensitivity and specificity, making it helpful for clinical diagnosis.
ANALYTICAL CHEMISTRY
(2022)
Review
Engineering, Biomedical
Ping Song, Lucia Ruojia Wu, Yan Helen Yan, Jinny X. Zhang, Tianqing Chu, Lawrence N. Kwong, Abhijit A. Patel, David Yu Zhang
Summary: This Review discusses the challenges and opportunities of technologies for the analysis of cell-free DNA for cancer diagnosis. It highlights the potential of cfDNA as biomarkers for guiding therapy, monitoring drug resistance, and early detection of cancers. However, the low concentrations and fragmented nature of cfDNA present challenges for clinical diagnostic applications. The Review describes state-of-the-art technologies and highlights the need to address biological and technical challenges to improve cancer diagnostics and patient care.
NATURE BIOMEDICAL ENGINEERING
(2022)
Article
Chemistry, Analytical
Kerou Zhang, Alessandro Pinto, Lauren Yuxuan Cheng, Ping Song, Peng Dai, Michael Wang, Luis Rodriguez, Cailin Weller, David Yu Zhang
Summary: In this study, we developed an occlusion system that functions as an efficient fluorescence indicator in HiFi qPCR reactions, improving the detection sensitivity for early cancer diagnosis and drug-resistance mutation identification.
ANALYTICAL CHEMISTRY
(2022)
Article
Biology
Andrew T. Sullivan, Vibha Rao, Tyler Rockwood, Jahnavi Gandhi, Sarah Gruzka, Logan O'Connor, Bonnie Wang, Katherine B. Ragan, David Yu Zhang, Dmitriy Khodakov
Summary: Detection of multiple RNA targets can be achieved rapidly and accurately using convective array PCR technology with tunable strand displacement probes, allowing for simultaneous amplification and detection of diverse RNA species with programmable sequence selectivity.
COMMUNICATIONS BIOLOGY
(2023)