Article
Multidisciplinary Sciences
Jungmin Yoo, Donghun Lee, Hyeryeon Im, Sangmi Ji, Sanghoon Oh, Minsang Shin, Daeho Park, Gwangrog Lee
Summary: The study reveals that during base excision repair, Exonuclease III creates a gap and transient ssDNA loop through an AP site anchor-based mechanism. The size of the gap is determined by the rigidity of the ssDNA loop and the duplex stability of the DNA.
Article
Biochemistry & Molecular Biology
Stefan H. Mueller, Lucy J. Fitschen, Afnan Shirbini, Samir M. Hamdan, Lisanne M. Spenkelink, Antoine M. van Oijen
Summary: Traditional enzyme characterization methods only provide population averages, while single-molecule methods can reveal kinetics and population heterogeneity but are often complex and time-consuming. We present a high-throughput single-molecule assay for rapidly characterizing DNA metabolism-related proteins by measuring changes in fluorescence intensity. Our method, combined with automated data analysis, can provide enzymatic activity data for thousands of molecules in less than an hour. We demonstrated three different enzyme activities and discovered a previously unknown activity of the UvrD helicase.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Chunmin Pu, Xiaoyan Liao, Xianming Shi, Yan Cui, Yalong Bai, Lili Chen
Summary: A novel method based on amino-modified silica-coated magnetic particles (ASMPs) was successfully developed for the extraction of short single-stranded DNA (ssDNA) from agarose gel. The method demonstrated remarkable efficiency and outperformed three commercially available DNA gel extraction products in aptamer screening.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biotechnology & Applied Microbiology
Imen Tanniche, Amanda K. Fisher, Frank Gillam, Eva Collakova, Chenming Zhang, David R. Bevan, Ryan S. Senger
Summary: Lambda-PCR is an effective method for DNA assembly and cloning, which utilizes overlap extension and different variants to achieve stable, efficient, and cost-effective assembly of DNA sequences.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Chemistry, Analytical
Zhou-Jie Liu, Liang-Yong Yang, Tai-Cheng Lu, Yu-Qi Liang, Meng-Meng Liu, Guang-Xian Zhong, Xin-Hua Lin, Pin-Fang Huang, Jin-Yuan Chen
Summary: This study presents a lambda exonuclease-assisted ligase chain reaction-based electrochemical biosensor, named lambda-eLCR, for highly sensitive and accurate genotyping of the CYP2C19*2 allele. The biosensor features a methylene blue-attached DNA probe and an inverted hybridization format, enabling zero-background analysis. The lambda-eLCR exhibited excellent performance in terms of a good linear range and low limit of detection, and successfully distinguished the CYP2C19*2 allele genotypes in human whole blood samples.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Chemistry, Multidisciplinary
Zhaohui Qin, Yu Liu, Linghao Zhang, Jiajia Liu, Xin Su
Summary: This study demonstrates a DNA-based artificial dissipative system with a molecular timer, which allows for dynamic enzyme catalysis and DNA nanostructure disassembly. This provides a useful tool for the development of artificial reaction networks and intelligent nanostructures.
Article
Chemistry, Multidisciplinary
Yajun Zhang, Licong Jia, Wei Wang, Meng Jiang, Hongying Zhang, LingMei Niu
Summary: A fluorescent aptamer sensor was constructed to detect trace amounts of 178-estradiol in various foods. The sensor showed good selectivity and specificity, and was successfully applied to the determination of milk samples. The results indicated that the concentration of E2 in water and milk was below safe limits, ensuring the safety of the foods in the market. However, continuous intake of trace amounts of E2 still poses a health risk.
ARABIAN JOURNAL OF CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Victoria E. Paluzzi, Cuizheng Zhang, Chengde Mao
Summary: Small ssDNA circles are difficult to prepare, as they often form concatemers instead of monomeric circles. This study presents a simple method to overcome this problem by designing complementary linker molecules. The method allows for the enzymatic ligation of ssDNA as short as 16 nts into monomeric circles at high concentration and high yield.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Analytical
Jianbo Sun, Changjiang Li, Yuqiang Hu, Yawen Ding, Tongbo Wu
Summary: A rapid, sensitive, and selective biosensor for UDG activity detection has been developed in this study based on the substrate preference of Lambda exonuclease. The proposed strategy exhibited high selectivity and sensitivity, and has been successfully applied to detect UDG in real biological samples and screen UDG inhibitors.
Article
Biochemical Research Methods
Fuming Sang, Suyao Yin, Jianxin Pan, Zhizhou Zhang
Summary: The novel aptasensor combines the plasmonic properties of gold nanoparticles (AuNPs) with exonuclease III (Exo III)-assisted target recycling for ultrasensitive detection of Hg2+, with a linear range from 5 pM to 0.6 nM and a detection limit of 0.2 pM. The sensor allows visual detection of Hg2+ as low as 50 pM by the naked eye and reliable determination of spiked Hg2+ in sea water samples.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Yoshiya Kikukawa, Ryoji Kawazoe, Ryo Miyahara, Takato Sakurada, Yusuke Nagata, Shigeki Sasaki, Yosuke Taniguchi
Summary: In this study, a method for detecting the presence of 8-oxo-2'-deoxyguanosine in DNA was developed, and the signal was successfully amplified. This has important implications for elucidating the pathogenesis of various diseases.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Matthew Eroglu, Bin Yu, W. Brent Derry
Summary: Highly efficient insertion of deletions, substitutions, and small insertions (up to 150 bp) into the Caenorhabditis elegans genome using CRISPR/Cas9 has been made easier with the use of single-stranded oligonucleotide donors. However, inserting larger sequences such as fluorescent markers and functional domains remains challenging due to uncertainty and labor-intensive protocols. In this study, a simplified method for generating long single-stranded DNA (ssDNA) donors in CRISPR/Cas9 is presented, which shows significantly increased insertion frequency compared to double-stranded DNA (dsDNA) donors. This approach complements the existing CRISPR/Cas9 toolkit for C. elegans and enables efficient insertion of longer sequences with a simple and standardized protocol.
Article
Biochemistry & Molecular Biology
Brian J. Caldwell, Andrew Norris, Ekaterina Zakharova, Christopher E. Smith, Carter T. Wheat, Deepanshu Choudhary, Marcos Sotomayor, Vicki H. Wysocki, Charles E. Bell
Summary: This study describes the research methods and results of oligomer formation of Red beta protein in different DNA binding states, as well as the measurement of its concentration in cells. Various techniques were used to characterize the oligomers formed by Red beta, revealing the dynamic nature on ssDNA and the stable complex on annealed duplex. The study provides new insights into the functional forms of Red beta in vivo.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Jun-Tao Guo, Fareeha Malik
Summary: Single-stranded DNA binding proteins (SSBs) play critical roles in maintaining genome stability and transcriptional regulation, and machine learning-based approaches have been developed for predicting SSBs from double-stranded DNA binding proteins (DSBs).
Article
Biochemistry & Molecular Biology
Shuming Zhang, Xue Xiao, Jingwei Kong, Ke Lu, Shuo-Xing Dou, Peng-Ye Wang, Lu Ma, Yuru Liu, Guohong Li, Wei Li, Huidong Zhang
Summary: Strand displacement DNA synthesis (SDDS) is a crucial step in DNA replication with complex kinetics. Experiments with magnetic tweezers show that the rate and processivity of SDDS are influenced by force and dNTP concentration. Moreover, GC content has a significant impact on the processivity and rate of SDDS and exonuclease activity.
Review
Chemistry, Analytical
Palaniyandi Velusamy, Chia-Hung Su, Palaniappan Ramasamy, Viswanathan Arun, Narayanan Rajnish, Pachaiappan Raman, Vaseeharan Baskaralingam, Sakkarapalayam Murugesan Senthil Kumar, Subash C. B. Gopinath
Summary: Biomarkers are biological molecules associated with physiological changes of the body, aiding in the detection and prediction of disease onset. Breath analysis, as a noninvasive, rapid, and inexpensive method, has become a research focus in early detection of health issues.
CRITICAL REVIEWS IN ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Xuekai Zhao, Subash C. B. Gopinath, Weichao Zhao
Summary: An immunosensor based on a multiwalled carbon nanotube-modified surface was developed in this study to quantify the CRP level in blood. By constructing specific anti-CRP on the multiwalled carbon nanotube surface, the sensor exhibited a dose-dependent linear pattern in the range of 200 to 3000 pM and was able to identify CRP in biological samples.
BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Hu Hui, Subash C. B. Gopinath, Zool H. Ismail, Yeng Chen, K. Pandian, Palaniyandi Velusamy
Summary: Myocardial infarction (MI) is a life-threatening condition that can cause cardiac arrest and organ damage. Current diagnostic techniques are not sensitive enough for early detection, but blood biomarker-based diagnosis, specifically the measurement of cardiac troponin I (cTnI), provides a potential solution. In this study, a sensor based on interdigitated electrodes was developed and used to detect cTnI. The use of aptamer-conjugated gold nanoparticles and detection antibodies in a sandwich pattern significantly improved the sensitivity of the detection. The developed sensor showed promising results for diagnosing MI.
BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Dapeng Qin, Qiuping Gong, Xin Li, Yanping Gao, Subash C. B. Gopinath, Yeng Chen, Zehua Yang
Summary: In this study, a gold nanoparticle-based colorimetric biosensing method was used to accurately and easily detect the specific target DNA for Mycoplasma pneumoniae. The color of the gold nanoparticles changes in the presence of the target DNA, allowing for the diagnosis of Mycoplasma pneumoniae.
BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY
(2023)
Review
Biotechnology & Applied Microbiology
Theivasanthi Thirugnanasambandan, Subash C. B. Gopinath
Summary: The storage of food grains against fungal infection is a major challenge for farmers, but nanotechnology offers a solution by replacing synthetic fungicides with inorganic nanoparticles such as silver and zinc oxide, as well as green synthesized nanoparticles. Plant extracts and essential oils show effective antifungal properties, and nanoparticles can be impregnated in packaging materials for safe food storage. This overview discusses the nanomaterials-mediated protection of food materials from mycotoxin contamination and its impact on the environment.
Article
Health Care Sciences & Services
Dayang Nooreffazleen Yahya, Rhanye Mac Guad, Yuan-Seng Wu, Siew Hua Gan, Subash C. B. Gopinath, Hasif Adli Zakariah, Rusdi Abdul Rashid, Maw Shin Sim
Summary: The rs4755404 gene polymorphism of SLC1A2 is significantly associated with METH-induced psychosis, especially for individuals with the GG homozygous genotype.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Review
Chemistry, Medicinal
Nur Syafiqah Rahim, Yuan Seng Wu, Maw Shin Sim, Appalaraju Velaga, Srinivasa Reddy Bonam, Subash C. B. Gopinath, Vetriselvan Subramaniyan, Ker Woon Choy, Sin-Yeang Teow, Ismail M. M. Fareez, Chandramathi Samudi, Shamala Devi Sekaran, Mahendran Sekar, Rhanye Mac Guad
Summary: There are six members of the transmembrane 4 superfamily (TM4SF) that have similar topology and sequence homology. Among these members, TM4SF1, TM4SF4, and TM4SF5 play crucial roles in cancer angiogenesis, progression, and chemoresistance. Targeting these TM4SF members has emerged as a promising strategy for cancer therapy.
Article
Chemistry, Physical
Evan T. Salim, Suhair R. Shafeeq, Mohammed Jalal AbdulRazzaq, Makram A. Fakhri, Subash C. B. Gopinath
Summary: This study presents the first use of silver (Ag) nanoparticles to enhance the pulsed laser fabricated Nb2O5 nanostructures. Ag NPs were incorporated into Nb2O5 nanomatrix structure by UV photo-activation mechanism. The results showed that the optical band gap of Nb2O5 was reduced and defects were reduced within the UV region of the emission wavelengths. XRD analysis confirmed the successful decoration of Ag NPs into the Nb2O5 nanostructure. SERS analysis demonstrated successful hot electrons transfer in the monoclinic (H-Nb2O5).
SURFACES AND INTERFACES
(2023)
Review
Engineering, Biomedical
Hong Hui Jing, Fevzi Bardakci, Sinan Akgol, Kevser Kusat, Mohd Adnan, Mohammad Jahoor Alam, Reena Gupta, Sumaira Sahreen, Yeng Chen, Subash C. B. Gopinath, Sreenivasan Sasidharan
Summary: Carbon dots (CDs) are a type of crystalline, quasi-spherical fluorescence nanomaterials with a size between 1 nm to 10 nm. Green CDs are synthesized from renewable biomass and have distinct advantages over physicochemical methods. Green CDs can be synthesized using various plant-based organic resources and have diverse applications in biomedical fields. This review focuses on the synthesis, characterization techniques, properties, and biomedical applications of green CDs.
JOURNAL OF FUNCTIONAL BIOMATERIALS
(2023)
Review
Engineering, Chemical
Hussaini Adam, Subash C. B. Gopinath, M. K. Md Arshad, Tijjani Adam, Uda Hashim, Zaliman Sauli, Makram A. Fakhri, Sreeramanan Subramaniam, Yeng Chen, Sreenivasan Sasidharan, Yuan Seng Wu
Summary: This study presents an electrochemically-based microfluidic nanobiosensor array for monoplex and multiplex detection of physiologically relevant analytes. The integrated system is portable and serves as a custom electrochemical reader. It has great potential for real-time profiling of immune-mediated treatment responses and as a point-of-care diagnostic device for conducting near-patient tests using biological samples.
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS
(2023)
Article
Biochemistry & Molecular Biology
Hussaini Adam, Subash C. B. Gopinath, Thirumananseri Kumarevel, M. K. Md Arshad, Tijjani Adam, Zaliman Sauli, Sreeramanan Subramaniam, Uda Hashim, Yeng Chen
Summary: In this study, a novel technique for the selective detection of amyloid fibrils was reported. Using a dipole moment on a dielectrode surface, this technique can sensitively detect the aggregation of alpha-synuclein, which is crucial for diagnosing Parkinson's disease. The stability and detection range of the sensor were confirmed through physical and electrical characterization.
PROCESS BIOCHEMISTRY
(2023)
Review
Green & Sustainable Science & Technology
Wan Yuen Tan, Subash C. B. Gopinath, Periasamy Anbu, Ahmad Radi Wan Yaakub, Sreeramanan Subramaniam, Yeng Chen, Sreenivasan Sasidharan
Summary: With the development of bionanotechnology, the field of nanobiocatalysts has grown rapidly and transformed various nanomaterials into novel nanocarriers for enzyme immobilization. Nanotubes, nanofibers, nanopores, nanoparticles, and nanocomposites have been successfully used as nanocarriers. The combination of enzymes and nanocarriers through different immobilization techniques has attracted attention due to their exceptional catalytic performance, stability, and reusability. The review discusses enzyme immobilization on nanocarriers and highlights the techniques, properties, preparations, and applications of nanoimmobilized enzymes.
Article
Engineering, Environmental
Mugashini Vasudevan, Sathaniswarman Remesh, Veeradasan Perumal, Pandian Bothi Raja, Mohammad Nasir Mohammad Ibrahim, Subash C. B. Gopinath, Saravanan Karuppanan, Mark Ovinis
Summary: This article presents the development and application of a green lignin-derived graphene biosensor for Troponin I, a biomarker for Acute Myocardial Infarction (AMI). The biosensor showed high analytical performance, high specificity, and a detection limit of 100 attomolar. The biosensor has a sensitivity of 31.45 mu A mM(-1) cm(-2), stability of 87%, with a relative standard deviation for reproducibility of 3.8%.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Multidisciplinary Sciences
Mohammed Mohammed, Jawad K. Oleiwi, Anwar Ja 'afar Mohamad Jawad, Aeshah M. Mohammed, Azlin F. Osman, Rozyanty Rahman, Tijjani Adam, Bashir O. Betar, Subash C. B. Gopinath, Omar S. Dahham
Summary: This study aimed to enhance the flexural properties of unsaturated polyester/kenaf fiber nanocomposites by using zinc oxide nanoparticles for surface treatment. The findings showed that the addition of ZnONPs significantly improved the performance of the composites, with 2% being the optimal loading, and surface treatment with ZnONPs resulted in kenaf fibers with improved flexural properties.
Article
Biotechnology & Applied Microbiology
Nagasathiya Krishnan, Roshini Iyer, Swati Priyadarshini, Arkadeep Kundu, Pradiksha Natarajan, Pinki Kumari Singh, Subash C. B. Gopinath, Pachaiappan Raman
Summary: This study investigated the impact of different abiotic elicitors on CPT production in N. nimmoniana cell suspension culture. The results showed that tryptophan and ethanol treatment significantly increased CPT production. However, the viability of the cells decreased when treated with calcium chloride and cadmium chloride.
BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY
(2023)
