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)
Article
Green & Sustainable Science & Technology
Muhammad Nur Aiman Uda, Subash C. B. Gopinath, Uda Hashim, Muhammad Nur Afnan Uda, Tijjani Adam, Nor Azizah Parmin, Sreeramanan Subramaniam, Suresh V. Chinni, Veeranjaneya Reddy Lebaka, Ramachawolran Gobinath
Summary: Rice is increasingly exposed to inorganic arsenic, affecting half of the world population as rice consumers. This study investigated the effects of silica and graphene nanomaterials treatment on varied arsenic levels, and found that silica nanoparticles showed the highest inhibition on arsenic accumulation. Arsenic adversely affected plant growth and even caused death at high concentrations, but silica nanoparticles demonstrated potential in reducing consumer health risks.
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
Microbiology
Suaidah Ramli, Yuan Seng Wu, Kalaivani Batumalaie, Rhanye Mac Guad, Ker Woon Choy, Ashok Kumar, Subash C. B. Gopinath, Md. Moklesur Rahman Sarker, Vetriselvan Subramaniyan, Mahendran Sekar, Neeraj Kumar Fuloria, Shivkanya Fuloria, Suresh V. Chinni, Gobinath Ramachawolran
Summary: This review focuses on the therapeutic efficacy and molecular mechanisms of Withania somnifera (WS) extracts and their phytochemicals against SARS-CoV-2 infection. It also discusses the use of molecular docking in developing potential inhibitors from WS to target the virus and host cell receptors. Additionally, the review explores the use of nanoformulations or nanocarriers in enhancing WS delivery for improved bioavailability and treatment efficacy.
Article
Infectious Diseases
Valiappan Ranjutha, Yeng Chen, Lamya Ahmed Al-Keridis, Mitesh Patel, Nawaf Alshammari, Mohd Adnan, Sumaira Sahreen, Subash C. B. Gopinath, Sreenivasan Sasidharan
Summary: Polyalthia longifolia is a medicinal plant used in traditional medicine for skin diseases. This study confirms the synergistic antimicrobial activity of Polyalthia longifolia methanol leaf extract (MEPL) and ceftriaxone against methicillin-resistant Staphylococcus aureus (MRSA) bacteria. The combination of MEPL and ceftriaxone significantly reduces the minimum inhibitory concentration of ceftriaxone and inhibits the expression of the resistant mecA gene in MRSA.
Article
Biology
Ramesh Thevendran, Sivalingam Rogini, Glenn Leighton, Atherton Mutombwera, Sarah Shigdar, Thean-Hock Tang, Marimuthu Citartan
Summary: Dengue infection poses a global threat and requires immediate and appropriate disease management. The current diagnosis methods for dengue infection are time-consuming, expensive, and require trained personnel. This study aimed to isolate RNA aptamers against the NS1 protein of dengue virus serotype 2 as a potential alternative to antibodies for early diagnosis. Two potent aptamers, DENV-3 and DENV-6, were obtained through SELEX cycles and showed high specificity against dengue NS1 without cross-reactivity to other viruses or proteins. These aptamers were further miniaturized and used in a sandwich ELASA, which achieved a low limit of detection of 2 nM in human serum.
Review
Multidisciplinary Sciences
A. L. Olatomiwa, Tijjani Adam, C. O. Edet, A. A. Adewale, Abdullah Chik, Mohammed Mohammed, Subash C. B. Gopinath, U. Hashim
Summary: This review provides a comprehensive overview of articles on the electronic and optical properties of graphene using density functional theory and machine learning approaches. It summarizes the thermodynamic stability parameters of various doped graphene systems and discusses the strengths and uncertainties of the used models and potentials. Future studies should explore the thermal properties, heterostructure modeling, superconducting behavior, and optimization of DFT models to enhance the potential of graphene.
Article
Green & Sustainable Science & Technology
Roslaili Abdul Aziz, Mok Yiwen, Mawaddah Saleh, Mohd Nazry Salleh, Subash C. B. Gopinath, Sunny Goh Eng Giap, Suresh V. Chinni, Ramachawolran Gobinath
Summary: This study evaluated the accumulation of trace elements, such as copper, zinc, and lead, in paddy fields and soil, and analyzed their transfer to rice plants. The findings show that the accumulation of heavy metals in soil varies depending on the location and the order of accumulation differs for different metals. The study also found that soil properties and metal abundance can influence the growth characteristics of rice plants.
Article
Food Science & Technology
Raja Hasnida Raja Hashim, Ahmad Anas Nagoor Gunny, Sam Sung Ting, Subash C. B. Gopinath, Yeong Yin Fong, Sunil Pareek, Muaz Mohd Zaini Makhtar, Hafiza Shukor
Summary: This study investigated the effect of Coleus aromaticus essential oil (CAEO) on an active film made of polylactic acid, chitosan, and cellulose nanocrystal for fruit packaging. The addition of CAEO improved the mechanical properties and antioxidant activity of the film, and exhibited inhibitory effects against pathogenic fungus. The results suggest that the PLA/Cs/CNC/CAEO films can enhance microbial safety and prolong the shelf life of fruits, potentially replacing petroleum-based plastics for fruit packaging applications.
JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION
(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
Engineering, Biomedical
S. Iswarya, T. Theivasanthi, Subash C. B. Gopinath
Summary: Sodium alginate/hydroxyapatite/nanocellulose (SA/HA/NC) nanocomposite films were prepared for bone tissue engineering using a simple solution casting method. The structure and properties of the composite films were studied by XRD, SEM, EDAX, and FTIR analysis. The results showed that the inclusion of different concentrations of NC improved the tensile strength of the biopolymer film. These bionanocomposite films have the potential to be used as biomaterials in bone tissue engineering.
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS
(2023)
