Article
Chemistry, Multidisciplinary
Ngozi A. Eze, Valeria T. Milam
Summary: Locked nucleic acids (LNAs) are synthetic analogues of natural oligonucleotides that offer superior nucleaseresistance and cytocompatibility. In this study, the competitive displacement of target strands immobilized on microspheres was measured using high throughputflow cytometry. The results show that the response of the primary duplex probe systems to unlabeled secondary targets varies.
Review
Oncology
Mohammad Javad Kamali, Mohammad Salehi, Somayeh Fatemi, Fereshteh Moradi, Azin Khoshghiafeh, Mohamadreza Ahmadifard
Summary: Cancer is a major cause of death globally, and traditional cancer treatments have limitations and side effects. RNA therapies, using tools such as antisense oligonucleotides (ASOs) and siRNAs, have shown potential for improving cancer treatment. Locked Nucleic Acids (LNAs) are a new type of RNA analog with unique properties that make them effective and safe for cancer treatment. LNAs also have applications in molecular diagnostics, providing accurate and rapid detection of mutations. This study reviews the special properties of LNA oligonucleotides and their potential in cancer treatment and molecular detection methods.
EXPERIMENTAL CELL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Layla R. Goddard, Charlotte E. Mardle, Hassan Gneid, Ciara G. Ball, Darren M. Gowers, Helen S. Atkins, Louise E. Butt, Jonathan K. Watts, Helen A. Vincent, Anastasia J. Callaghan
Summary: The increase in antibacterial resistance poses challenges for health and defense sectors, necessitating novel antibacterial targets and strategies. Targeting the translation initiation region of Escherichia coli rne mRNA using antisense oligonucleotides shows promise in inhibiting translation and facilitating RNase H-mediated mRNA cleavage.
Article
Chemistry, Analytical
Kaiyue Tan, Longsheng Chen, Donglin Cao, Wei Xiao, Qian Lv, Lili Zou
Summary: As a promising biomarker of liquid biopsy, circulating tumor DNA (ctDNA) plays a significant role in the early diagnosis of noninvasive cancer. This study presents a locked nucleic acid (LNA)-incorporated CHA circuit for the rapid and sensitive detection of target ctDNA. The LNA-assisted CHA system demonstrates excellent performance in target ctDNA detection and provides a general and robust platform for the sensitive detection of biomarkers of interest.
ANALYTICAL METHODS
(2023)
Article
Chemistry, Analytical
Kaiyue Tan, Longsheng Chen, Donglin Cao, Wei Xiao, Qian Lv, Lili Zou
Summary: The CHA strategy combined with LNA can be used for highly sensitive detection of ctDNA in liquid biopsy and has been successfully applied to the analysis of clinical samples from breast cancer patients.
ANALYTICAL METHODS
(2023)
Article
Chemistry, Medicinal
Hiroaki Sawamoto, Takashi Sasaki, Tomo Takegawa-Araki, Masayuki Utsugi, Hiroyuki Furukawa, Yoko Hirakawa, Fumiko Yamairi, Takashi Kurita, Karin Murahashi, Katsuya Yamada, Tetsuya Ohta, Shinji Kumagai, Akihiro Takemiya, Satoshi Obika, Jun Kotera
Summary: In this study, a novel nucleic acid, 2'-N-methanesulfonyl-2'-amino-locked nucleic acid (ALNA[Ms]), was synthesized and compared to conventional nucleic acids in terms of physical and pharmacological properties. ALNA[Ms] exhibited similar binding affinities for complementary RNA strands as conventional nucleic acids. ALNA[Ms] showed distinct biological activities from conventional constrained nucleic acids, indicating its potential as a novel modified nucleic acid in oligonucleotide therapeutics.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2023)
Review
Immunology
Ana Barbosa, Sonia Miranda, Nuno F. Azevedo, Laura Cerqueira, Andreia S. Azevedo
Summary: Biofilms are complex structures with intricate relationships between microorganisms, matrix, and environment. There is growing interest in biofilms due to their presence in diverse fields. Molecular techniques have been used to study biofilms but disrupt the spatial structure. Fluorescence in situ hybridization (FISH) is a widely used method to analyze the spatial distribution, and different FISH variants have been explored. These variants, combined with confocal microscopy, provide a powerful approach to visualize, quantify, and locate biofilm components. Future research directions focus on developing robust and accurate FISH-based methods for deeper understanding of biofilm structure and function.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Chemistry, Analytical
Huo Xu, Yanhui Zheng, Danlong Chen, Yinghao Cheng, Xiaojun Fang, Chunlian Zhong, Xinmei Huang, Qi Huang, Jiawei Xu, Jianguo Xu, Chang Xue
Summary: The use of a branch-shaped trapping device in a spatial confinement reactor showed accelerated miRNA imaging, improving localized concentration and shortening physical distance. In vitro and in situ analyses demonstrated that the T-CHA outperformed the D-CHA in stability, reaction speed, and amplification sensitivity. The platform showed potential for accurately and timely revealing miRNA in biological systems, benefiting from the unique nanoarchitecture of the FEN.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Mary Catherine Adams, Valeria T. Milam
Summary: Double-stranded oligonucleotide probes outperform single-stranded probes in terms of target sequence specificity without target labeling. Flow cytometry combined with Forster resonance energy transfer (FRET) is used to rapidly screen and detect the stability and selective responsiveness of LNA and DNA probes to SARS-CoV-2 RNA. Titration studies were conducted to examine the quenching range of residual quencher-capped hybridization partners in the probes.
ANALYTICAL CHEMISTRY
(2023)
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.
Article
Chemistry, Physical
Min Seok Lee, Hwi Hyun, Inwon Park, Sungho Kim, Dong-Hyun Jang, Seonghye Kim, Jae-Kyeong Im, Hajin Kim, Jae Hyuk Lee, Taejoon Kwon, Joo H. Kang
Summary: This study developed a novel technology called mu FISH, which uses mu FISH probes based on 16S rRNA sequences to quantitatively identify and detect bacteria in blood samples. It is a more sensitive method compared to traditional bacterial detection methods.
Article
Multidisciplinary Sciences
Chen Chen, Zhilun Zhao, Naixin Qian, Shixuan Wei, Fanghao Hu, Wei Min
Summary: The research team developed a multi-parameter measurement system that can simultaneously quantify cell surface proteins, endocytosis activities, and metabolic dynamics of single live cells. This technique allows for analysis of 14 parameters under drug perturbations, enabling powerful clustering, correlation, and network analysis.
NATURE COMMUNICATIONS
(2021)
Article
Biophysics
Agustin Robles-Remacho, M. Angelica Luque-Gonzalez, F. Javier Lopez-Delgado, Juan J. Guardia-Monteagudo, Mario Antonio Fara, Salvatore Pernagallo, Rosario M. Sanchez-Martin, Juan Jose Diaz-Mochon
Summary: The detection of genomic variations in repetitive sequences is crucial for understanding their biological implications. However, there is a lack of techniques to validate the sequencing data obtained from repetitive sequences, especially in the case of single-nucleotide variations (SNVs). This study presents chemFISH, an innovative method for detecting SNVs in repetitive sequences, using dynamic chemistry labelling and abasic peptide nucleic acid probes. ChemFISH allows for rapid and accurate detection of alpha-satellite DNA with single-base resolution. The method demonstrates high sensitivity and specificity, making it a potential tool for validating and discovering SNVs in repetitive sequences.
BIOSENSORS & BIOELECTRONICS
(2023)
Review
Biochemistry & Molecular Biology
Yu-Sheng Wang, Jia Guo
Summary: The ability to quantify a large number of varied transcripts in single cells in their native spatial context is crucial for understanding health and disease, and recent advances in multiplexed FISH methods have enabled comprehensive RNA profiling in individual cells.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Arkaja Goswami, Ashok K. Prasad, Jyotirmoy Maity, Neerja Khaneja
Summary: This article discusses the synthesis and applications of modified locked nucleic acids (LNAs) with various modifications and restricted conformations as antisense oligonucleotides.
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS
(2022)
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)