Article
Chemistry, Multidisciplinary
Diego Nunez-Villanueva, Christopher A. Hunter
Summary: The template-directed synthesis of nucleic acids in the polymerase chain reaction was achieved by attaching a high affinity primer to a mixed sequence template. The study demonstrated a substantial template effect through H-bonding interactions between the phenols on the template and phosphine oxides on the azide. The use of a compound with multiple H-bonding capability resulted in the highest rate acceleration.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Ryan P. Connelly, Pedro F. Madalozzo, Jack E. Mordeson, Andrew D. Pratt, Yulia Gerasimova
Summary: The research demonstrates the conversion of a dapoxyl DNA aptamer into a sensor generating fluorescence signal at different wavelengths for detecting drug-resistant tuberculosis gene fragments. The promiscuity of the aptamer in binding to fluorogenic dyes has been discovered, laying the foundation for its application as a versatile sensing platform.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Yu Zhang, Mengke Su, Xingru Fang, Wenwen Huang, Hao Jiang, Qi Li, Nisar Hussain, Mao Ye, Honglin Liu, Weihong Tan
Summary: In this study, a novel nanometal surface energy transfer (NSET) nanoruler with a single-nucleobase resolution was proposed for in situ identification of aptamer-binding targets on living cell membrane surfaces. The nanoruler consisted of FAM-labeled aptamers and single-sized gold nanoparticle (GNP) antibody conjugates as a donor and an acceptor, respectively. Experimental evidence demonstrated the single nucleobase resolution of the nanoruler by molecular size, orientation, quenching nature, and other dye-GNP pairs. The nanoruler showed high reproducibility and precision for measuring molecule distance on living cell membranes at the nanometer level due to the use of only single-sized antibody-capped GNPs. The proposed strategy represents a solid step towards the wider application of optical-based rulers for observing molecular structural configuration and dynamic transitions on the membrane surface of living cells.
Article
Chemistry, Multidisciplinary
Juan Canoura, Haixiang Yu, Obtin Alkhamis, Daniel Roncancio, Rifat Farhana, Yi Xiao
Summary: The study introduces a generalizable method using exonuclease III and exonuclease I for rapid detection of small-molecule-binding aptamers' binding properties. This method can enhance aptamer binding characteristics and successfully identify two new high-affinity aptamers.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Review
Chemistry, Multidisciplinary
Obtin Alkhamis, Juan Canoura, Phuong T. Ly, Yi Xiao
Summary: This article introduces the research results of using nucleases to improve the sensitivity, specificity, and cost-effectiveness of aptamer sensors. The author serendipitously discovered that the digestion of DNA aptamers by exonucleases is inhibited when an aptamer is bound to a ligand, which laid the foundation for the development of three novel aptamer-related methodologies. The enzymatic technologies described in this article can greatly streamline the aptamer characterization and sensor development process.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Multidisciplinary Sciences
Alex M. Yoshikawa, Alexandra E. Rangel, Liwei Zheng, Leighton Wan, Linus A. Hein, Amani A. Hariri, Michael Eisenstein, H. Tom Soh
Summary: Aptamer-based molecular switches have various applications such as imaging metabolites, drug delivery, and biomolecule detection. Conventional aptamer selection methods do not produce aptamers with structure-switching functionality, so post-selection modification is necessary. This study presents a screening-based strategy that can convert any aptamer into a molecular switch without prior knowledge of its structure.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Applied
Aloys Hitabatuma, Yue-hong Pang, Li-hong Yu, Xiao-fang Shen
Summary: An ultrasensitive method for rapid and specific detection of Ochratoxin A (OTA) was designed using complementary sequence to aptamer as a target of molecular beacons. The method showed linear increase in fluorescence intensity with OTA concentration and a detection limit of 0.247 pg mL(-1), making it a potential sensing platform for OTA detection in wheat samples when compared to traditional HPLC-MS/MS method.
Review
Chemistry, Analytical
Ke Ma, Xing Li, Bin Xu, Wenjing Tian
Summary: Bioassays using fluorophore and DNA aptamer have been extensively developed due to the ultra-sensitivity of fluorophores and recognition ability of DNA aptamers. A label-free aptasensing strategy has been introduced, utilizing flexible fluorophore indicators and ssDNA aptamers for various sensing and assay applications. The conformational change of the DNA aptamer in the presence of the target results in dramatic fluorescence recovery and amplification.
ANALYTICA CHIMICA ACTA
(2021)
Article
Chemistry, Analytical
Yao Yao, Jingyu Kuang, Jiahe Ju, Tao Hu, Wei Shen, Sheng Tang, Chang Liu, Dezhao Kong, Haiwei Shi, Hian Kee Lee
Summary: A simple fluorescence sensing device based on solvent-free magnetic-tip microextraction was developed and successfully applied for the fluorescence detection of chloramphenicol (CAP) in genuine milk and urine samples.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Biochemistry & Molecular Biology
Hu Xing, Yiting Zhang, Markus Kraemer, Ann-Kathrin Kissmann, Valerie Amann, Heinz Fabian Raber, Tanja Weil, Kai R. Stieger, Uwe Knippschild, Marius Henkel, Jakob Andersson, Frank Rosenau
Summary: This article describes a FluCell-SELEX polyclonal aptamer library specific for R. intestinalis, which can be used for fluorescence microscopy and binding assays. The application of this library shows potential as an effective, rapid, and cost-effective method for quantifying R. intestinalis, providing a new tool for the diagnosis of gut microbiome-related diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Canyu Zhang, Qingting Li, Tianbin Xu, Wei Li, Yungang He, Hongzhou Gu
Summary: This study identified two new classes of DNA-hydrolyzing deoxyribozymes by programming a terminal hybridization stem, in addition to the previously reported classes, using the old selection strategy. These new deoxyribozymes can specifically hydrolyze DNA in the presence of Zn2+ and may have potential applications in engineering DNA-responsive DNA hydrolyzers for detecting target ssDNA sequences.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Environmental Sciences
Xianglin Zhang, Jie Xue, Yi Xiao, Zhou Shi, Songchao Chen
Summary: Soil visible and near-infrared (Vis-NIR, 350-2500 nm) spectroscopy has been proven as an alternative to conventional laboratory analysis. The study evaluated seven variable selection algorithms and three predictive algorithms in predicting soil properties using a regional soil Vis-NIR spectral library. The results showed that Cubist outperformed partial least squares regression (PLSR) and random forests (RF) in most soil properties when using the full spectra. The study provides valuable insights for predicting soil information using spectroscopic techniques and variable selection algorithms.
Article
Biochemistry & Molecular Biology
Li Li, Zhengbo Chen
Summary: In this study, a high specificity, flexibility, and simplicity aptasensor strategy was designed using a triblock DNA probe. It was found that the polyA fragment could assemble on the gold electrode surface via polyA instead of traditional Au-S bonds, leading to improved hybridization stability. The electrochemical aptasensor showed good repeatability, stability, and specificity.
BIOELECTROCHEMISTRY
(2023)
Article
Biophysics
Wan Huang, Danyan Zhan, Yiming Xie, Xin Li, Guosong Lai
Summary: The researchers successfully formed a tripedal DNAzyme-DNA walker using a dual-catalytic hairpin assembly strategy, and developed a novel proteinase-free dual-mode biosensing method for kanamycin antibiotic detection.
BIOSENSORS & BIOELECTRONICS
(2022)
Article
Chemistry, Multidisciplinary
Aitor Patino Diaz, Sara Bracaglia, Simona Ranallo, Tania Patino, Alessandro Porchetta, Francesco Ricci
Summary: This study developed a cell-free in vitro transcription system for the detection of specific target antibodies. The system uses programmable antigen-conjugated DNA-based conformational switches that can trigger cell-free transcription upon binding to a target antibody, resulting in the production of a light-up fluorescence-activating RNA aptamer. The system combines the programmability and responsiveness of DNA-based systems with the specificity and sensitivity offered by in vitro genetic circuitries and commercially available transcription kits. The study demonstrates that cell-free transcriptional switches can efficiently measure antibody levels directly in blood serum and can be adapted to different antibodies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)