Review
Chemistry, Analytical
Zhaohe Huang, Sitong Liu, Xiaojing Pei, Shujing Li, Yifan He, Yigang Tong, Guoqi Liu
Summary: This review discusses the importance and development of CRISPR/Cas system in nucleic acid detection applications. The combination of CRISPR with various signal-readout techniques has wide applications in molecular diagnostics. Fluorescence is a dominant read-out technique, and understanding fluorescence readout types and variables affecting the signals can improve experimental designs.
Article
Chemistry, Multidisciplinary
Obianuju A. Nwokolo, Brant Kidd, Te'Kara Allen, Alexander S. Minasyan, Suchitra Vardelly, Kristopher D. Johnson, Irina V. Nesterova
Summary: In this study, a memory-based sensor was designed based on the unique kinetic properties of nucleic acid quadruplexes to measure heat changes in small open systems. The sensors are biocompatible, operate homogeneously, and measure small heats released over long time periods, and have been successfully applied to water/propanol mixing and ligand/protein binding.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Yifan Chen, Sijian Ye, Chongling Cheng, Renguo Xie, Dayang Wang
Summary: In this work, NR was loaded into mesopores of MCM-41 particles through hydrogen bonding-driven adsorption in organic media. The resulting NR-borne MCM-41 particles were used as mesoporous luminescent donors for detecting hydrophilic TPM dyes in aqueous media based on NR-to-TPM FRET. The method allowed for determination of TPM concentration from ca. 1 μmol L-1 to ca. 1 nmol L-1, with a detection limit of 0.1 nmol L-1 (0.1 ppb) due to the 1000-fold enrichment of TPM dyes in the NR-borne MCM-41 mesopores. The fluorescence quenching constant of NR-borne MCM-41 particles induced by TPM was empirically connected to their NR uptake, allowing for identification of TPM dyes. Additionally, an image analysis and processing protocol was developed to convert fluorescence images of microtiter plates into multiplex, FRET-encoded matrices, enabling molecular identification and sub-ppb-level determination of TPM concentrations.
MATERIALS CHEMISTRY FRONTIERS
(2022)
Article
Biochemistry & Molecular Biology
Aren Mirzakhanian, Michael Khoury, Donald E. Trujillo, Byoula Kim, Donnie Ca, Thomas Minehan
Summary: Different compounds bind to DNA in different ways, some to the major groove and some to the minor groove. The design of major groove binding ligands should consider the spatial structure of the compounds and the stereoelectronic interactions with DNA.
BIOORGANIC & MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Javier Cabello-Garcia, Wooli Bae, Guy-Bart Stan, Thomas E. Ouldridge
Summary: The use of templates for sequence-controlled assemblies, particularly in long polymers, is a well-established method. However, the transient template recognition interactions during the biogenesis of sequence-controlled polymers can disrupt the equilibrium, leading to the production of far-from-equilibrium output. Handhold-mediated strand displacement (HMSD) is proposed as an alternative mechanism to generate out-of-equilibrium products by decoupling drive and specificity in DNA-based reactions.
Review
Chemistry, Inorganic & Nuclear
Min Yang, Longjiao Zhu, Wenping Yang, Wentao Xu
Summary: This article provides a comprehensive review of the recent advances in nucleic acid-mediated silver nanoclusters that first emerged in 2007. It focuses on the properties and structures of nucleic acid-templated silver nanoclusters, as well as the regulation of their properties by nucleic acid sequences, conformation, and structure. The most recent advances in nucleic acid-templated silver nanoclusters in biological detection are highlighted. Current challenges, prospects, and future directions are also discussed.
COORDINATION CHEMISTRY REVIEWS
(2023)
Article
Chemistry, Physical
Dhananjoy Maity, Shubhra Kanti Bhaumik, Supratim Banerjee
Summary: Dimeric cationic cyanostilbenes with peripheral alkyl chains formed aggregates in water and produced luminescent nano-assemblies, depending on the hydrophobic segment length. In the presence of heparin, the self-assembled structures showed higher-order formations, while non-assembling dimers exhibited heparin-induced supramolecular structures. The emission was significantly enhanced in both cases, enabling the detection of heparin in various aqueous solutions with fluorescence response. Interestingly, these derivatives also exhibited luminescence variation in the presence of ctDNA, but with a turn-off fluorescence response. Different DNA binding modes were observed based on the length of the alkyl segment.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Review
Chemistry, Physical
Yuchan Yuan, Netzahualcoyotl Arroyo-Curras
Summary: Nucleic acid-based electrochemical (NBE) sensors offer real-time and reagent-free sensing capabilities by using affinity-based molecular detection. These sensors are modular and versatile, allowing the monitoring of various molecular targets by swapping recognition probes. However, their performance in vivo has not been rigorously validated relative to benchmark methods. This article highlights recent reports evaluating the in vivo performance of NBE sensors, aiming to inspire future translational efforts for clinical applications and commercial development.
CURRENT OPINION IN ELECTROCHEMISTRY
(2023)
Review
Chemistry, Analytical
Ya-peng Huo, Sha Liu, Zhi-xian Gao, Bao-an Ning, Yu Wang
Summary: Metal-organic frameworks (MOFs) have attracted significant attention in the sensing analysis field due to their unique properties. MOFs are extensively studied as fluorescence quenchers, used in switch fluorescence biosensors for specific and sensitive detection of various analytes. The research focuses on both in vitro and intracellular analytes, showcasing the potential for biomedical applications.
Article
Chemistry, Organic
Imrich Geci, Maha Fatthalla, Maike Heintz, Per T. Jorgensen, Erik B. Pedersen
Summary: In this study, we synthesized a DNA intercalator called TINA and found that it can improve the binding ability of triplex DNA and duplex DNA. The introduction of TINA monomer Y can stabilize the oligodeoxynucleotide sequence, resulting in enhanced thermal stability.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2022)
Article
Chemistry, Analytical
Lu Gao, Liying Liu, Yunfei Tian, Qianfan Yang, Peng Wu, Chunhai Fan, Qiang Zhao, Feng Li
Summary: The development of robust analytical tools is essential for understanding and manufacturing DNA-based materials. We introduced a real-time fluorescence anisotropy assay and DNA reaction termination probes (DRTPs) to explore the formation mechanisms of DNA nanostructures, focusing on the tetrahedral DNA nanostructure (TDN). By revealing the dominance of simultaneous hybridization and the impact of reaction temperature on TDN formation, we engineered magnetic DRTPs for single-step purification, leading to significant improvement in target product purity. These tools enabled one-pot synthesis and purification of TDN, showcasing their potential for structural DNA nanotechnology.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Theresa Kolmar, Antonia Becker, Ronja A. Pfretzschner, Alina Lelke, Andres Jaeschke
Summary: This article discusses the systematic variation of the core structure in nucleoside-based diarylethenes to achieve reversible modulation of fluorescence signals by light. The introduction of different aromatic bridging units affects the absorption peak and switch efficiency of the closed-ring form, while the substitution of different aryl units in the core improves stability and fluorescence properties, holding potential applications in fluorescence-switchable DNA.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Nanoscience & Nanotechnology
Fangfei Yin, Haipei Zhao, Shasha Lu, Juwen Shen, Min Li, Xiuhai Mao, Fan Li, Jiye Shi, Jiang Li, Baijun Dong, Wei Xue, Xiaolei Zuo, Xiurong Yang, Chunhai Fan
Summary: The article introduces a DNA-encoded molecular classifier that can classify multidimensional molecular clinical data and has been tested in prostate cancer patients.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Applied
Chunyan Sun, Zheng Liu, Xinyue Ma, Chuanyu Yang, Ying Li, Ni Liu, Ting Lv, Junyang Wang
Summary: A biosensor based on single-stranded DNA and Tb3+ fluorescent probe was developed for the rapid detection of the highly dangerous pollutant, Hg2+. The detection method utilizes a single DNA strand with a G-rich sequence serving as the Tb3+ luminescent antenna ligand and a T-rich sequence acting as the Hg2+ recognition probe. The designed fluorescent probe exhibited simplicity and functionality, making it suitable for applications in food safety and environmental pollution.
Review
Chemistry, Multidisciplinary
Xiaotong Yao
Summary: Acids and anions are widely distributed in plants, animals and biotechnological products, and their detection is of great importance. Molecular imprinting technology can achieve high sensitivity and selectivity for the detection of acids and anions, with fluorescent molecularly imprinted polymers considered as promising candidates.
ARABIAN JOURNAL OF CHEMISTRY
(2022)
