By integrating ATP aptamer into the linker DNA, a novel DNA hydrogel was designed, with mechanical properties that could be tuned into three phases. Based on the unique interaction between ATP and its aptamer, the mechanical strength of the hydrogel increased from 204 Pa to 380 Pa after adding ATP. Furthermore, with the addition of the complementary sequence to the ATP aptamer, the mechanical strength could be increased to 570 Pa.
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http://dx.doi.org/10.3390/ijms19061633 | DOI Listing |
Anal Chem
January 2025
State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
() is a prominent pathogen responsible for intestinal infections, primarily transmitted through contaminated food and water. This underscores the critical need for precise and biocompatible technologies enabling early detection and intervention of bacterial colonization . Herein, a multifunctional nanoplatform (IR808-Au@ZIF-90-Apt) was designed, utilizing an -specific aptamer to initiate cascade responses triggered by intracellular ATP and GSH.
View Article and Find Full Text PDFAnal Chem
January 2025
Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.
DNA reaction equilibrium-based calculations have great potential in thermodynamic characterization, but their widespread applications are hindered by significant measurement deviation of equilibrium concentration. Here, we report the advantages of metastable DNA hybridization in reducing quantification deviation of equilibrium concentration and propose a universal and standardized strategy for measuring aptamer binding energy, termed metastable DNA reference calorimetry (MDRC). We built different MDRC-based algorithms tailored to different aptamer binding models, enabling the calculation of thermodynamic parameters for aptamers with one or more binding sites.
View Article and Find Full Text PDFAngew Chem Int Ed Engl
January 2025
School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
Adenosine triphosphate (ATP), the primary energy currency in cells, is dynamically regulated across different subcellular compartments. The ATP interplay between mitochondria and endoplasmic reticulum (ER) underscores their coordinated roles in various biochemical processes, highlighting the necessity for precise profiling of subcellular ATP dynamics. Here we present an exogenously and endogenously dual-regulated DNA nanodevice for spatiotemporally selective, subcellular-compartment specific signal amplification in ATP sensing.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States.
Genetically encoded fluorescent protein and fluorogenic RNA sensors are indispensable tools for imaging biomolecules in cells. To expand the toolboxes and improve the generalizability and stability of this type of sensor, we report herein a genetically encoded fluorogenic DNA aptamer (GEFDA) sensor by linking a fluorogenic DNA aptamer for dimethylindole red with an ATP aptamer. The design enhances red fluorescence by 4-fold at 650 nm in the presence of ATP.
View Article and Find Full Text PDFMikrochim Acta
December 2024
State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, 130012, People's Republic of China.
A highly sensitive aptamer sensor (aptasensor) is proposed based on metal-organic frameworks-silver nanoparticles (AgNPs@MOF) to detect sulfadimethoxine (SDM) by surface-enhanced Raman spectroscopy (SERS). AgNPs@MOF with SERS activity was successfully fabricated by synthesizing AgNPs in situ on the surface of MIL-101(Fe), and SDM aptamer and Raman reporter 4-aminophenthiophenol (4-ATP) were selected as specific recognition elements and signal probes, respectively. When SDM was absent, the SDM aptamers were effectively adsorbed on the surface of AgNPs@MOF, thus keeping AgNPs@MOF in a dispersed state, resulting in a weakened SERS signal of 4-ATP.
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