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Energy Landscapes in Chemical Reactions and Transport.
Chemphyschem
January 2025
Fachbereich Chemie, Philipps-Universität Marburg, 35032, Marburg, Germany.
Both, molecular chemical reactions and transport of atoms in solid media are determined by the energy landscape in which the seemingly different processes take place. Chemical reactions can be described as cooperative translocation of two chemical entities on a common potential energy surface. Transport of atoms in a solid can be envisaged as the translocation of a single particle in the potential energy landscape of all other particles constituting the solid.
View Article and Find Full Text PDFSingle-molecule analysis of transcription activation: dynamics of SAGA coactivator recruitment.
Nat Struct Mol Biol
January 2025
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
Transcription activators are said to stimulate gene expression by 'recruiting' coactivators, yet this vague term fits multiple kinetic models. To directly analyze the dynamics of activator-coactivator interactions, single-molecule microscopy was used to image promoter DNA, a transcription activator and the Spt-Ada-Gcn5 acetyltransferase (SAGA) complex within yeast nuclear extract. SAGA readily but transiently binds nucleosome-free DNA without an activator, while chromatin association occurs primarily when an activator is present.
View Article and Find Full Text PDFFrom Radioactive Effluent to Drinking Water: Efficient Removal of Trace TcO /ReO by Cationic Porous Aromatic Framework.
Adv Sci (Weinh)
January 2025
Department of Chemistry, University of North Texas1508 W Mulberry St, Denton, TX, 76201, USA.
Efficient removal of TcO from radioactive effluents while recovering drinking water remains a challenge. Herein, an excellent ReO (a nonradioactive surrogate of TcO ) scavenger is presented through covalently bonding imidazolium poly(ionic liquids) polymers with an ionic porous aromatic framework (iPAF), namely iPAF-P67, following an adsorption-site density-addition strategy. It shows rapid sorption kinetics, high uptake capacity, and exceptional selectivity toward ReO .
View Article and Find Full Text PDFPretrained Deep Neural Network Kin-SiM for Single-Molecule FRET Trace Idealization.
J Phys Chem B
January 2025
Single Molecule Analysis Group, Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109, United States.
Single-molecule fluorescence resonance energy transfer (smFRET) has emerged as a pivotal technique for probing biomolecular dynamics over time at nanometer scales. Quantitative analyses of smFRET time traces remain challenging due to confounding factors such as low signal-to-noise ratios, photophysical effects such as bleaching and blinking, and the complexity of modeling the underlying biomolecular states and kinetics. The dynamic distance information shaping the smFRET trace powerfully uncovers even transient conformational changes in single biomolecules both at or far from equilibrium, relying on trace idealization to identify specific interconverting states.
View Article and Find Full Text PDFStructure switching aptamer enhance sensitivity and specificity of photonic crystal-based sensors for RSV-G protein detection.
Biosens Bioelectron
January 2025
Beijing Institute of Technology School of Chemistry and Chemical Engineering, China. Electronic address:
Photonic crystal-based aptasensors for viral proteins detection offer the advantage of producing visible readouts. However, they usually suffer from limited sensitivity and high non-specific background noise. A significant contributing factor to these issues is the use of fixed-conformation aptamers in these sensors.
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