The unique properties of the photoswitchable protein Dreiklang are attributed to a reversible hydration/dehydration reaction at the imidazolinone ring of the chromophore. Recovery of the fluorescent state, which is associated with a chemical reaction of the chromophore's dehydration, is an important part of the photocycle of this protein. Here we characterize the fluorescent (ON) and nonfluorescent (OFF) states of Dreiklang and simulate the thermal recovery reaction OFF → ON using computational approaches. By using molecular modeling methods including the quantum mechanics/molecular mechanics (QM/MM) technique, we characterize the structures and spectra of the ON- and OFF-states. The results are consistent with available experimental data. The computed reaction profile explains the observed recovery reaction and clarifies the mechanism of chemical transformations in the chromophore-containing pocket in Dreiklang.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1021/acs.jpcb.9b06988 | DOI Listing |
J Fluoresc
January 2025
College of Chemistry and Chemical Engineering, Donghua University, Shanghai, 201620, China.
Construction of single probes for simultaneous detection of common trivalent metal ions has attracted much attention due to higher efficiency in analysis and cost. A naphthalimide-based fluorescent probe K1 was synthesized for selective detection of Al, Cr and Fe ions. Fluorescence emission intensity at 534 nm of probe K1 in DMSO/HO (9:1, v/v) was significantly enhanced upon addition of Al, Cr and Fe ions while addition of other metal ions (Li, Na, K, Ag, Cu, Fe, Zn, Co, Ni, Mn, Sr, Hg, Ca, Mg, Ce, Bi and Au) did not bring about substantial change in fluorescence emission.
View Article and Find Full Text PDFACS Nano
January 2025
Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
Controlling the light emitted by individual molecules is instrumental to a number of advanced nanotechnologies ranging from super-resolution bioimaging and molecular sensing to quantum nanophotonics. Molecular emission can be tailored by modifying the local photonic environment, for example, by precisely placing a single molecule inside a plasmonic nanocavity with the help of DNA origami. Here, using this scalable approach, we show that commercial fluorophores may experience giant Purcell factors and Lamb shifts, reaching values on par with those recently reported in scanning tip experiments.
View Article and Find Full Text PDFNucleic Acids Res
January 2025
Department of Physics, 845 W Taylor St, University of Illinois Chicago, Chicago, IL 60607, USA.
Altered DNA dynamics at lesion sites are implicated in how DNA repair proteins sense damage within genomic DNA. Using laser temperature-jump (T-jump) spectroscopy combined with cytosine-analog Förster Resonance Energy Transfer (FRET) probes that sense local DNA conformations, we measured the intrinsic dynamics of DNA containing 3 base-pair mismatches recognized in vitro by Rad4 (yeast ortholog of XPC). Rad4/XPC recognizes diverse lesions from environmental mutagens and initiates nucleotide excision repair.
View Article and Find Full Text PDFSmall Methods
January 2025
Department of Laboratory Medicine, Guangdong Provincial Key Laboratory of Precision Medical Diagnostics, Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, P. R. China.
Antimicrobial resistance (AMR) has emerged as a global challenge in treating bacterial infections, creating an urgent need for broad-spectrum antimicrobial agents that can effectively combat multidrug-resistant (MDR) bacteria. Despite advancements in novel antimicrobial agents, many fail to comprehensively cover common resistant bacterial strains or undergo rigorous multi-center validation. Herein, a cationic AIE-active photosensitizers are developed, ITPM, derived from a triphenylamine-pyridine backbone to address the MDR challenge.
View Article and Find Full Text PDFBiophys J
January 2025
Department of Physics, Northeastern University, Boston, MA, 02115, USA. Electronic address:
Binuclear ruthenium complexes have been investigated for potential DNA-targeted therapeutic and diagnostic applications. Studies of DNA threading intercalation, in which DNA base pairs must be broken for intercalation, have revealed means of optimizing a model binuclear ruthenium complex to obtain reversible DNA-ligand assemblies with the desired properties of high affinity and slow kinetics. Here, we used single-molecule force spectroscopy to study a binuclear ruthenium complex with a longer semi-rigid linker relative to the model complex.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!