Simulation of FRET dyes allows quantitative comparison against experimental data.

Fully understanding biomolecular function requires detailed insight into the systems' structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to such dynamic information yet have to be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles these challenges. While requiring only few parameters, we maintain full protein flexibility and include all heavy atoms of proteins, linkers, and dyes. We are able to sufficiently reduce computational demands to simulate large or heterogeneous structural dynamics and ensembles on slow time scales found in, e.g., protein folding. The simulations allow for calculating FRET efficiencies which quantitatively agree with experimentally determined values. By providing atomically resolved trajectories, this work supports the planning and microscopic interpretation of experiments. Overall, these results highlight how simulations and experiments can complement each other leading to new insights into biomolecular dynamics and function.

Fast Folding Dynamics of an Intermediate State in RNase H Measured by Single-Molecule FRET.

We have studied the folding kinetics of the core intermediate (I) state of RNase H by using a combination of single-molecule FRET (smFRET) and hidden Markov model analysis. To measure fast dynamics in thermal equilibrium as a function of the concentration of the denaturant GdmCl, a special FRET labeled variant, RNase H 60-113, which is sensitive to folding of the protein core, was immobilized on PEGylated surfaces. Conformational transitions between the unfolded (U) state and the I state could be described by a two-state model within our experimental time resolution, with millisecond mean residence times. The I state population was always a minority species in the entire accessible range of denaturant concentrations. By introducing the measured free energy differences between the U and I states as constraints in global fits of the GdmCl dependence of FRET histograms of a differently labeled RNase H variant (RNase H 3-135), we were able to reveal the free energy differences and, thus, population ratios of all three macroscopic state ensembles, U, I and F (folded state) as a function of denaturant concentration.

Intracellular thermometry by using fluorescent gold nanoclusters.

The "gold standard" for nanothermometry: The application of ultrasmall, near-IR-emitting fluorescent gold nanoclusters (AuNCs) for temperature sensing has been explored. AuNC-based fluorescent nanothermometry features excellent thermal sensitivity and simultaneous temperature sensing and imaging in HeLa cells.

Microwave-assisted rapid synthesis of luminescent gold nanoclusters for sensing Hg2+ in living cells using fluorescence imaging.

A microwave-assisted strategy for synthesizing dihydrolipoic acid (DHLA) capped fluorescent gold nanoclusters (AuNCs) has been developed. Irradiation with microwaves during synthesis enhanced the fluorescence quantum yield (QY) of AuNCs by about five-fold and shortened the reaction time from hours to several minutes. The as-synthesized DHLA-AuNCs possessed bright near-infrared fluorescence (QY: 2.9%), ultrasmall hydrodynamic diameter (3.3 nm), good colloidal stability over the physiologically relevant pH range of 5-10 as well as low cytotoxicity toward HeLa cells. Moreover, these DHLA-AuNCs were capable of sensing Hg(2+) through the specific interaction between Hg(2+) and Au(+) on the surface of AuNCs; the limit of detection (LOD) was 0.5 nM. A potential application in imaging intracellular Hg(2+) in HeLa cells was demonstrated by using spinning disc confocal microscopy.

Effect of protein adsorption on the fluorescence of ultrasmall gold nanoclusters.

The interaction of proteins with ultrasmall gold nanoclusters (Au NCs) is investigated. Upon protein association, the fluorescence of Au NCs is significantly enhanced and, concomitantly, their luminescence lifetime is prolonged. The results stress the importance of investigating the behavior of fluorescent metal NCs in complex biological environment for advancing their bio-nanotechnology applications.

One-pot synthesis of near-infrared fluorescent gold clusters for cellular fluorescence lifetime imaging.

A facile strategy to synthesize water-soluble fluorescent gold nanoclusters (Au NCs) stabilized with the bidentate ligand dihydrolipoic acid (DHLA) is reported. The DHLA-capped Au NCs are characterized by UV-vis absorption spectroscopy, fluorescence spectroscopy, transmission electron microscopy, and X-ray photoelectron spectroscopy. The Au NCs possess many attractive features including ultrasmall size, bright near-infrared luminescence, high colloidal stability, and good biocompatibility, making them promising imaging agents for biomedical and cellular imaging applications. Moreover, their long fluorescence lifetime (>100 ns) makes them attractive as labels in fluorescence lifetime imaging (FLIM) applications. As an example, the internalization of Au NCs by live HeLa cells is visualized using the FLIM technique.