Simultaneous time and frequency resolved fluorescence microscopy of single molecules.

Single molecule fluorophores were studied for the first time with a new confocal fluorescence microscope that allows the wavelength and emission time to be simultaneously measured with single molecule sensitivity. In this apparatus, the photons collected from the sample are imaged through a dispersive optical system onto a time and position sensitive detector. This detector records the wavelength and emission time of each detected photon relative to an excitation laser pulse. A histogram of many events for any selected spatial region or time interval can generate a full fluorescence spectrum and correlated decay plot for the given selection. At the single molecule level, this approach makes entirely new types of temporal and spectral correlation spectroscopy of possible. This report presents the results of simultaneous time- and frequency-resolved fluorescence measurements of single rhodamine 6G (R6G), tetramethylrhodamine (TMR), and Cy3 embedded in thin films of polymethylmethacrylate (PMMA)

Characterization of fluorescein arsenical hairpin (FIAsH) as a probe for single-molecule fluorescence spectroscopy

Sherpa Romeo green journal. Open access article. Creative Commons Attribution 4.0 International License (CC BY 4.0) appliesIn recent years, new labelling strategies have been developed that involve the genetic insertion of small amino-acid sequences for specific attachment of small organic fluorophores. Here, we focus on the tetracysteine FCM motif (FLNCCPGCCMEP), which binds to fluorescein arsenical hairpin (FlAsH), and the ybbR motif (TVLDSLEFIASKLA) which binds fluorophores conjugated to Coenzyme A (CoA) via a phosphoryl transfer reaction. We designed a peptide containing both motifs for orthogonal labelling with FlAsH and Alexa647 (AF647). Molecular dynamics simulations showed that both motifs remain solvent-accessible for labelling reactions. Fluorescence spectra, correlation spectroscopy and anisotropy decay were used to characterize labelling and to obtain photophysical parameters of free and peptide-bound FlAsH. The data demonstrates that FlAsH is a viable probe for single-molecule studies. Single-molecule imaging confirmed dual labeling of the peptide with FlAsH and AF647. Multiparameter single-molecule Förster Resonance Energy Transfer (smFRET) measurements were performed on freely diffusing peptides in solution. The smFRET histogram showed different peaks corresponding to different backbone and dye orientations, in agreement with the molecular dynamics simulations. The tandem of fluorophores and the labelling strategy described here are a promising alternative to bulky fusion fluorescent proteins for smFRET and single-molecule tracking studies of membrane proteins.Ye

Advanced microscopy :time-resolved multi-spectral imaging of single biomolecules.

Over the past few years we have developed the ability to acquire images through a confocal microscope that contain, for each pixel, the simultaneous fluorescence lifetime and spectra of multiple fluorophores within that pixel. We have demonstrated that our system has the sensitivity to make these measurements on single molecules. The spectra and lifetimes of fluorophores bound to complex molecules contain a wealth of information on the conformational dynamics and local chemical environments of the molecules. However, the detailed record of spectral and temporal information our system provides from fluorophores in single molecules has not been previously available. Therefore, we have studied several fluorophores and simple fluorophore-molecule systems that are representative of the use of fluorophores in biological systems. Experiments include studies of a simple fluorescence resonance energy transfer (FRET) system, green fluorescent probe variants and quantum dots. This work is intended to provide a basis for understanding how fluorophores report on the chemistry of more complex biological molecules

An Adequate Account of Excluded Volume Is Necessary To Infer Compactness and Asphericity of Disordered Proteins by Förster Resonance Energy Transfer

Single-molecule Förster resonance energy transfer (smFRET) is an important tool for studying disordered proteins. It is commonly utilized to infer structural properties of conformational ensembles by matching experimental average energy transfer ⟨<i>E</i>⟩_exp with simulated ⟨<i>E</i>⟩_sim computed from the distribution of end-to-end distances in polymer models. Toward delineating the physical basis of such interpretative approaches, we conduct extensive sampling of coarse-grained protein chains with excluded volume to determine the distribution of end-to-end distances conditioned upon given values of radius of gyration <i>R</i>_g and asphericity <i>A</i>. Accordingly, we infer the most probable <i>R</i>_g and <i>A</i> of a protein disordered state by seeking the best fit between ⟨<i>E</i>⟩_exp and ⟨<i>E</i>⟩_sim among various (<i>R</i>_g,<i>A</i>) subensembles. Application of our method to residues 1–90 of the intrinsically disordered cyclin-dependent kinase (Cdk) inhibitor Sic1 results in inferred ensembles with more compact conformations than those inferred by conventional procedures that presume either a Gaussian chain model or the mean-field Sanchez polymer theory. The Sic1 compactness we infer is in good agreement with small-angle X-ray scattering data for <i>R</i>_g and NMR measurement of hydrodynamic radius <i>R</i>_h. In contrast, owing to neglect or underappreciation of excluded volume, conventional procedures can significantly overestimate the probabilities of short end-to-end distances, leading to unphysically large smFRET-inferred <i>R</i>_g at high [GdmCl]. It follows that smFRET Sic1 data are incompatible with the presumed homogeneously expanded or contracted conformational ensembles in conventional procedures but are consistent with heterogeneous ensembles allowed by our subensemble method of inference. General ramifications of these findings for smFRET data interpretation are discussed