14.3 Single-molecule fluorescence spectroscopy

Single-molecule fluorescence spectroscopy is a game-changer in biophysics. It lets us peek at individual molecules, revealing their unique behaviors and interactions. This technique uses super-sensitive detectors to catch the faint glow of single fluorescent molecules.

From protein folding to enzyme activity, this method uncovers hidden details in biological processes. It's like having a microscopic spotlight on the nanoscale world, showing us things we'd miss with traditional bulk measurements.

Principles of single-molecule fluorescence

Fundamentals of single-molecule fluorescence spectroscopy

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• Single-molecule fluorescence spectroscopy detects the fluorescence signal from individual molecules providing information on their behavior, dynamics, and interactions at the molecular level
• Fluorescence occurs when a fluorophore absorbs a photon, transitions to an excited electronic state, and emits a photon of longer wavelength as it relaxes back to the ground state
• Single-molecule fluorescence spectroscopy requires sensitive detectors, such as avalanche photodiodes (APDs) or electron-multiplying charge-coupled devices (EMCCDs), to detect the weak fluorescence signal from individual molecules

Techniques used in single-molecule fluorescence spectroscopy

• Total internal reflection fluorescence (TIRF) microscopy is a common technique used in single-molecule fluorescence spectroscopy which selectively excites fluorophores near a glass-water interface using an evanescent wave
• Confocal microscopy is another technique used in single-molecule fluorescence spectroscopy which uses a pinhole to reject out-of-focus light and achieve high spatial resolution
• Fluorescence resonance energy transfer (FRET) is a technique used in single-molecule fluorescence spectroscopy to measure the distance between two fluorophores and study protein conformational changes and interactions
• Single-molecule fluorescence spectroscopy can be combined with other techniques such as optical tweezers or atomic force microscopy to manipulate and study individual molecules

Applications of single-molecule fluorescence

Studying protein folding and dynamics

• Single-molecule fluorescence spectroscopy can be used to study protein folding and unfolding dynamics by monitoring the fluorescence of individual protein molecules over time
• Single-molecule FRET can be used to measure the conformational changes of proteins, such as the opening and closing of ion channels (potassium channels) or the movement of motor proteins (kinesin)
• Single-molecule fluorescence can be used to study the diffusion and transport of proteins in living cells, providing insights into cellular processes such as signal transduction (G protein-coupled receptors) and membrane trafficking (vesicle fusion)

Investigating protein-protein interactions and enzyme activity

• Single-molecule fluorescence spectroscopy can be used to study protein-protein interactions, such as the formation of protein complexes (ribosome assembly) or the binding of ligands to receptors (neurotransmitter binding to receptors)
• Single-molecule fluorescence spectroscopy can be used to study the activity of enzymes at the single-molecule level, revealing the kinetics and mechanisms of enzymatic reactions (DNA polymerase activity during replication)
• Single-molecule fluorescence can be used to investigate the stoichiometry and dynamics of multi-protein complexes, such as the transcription machinery (RNA polymerase and transcription factors) or the DNA repair machinery (DNA repair enzymes)

Data analysis for single-molecule fluorescence

Analyzing fluorescence intensity traces

• Single-molecule fluorescence data typically consists of fluorescence intensity traces over time, which can be analyzed to extract biophysical parameters such as kinetic rates and equilibrium constants
• Hidden Markov models (HMMs) can be used to analyze single-molecule fluorescence data and identify distinct states and transitions between them, such as the open and closed states of an ion channel
• Fluorescence correlation spectroscopy (FCS) can be used to analyze the fluctuations in fluorescence intensity over time and extract parameters such as diffusion coefficients and concentrations

Statistical methods for parameter estimation

• Single-molecule FRET data can be analyzed to determine the distance between two fluorophores and the conformational changes of proteins over time
• Statistical methods, such as maximum likelihood estimation and Bayesian inference, can be used to fit single-molecule fluorescence data to mathematical models and extract biophysical parameters with confidence intervals
• Bootstrapping and other resampling techniques can be used to assess the robustness and uncertainty of the estimated parameters from single-molecule fluorescence data

Single-molecule vs ensemble fluorescence

Advantages of single-molecule fluorescence spectroscopy

• Single-molecule fluorescence spectroscopy can reveal heterogeneity and rare events that are masked in ensemble measurements, providing a more detailed understanding of molecular behavior and interactions
• Single-molecule fluorescence spectroscopy is more suitable for measuring slow kinetics and small-scale conformational changes compared to ensemble techniques
• Single-molecule fluorescence spectroscopy allows for the direct observation of individual molecular events, such as the stepping of motor proteins (myosin) or the opening and closing of ion channels (ligand-gated ion channels)

Complementary nature of single-molecule and ensemble techniques

• Ensemble fluorescence techniques, such as bulk fluorescence spectroscopy, measure the average behavior of a large number of molecules, while single-molecule fluorescence spectroscopy measures the behavior of individual molecules
• Ensemble fluorescence techniques typically have higher signal-to-noise ratios and are more suitable for measuring fast kinetics and large-scale conformational changes, while single-molecule fluorescence spectroscopy is more suitable for measuring slow kinetics and small-scale conformational changes
• Single-molecule fluorescence spectroscopy requires more advanced instrumentation and data analysis techniques compared to ensemble fluorescence techniques, but provides unique insights into molecular behavior and interactions
• Ensemble fluorescence techniques and single-molecule fluorescence spectroscopy can be used in combination to provide a comprehensive understanding of biological systems at different scales and levels of detail (protein folding studied by both ensemble and single-molecule FRET)