Single-molecule dynamics of semiflexible Gaussian chains

Abstract

Theory of linear viscoelasticity of semiflexible rods in dilute solutionA semiflexible Gaussian chain model is used to determine the statistics and correlations of single-molecule fluorescence resonant energy transfer ͑FRET͒ experiments on biological polymers. The model incorporates a persistence length in a Rouse chain and describes single-chain dynamics with normal modes. The hydrodynamic interaction is included in the dynamics of the semiflexible Gaussian chain on the preaveraging level. The distribution functions of the fluorescence lifetime and the FRET efficiency provide direct measures of the chain stiffness, and their correlation functions probe the intrachain dynamics at the single-molecule level. When measured with finite time resolution, the instantaneous diffusion coefficient for FRET is much smaller in the collapsed structure than in the coiled structure, and the variation has a quadratic dependence on the donoracceptor distance. In the fast reaction limit, single-molecule FRET lifetime measurements can be used to map out the equilibrium distribution function of interfluorophore distance. As an example of microrheology, the intrinsic viscoelasticity can be extracted from single-molecule tracking of the Brownian dynamics of polymers in solution.

Measuring distances within unfolded biopolymers using fluorescence resonance energy transfer: The effect of polymer chain dynamics on the observed fluorescence resonance energy transfer efficiency

“…͑3͒ cannot be generally evaluated analytically except in certain asymptotic limits. 5,13 To examine how the observed FRET efficiency depends on the donor lifetime and on the polymer dynamics we thus instead resort to simulations. We have used Langevin dynamics to simulate FRET kinetics for donor-acceptor pairs located at the ends of polypeptide chains in water.…”

“…That is, in practice the instantaneous values of E ͑and accordingly R͒ cannot be measured because the donoracceptor distance fluctuates on a time scale that is much faster than the time resolution of the experiment. [1][2][3] It is commonly assumed that the observed value of the FRET efficiency is equal to the ensemble average value of E, [3][4][5][6][7][8][9][10][11][12] …”

Theoretical analysis and computer simulation of fluorescence lifetime measurements. I. Kinetic regimes and experimental time scales

“…III, we calculate the full kinetics of the fluorescence quenching in a semiflexible Gaussian chain with a normal mode decomposition scheme. 21 Our calculations demonstrate that the first-a͒ Author to whom correspondence should be addressed. Electronic mail: jianshu@mit.edu order inhomogeneous cumulant expansion and the WF approximation provide lower and upper bounds for the real survival probability, respectively.…”

Comparison of Different Fluorescence Fluctuation Methods for their Use in FRET Assays: Monitoring a Protease Reaction

“…(5)), the statistical precision is given by the relative standard deviation of a single measurement, the accuracy denotes the standard deviation from one measurement to another (i.e., sample-to-sample variations) as determined by the average relative deviation of the measurement points from the exponential fit, the dynamic range marks the difference between the data recorded at incubation time t = 0 min and at incubation time t = 60 min, and the Z'-factor is determined according to Eq. (20). The synonyms given are: "un" and "n", unnormalized and normalized correlation data.…”

“…Furthermore, the improvements in the field of confocal microscopy enabled the direct observation of single fluorescing molecules. Due to their substantial sensitivity and selectivity, biochemical applications increasingly apply FRET-based single-molecule experiments [6,7,[18][19][20][21][22][23][24], ultimately refined in the simultaneous detection and analysis of multiple fluorescence parameters [25]. Alternating FRET and direct laser excitation of the acceptor introduces further accuracy and variability to the analysis of single-molecule FRET measurements.…”