Fretting about FRET: Correlation between κ and R

Electronic excitation energy transfer (EET) is described theoretically for the chromophore complex P(4) formed by a butanediamine dendrimer to which four pheophorbide-a molecules are covalently linked. To achieve a description with atomic resolution, and to account for the effect of an ethanol solvent, a mixed quantum-classical methodology is utilized. Room-temperature molecular dynamics simulations are used to describe the nuclear dynamics, and EET is accounted for in utilizing a mixed quantum-classical formulation of the transition rates. Therefore, the full quantum expression of the EET rates is given and the change to a mixed quantum-classical version is briefly explained. The description results in the calculation of transition rates which coincide rather satisfactory with available experimental data on P(4). It is also shown that different assumptions of classical Förster theory are not valid for P(4). The temporal behavior of EET deduced from the rate equations is confronted with that following from the solution of the time-dependent Schrödinger equation entering the mixed quantum-classical description of EET. From this we can conclude that EET in flexible chromophore complexes such as P(4) can be rather satisfactory estimated by single transition rates. A correct description, however, is only achievable by using a sufficiently large set of rates that correspond to the various possible equilibrium configurations of the complex.

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“…(19)] cannot be applied to the EET in P 4 (we also refer to similar discussions in ref. [43][44][45]). …”

Section: Simulations and Dft/td-dft Calculationsmentioning

confidence: 99%

A Mixed Quantum–Classical Description of Excitation Energy Transfer in Supramolecular Complexes: Förster Theory and beyond

et al. 2011

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“…The orientation dependence is likely to be most significant where the fluorophores are constrained (5)(6)(7)(8)(9). This has been demonstrated experimentally by using a fluorophore that was terminally affixed to duplex DNA by two points of covalent attachment (10), thereby seriously constraining its motion.…”

mentioning

confidence: 99%

Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids

Iqbal

Arslan

Okumuş

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

318

369

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We have found that the efficiency of fluorescence resonance energy transfer between Cy3 and Cy5 terminally attached to the 5 ends of a DNA duplex is significantly affected by the relative orientation of the two fluorophores. The cyanine fluorophores are predominantly stacked on the ends of the helix in the manner of an additional base pair, and thus their relative orientation depends on the length of the helix. Observed fluorescence resonance energy transfer (FRET) efficiency depends on the length of the helix, as well as its helical periodicity. By changing the helical geometry from B form double-stranded DNA to A form hybrid RNA/DNA, a marked phase shift occurs in the modulation of FRET efficiency with helix length. Both curves are well explained by the standard geometry of B and A form helices. The observed modulation for both polymers is less than that calculated for a fully rigid attachment of the fluorophores. However, a model involving lateral mobility of the fluorophores on the ends of the helix explains the observed experimental data. This has been further modified to take account of a minor fraction of unstacked fluorophore observed by fluorescent lifetime measurements. Our data unequivocally establish that Fö rster transfer obeys the orientation dependence as expected for a dipole-dipole interaction.cyanine fluorophores ͉ FRET ͉ kappa squared ͉ single-molecule FRET F luorescence resonance energy transfer (FRET) has become widely used to report on distances over the macromolecular scale in biology (1), reviewed in refs. 2-4. The method is highly sensitive, and consequently has been widely exploited in singlemolecule experiments in biological systems. Energy transfer results from dipolar coupling between the transition moments of two fluorophores, and the efficiency of the process (E FRET ) depends on the separation between the donor and acceptor fluorophores, raised to the sixth power. Although such data are frequently interpreted on the assumption of a simple relationship between E FRET and distance, E FRET should also depend on the relative orientation of the transition dipole vectors.The orientation dependence is likely to be most significant where the fluorophores are constrained (5-9). This has been demonstrated experimentally by using a fluorophore that was terminally affixed to duplex DNA by two points of covalent attachment (10), thereby seriously constraining its motion. This situation is not typical of most FRET studies involving nucleic acids. Fluorophores are normally tethered by a single point of attachment, and in theory would be significantly less constrained. But if the fluorophores adopt a rigid manner of attachment to the helix, an orientational dependence could be observed.Cy3 and Cy5 are a commonly used fluorophore pair, especially in single-molecule experiments. Our earlier NMR studies have shown that when these are attached to the 5Ј termini of duplex DNA via a 3-carbon linker to the 5Ј-phosphate they are predominantly stacked onto the ends of the helix in the manner of an additio...

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“…This is referred to as the "isotropic averaging regime," in which case a constant value of κ 2 = 2/3 can be used. 25 The assumption of κ 2 = 2/3 has been questioned in several studies 12,[18][19][20] but can be tested experimentally, e.g., by measuring time-dependent fluorescence anisotropy decays. 14 …”

Section: A Förster Resonance Energy Transfermentioning

confidence: 99%

“…17 Molecular dynamics simulations also allow testing assumptions such as approximating the mutual dye-dye orientation factor κ 2 with 2/3, which is questioned in several studies, 18,19 in particular, for low linker flexibilities. 20 Many simulation protocols have computationally prohibitive demands to reach sufficiently long simulation times for accurate calculations of experimentally accessible properties. 21 In particular, it is challenging to account for slow or large-scale conformational transitions, structurally diverse ensembles such as unfolded proteins, very large systems, or intrinsically disordered proteins.…”

Section: Introductionmentioning

confidence: 99%

Simulation of FRET dyes allows quantitative comparison against experimental data

Reinartz

Sinner

Nettels

et al. 2018

The Journal of Chemical Physics

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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.

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Fretting about FRET: Correlation between κ and R

Cited by 101 publications

References 73 publications

A Mixed Quantum–Classical Description of Excitation Energy Transfer in Supramolecular Complexes: Förster Theory and beyond

A Mixed Quantum–Classical Description of Excitation Energy Transfer in Supramolecular Complexes: Förster Theory and beyond

Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids

Simulation of FRET dyes allows quantitative comparison against experimental data

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