Förster’s resonance excitation transfer theory: not just a formula

Knox, Robert

doi:10.1117/1.jbo.17.1.011003

Cited by 36 publications

(41 citation statements)

References 32 publications

(22 reference statements)

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“…3C) suggested a much smaller overlap with the near-perpendicular reciprocal orientations of dyes suggesting lower probability of close inter-dye interactions. This dye orientation also suggests near-perpendicular orientation of transition dipole moments of the cyanine donor and acceptor at the equilibrium that results in low values of orienation κ 2 factor 26 corresponding to near-zero FRET efficiency 27 (Fig. 3C).…”

Section: Resultsmentioning

confidence: 85%

The three-dimensional context of a double helix determines the fluorescence of the internucleoside-tethered pair of fluorophores

Metelev¹,

Zhang²,

Tabatadze³

et al. 2013

Mol. BioSyst.

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We report a general phenomenon of the formation of either a fluorescent, or of an entirely quenched oligodeoxynucleotide (ODN) duplex system by hybridizing pairs of complementary ODNs with identical chemical composition. The ODNs carried internucleoside tether-linked cyanines, where the cyanines were chosen to form a Förster's resonance energy transfer (FRET) doner/acceptor pair. The fluorescent and quenched ODN duplex systems differed only in that the cyanines linked to the respective ODNs s were linked either closer to the 5′-, or closer to the 3′-ends of the molecule. In either case however, the dyes were separated by an identical number (7 or 8) of base pairs. Characterization by molecular modeling and energy minimization using a conformational search algorithm in a molecular operating environment (MOE) revealed that linking of the dyes closer to the 5′-ends resulted in their reciprocal orientation across the major groove which allowed a closely interacting dye pair to be formed. This overlap between the donor and acceptor dye molecules resulted in changes of absorbance spectra consistent with the formation of H-aggregates. Conversly, dyes linked closer to 3′-ends exhibited emissive FRET and formed a pair of dyes that interacted with the DNA helix only weakly. Induced CD spectra analysis suggested that interaction with the double helix was weaker than in the case of the closely interacting cyanine dye pair. Linking the dyes such that the base pair separation was 10 or 0 favored energy transfer with subsequent acceptor emission. Our results suggest that when interpreting FRET measurements from nucleic acids, the use of a “spectroscopic ruler” principle which takes into account the 3D helical context of the double helix will allow more accurate interpretation of fluorescence emission.

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Section: Resultsmentioning

confidence: 85%

The three-dimensional context of a double helix determines the fluorescence of the internucleoside-tethered pair of fluorophores

Metelev¹,

Zhang²,

Tabatadze³

et al. 2013

Mol. BioSyst.

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“…FRET between fluorophores requires that (1) the emission spectrum of the donor must overlap the excitation spectrum of the acceptor; (2) the transition dipoles of the two molecules be in a favorable (i.e, nonorthogonal) orientation; and (3) the two molecules be in very close spatial proximity (Foerster, 1946; Knox, 2012; Pietraszewska-Bogiel & Gadella, 2011; Sun et al, 2011). The hallmark of FRET is that when the sample is illuminated at the excitation wavelength of the donor, emission from the acceptor is detected and occurs concomitant with a decrease in the emission of the donor.…”

Section: Protein Preparation and Labelingmentioning

confidence: 99%

“…In this regard, unlike assembly of F-actin from monomeric G-actin, or assembly of microtubules from α-β tubulin dimers, formation of higher-order septin-based structures involves the assembly of a building block that has a very elongated geometry (4 × 32 nm). Given the linear organization and extended shape of septin heterooctamers, the method in fluorescence spectrometry that should be ideal for assessing their interactions is Förster resonance energy transfer (FRET) (Foerster, 1946; Knox, 2012; Pietraszewska-Bogiel & Gadella, 2011; Sun, Wallrabe, Seo, & Periasamy, 2011). To assess protein–protein interaction using FRET, one set of molecules is labeled with a donor fluorophore at a defined position that is not rotationally constrained and mixed with another set of molecules labeled with an acceptor fluorophore, also at a defined position that is not rotationally constrained.…”

Section: Introductionmentioning

confidence: 99%

A FRET-based method for monitoring septin polymerization and binding of septin-associated proteins

Booth

Thorner

2016

Methods in Cell Biology

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Much about septin function has been inferred from in vivo studies using mainly genetic methods, and much of what we know about septin organization has been obtained through examination of static structures in vitro primarily by electron microscopy. Deeper mechanistic insight requires real-time analysis of the dynamics of the assembly of septin-based structures and how other proteins associate with them. We describe here a Förster resonance energy transfer (FRET)-based approach for measuring in vitro the rate and extent of filament formation from septin complexes, binding of other proteins to septin structures, and the apparent affinities of these interactions. FRET is particularly well suited for interrogating protein–protein interactions, especially on a rapid timescale; the spectral change provides an unambiguous indication of whether two elements within the system under study are associating and serves as a molecular-level “ruler” because it is very sensitive to the separation between the donor and acceptor fluorophores over biologically relevant distances (≤ 10 nm). The necessary procedures involve generation of appropriate cysteine-less and single cysteine-containing septin variants, expression and purification of the heterooctameric complexes containing them, efficient labeling of the purified complexes with desired fluorophores, fluorimetric measurement of FRET, and appropriate safeguards and controls in data acquisition and analysis. Our methods can be used to interrogate the effects of buffer conditions, small molecules, and septin-binding proteins on septin filament assembly or stability; determine the effect of alternative septin subunits, mutational alterations, or posttranslational modifications on assembly; and, delineate the location of septin-binding proteins.

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“…InĤ − , the individual anti-correlated motions add up according to Eq. (25) to give rise to the generalized anti-correlated tuning vector…”

Section: Correlated and Anti-correlated Delocalized Vibrationsmentioning

confidence: 99%

“…The presence of vibrational-electronic resonance on the excited state leads to eigenfunctions with rapidly changing electronic character over the whole range of anti-correlated vibrational coordinates. This breakdown of the Born-Oppenheimer approximation 24 over the whole range of vibrational coordinates renders the adiabatic framework, under which electronic energy transfer has been traditionally studied (in both the adiabatic strong coupling and non-adiabatic weak coupling limits), 7,25 invalid. The resulting "unavoidable nested funnel" 22 is different from a conical funnel 26,27 because a finite Coulomb coupling between two pigments does not allow an energetically accessible intersection between their excited state adiabatic potential energy surfaces.…”

Section: Introductionmentioning

confidence: 99%

Electronic energy transfer through non-adiabatic vibrational-electronic resonance. I. Theory for a dimer

Tiwari

Jonas

2017

The Journal of Chemical Physics

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Non-adiabatic vibrational-electronic resonance in the excited electronic states of natural photosynthetic antennas drastically alters the adiabatic framework, in which electronic energy transfer has been conventionally studied, and suggests the possibility of exploiting non-adiabatic dynamics for directed energy transfer. Here, a generalized dimer model incorporates asymmetries between pigments, coupling to the environment, and the doubly excited state relevant for nonlinear spectroscopy. For this generalized dimer model, the vibrational tuning vector that drives energy transfer is derived and connected to decoherence between singly excited states. A correlation vector is connected to decoherence between the ground state and the doubly excited state. Optical decoherence between the ground and singly excited states involves linear combinations of the correlation and tuning vectors. Excitonic coupling modifies the tuning vector. The correlation and tuning vectors are not always orthogonal, and both can be asymmetric under pigment exchange, which affects energy transfer. For equal pigment vibrational frequencies, the nonadiabatic tuning vector becomes an anti-correlated delocalized linear combination of intramolecular vibrations of the two pigments, and the nonadiabatic energy transfer dynamics become separable. With exchange symmetry, the correlation and tuning vectors become delocalized intramolecular vibrations that are symmetric and antisymmetric under pigment exchange. Diabatic criteria for vibrational-excitonic resonance demonstrate that anti-correlated vibrations increase the range and speed of vibronically resonant energy transfer (the Golden Rule rate is a factor of 2 faster). A partial trace analysis shows that vibronic decoherence for a vibrational-excitonic resonance between two excitons is slower than their purely excitonic decoherence.

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Förster’s resonance excitation transfer theory: not just a formula

Cited by 36 publications

References 32 publications

The three-dimensional context of a double helix determines the fluorescence of the internucleoside-tethered pair of fluorophores

The three-dimensional context of a double helix determines the fluorescence of the internucleoside-tethered pair of fluorophores

A FRET-based method for monitoring septin polymerization and binding of septin-associated proteins

Electronic energy transfer through non-adiabatic vibrational-electronic resonance. I. Theory for a dimer

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