Real-Time Detection of Amplification Products Through Fluorescence Quenching or Energy Transfer

Huang, Shihai

doi:10.1007/978-1-4614-3970-7_24

Cited by 1 publication

(2 citation statements)

References 87 publications

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“…However, the dye is reported to have absorption and emission maxima close to its precursor . The same holds true for Cy5 compared to its nonsulfonated precursor Quasar 670 . Therefore, we assume the simplifications to be justified for our purposes.…”

Section: Theoretical Methodsmentioning

confidence: 99%

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Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ² Values

Spiegel¹,

Kleinschmidt²,

Gohlke³

et al. 2016

J. Phys. Chem. B

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Förster resonance energy transfer (FRET) is analyzed in terms of distance- and orientation-dependent interactions between the transition dipole moments of the involved donor and acceptor molecules. However, the ideal dipole approximation (IDA) is known to fail at short donor-acceptor distances. In this work, we model FRET in a Cy5- and Alexa Fluor 488-labeled double-stranded RNA by means of combined molecular dynamics (MD) simulations and quantum-chemical calculations involving the IDA as well as the more sophisticated monomer transition density (MTD) approach. To this end, the relaxed ground-state geometries of the dyes were fitted to the MD-based structures. Although substantial deviations between IDA and MTD results can be observed for individual snapshots, the statistical impact of the failure on the FRET rates is negligible in the chosen examples. Our results clearly demonstrate that the IDA-based Förster model can still be applied to systems with small donor-acceptor distances, provided that the dyes are not trapped in arrangements with a high IDA failure and that the distribution of the relative transition dipole orientations is fairly isotropic.

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Section: Theoretical Methodsmentioning

confidence: 99%

“…42 The same holds true for Cy5 compared to its nonsulfonated precursor Quasar 670. 43 Therefore, we assume the simplifications to be justified for our purposes. Furthermore, we performed test calculations on Alexa Fluor 488 and Cy5 including the sulfonate substituents with and without explicit solvation.…”

Section: = + +mentioning

confidence: 99%

Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ² Values

Spiegel¹,

Kleinschmidt²,

Gohlke³

et al. 2016

J. Phys. Chem. B

View full text Add to dashboard Cite

show abstract

Real-Time Detection of Amplification Products Through Fluorescence Quenching or Energy Transfer

Cited by 1 publication

References 87 publications

Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ² Values

Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ² Values

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Real-Time Detection of Amplification Products Through Fluorescence Quenching or Energy Transfer

Cited by 1 publication

References 87 publications

Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ2 Values

Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ2 Values

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Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ² Values

Failure of the IDA in FRET Systems at Close Inter-Dye Distances Is Moderated by Frequent Low κ² Values