With recent growth in the use of fluorescence-detected resonance energy transfer (FRET), it is being applied to complex systems in modern and diverse ways where it is not always clear that the common approximations required for analysis are applicable. For instance, the ideal dipole approximation (IDA), which is implicit in the Forster equation, is known to break down when molecules get ‘‘too close’’ to each other. Yet, no clear definition exists of what is meant by ‘‘too close’’. Here we examine several common fluorescent probe molecules to determine boundaries for use of the IDA. We compare the Coulombic coupling determined essentially exactly with a linear response approach with the IDA coupling to find the distance regimes over which the IDA begins to fail. We find that the IDA performs well down to roughly 20 A separation, provided the molecules sample an isotropic set of relative orientations. However, if molecular motions are restricted, the IDA performs poorly at separations beyond 50 A. Thus, isotropic probe motions help mask poor performance of the IDA through cancellation of error. Therefore, if fluorescent probe motions are restricted, FRET practitioners should be concerned with not only the well-known k2 approximation, but also possible failure of the IDA.
Fretting about FRET: Failure of the Ideal Dipole Approximation
MENNUCCI, BENEDETTA
2009-01-01
Abstract
With recent growth in the use of fluorescence-detected resonance energy transfer (FRET), it is being applied to complex systems in modern and diverse ways where it is not always clear that the common approximations required for analysis are applicable. For instance, the ideal dipole approximation (IDA), which is implicit in the Forster equation, is known to break down when molecules get ‘‘too close’’ to each other. Yet, no clear definition exists of what is meant by ‘‘too close’’. Here we examine several common fluorescent probe molecules to determine boundaries for use of the IDA. We compare the Coulombic coupling determined essentially exactly with a linear response approach with the IDA coupling to find the distance regimes over which the IDA begins to fail. We find that the IDA performs well down to roughly 20 A separation, provided the molecules sample an isotropic set of relative orientations. However, if molecular motions are restricted, the IDA performs poorly at separations beyond 50 A. Thus, isotropic probe motions help mask poor performance of the IDA through cancellation of error. Therefore, if fluorescent probe motions are restricted, FRET practitioners should be concerned with not only the well-known k2 approximation, but also possible failure of the IDA.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
