A schematic representation of a polymer chain containing monomers. The FRET dyes are assumed to be located at positions and along the chain. The distance between the two monomers fluctuates on a time scale associated with the monomer-dependent reconfiguration time .
The reconfiguration time inferred from the fluctuations of the distance between monomers and strongly depends on the choice of the monomers. It is close to the Rouse time when the monomers are located near the chain ends.
The reconfiguration time extracted from the fluctuations of the distance between monomers 0 and increases if a tail of length is attached to one of the monomers.
Reconfiguration time inferred from FRET efficiency fluctuations as a function of the sequence separation between the donor and the acceptor. Inset: rms donor-acceptor separation as a function of .
The reconfiguration time is determined by the folding/refolding time scales of the helix enclosed by A and B and thus can be much longer than .
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