Nonexponential kinetics of a single tRNA ^Phe molecule under physiological conditions

Abstract

The f luorescence decay functions of individual, specifically labeled tRNA Phe molecules exhibit nonexponential character as a result of conformational dynamics occurring during the measurement on a single molecule. tRNA Phe conformational states that interchange much more slowly are evidenced by the distribution of lifetimes observed for many individual molecules. A structural model for the nonexponential decay indicates that the tRNA Phe -probe adduct f luctuates between two states, one of which provides conditions that quench the probe f luorescence.

Optical Studies of Single Molecules at Room Temperature

“…In a more recent work, Rigler and coworkers were able to directly observe the conformational motion in real time by recording an emission intensity trajectory (66). (67). The specifically labeled single TMR molecules also exhibit double exponential decays ( Figure 12A), corresponding to two conformational states interchanging during the course of the measurements.…”

Statistical Analyses and Theoretical Models of Single-Molecule Enzymatic Dynamics

“…Prompted by the room-temperature observations of double exponential fluorescence decays of single dye molecules in DNA complexes, 11, 12 Geva and Skinner recast a two-state jump model in terms of population distributions as a function of data collection times. 13 Similar to "motional narrowing" in molecular spectroscopy, 14 this approach allowed the extraction of the time scale of conformational transitions of the systems.…”

“…8 The underlying dynamics of that system is tunneling of two-level systems, which was described by a two-state jump model, 6-7 and analyzed with autocorrelation functions of the transition frequency. Silbey and co-workers 9 and Klafter and co-workers 10 have also pursued this stochastic approach to two-level systems.Prompted by the room-temperature observations of double exponential fluorescence decays of single dye molecules in DNA complexes, 11,12 Geva and Skinner recast a two-state jump model in terms of population distributions as a function of data collection times. 13 Similar to "motional narrowing" in molecular spectroscopy, 14 this approach allowed the extraction of the time scale of conformational transitions of the systems.…”

Markov Chain Monte Carlo in the Analysis of Single-Molecule Experimental Data

“…In the hairpin's close state the quenching is strong, and thus very few photons from the donors are detected; in the open state the quenching is weak, and many photons from the donor are detected. The open/close of the DNA hairpin can hence be inferred indirectly from the detected photon arrivals ( [10], [7], [4]). …”