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. Author manuscript; available in PMC: 2014 Apr 25.
Published in final edited form as: J Phys Chem B. 2012 May 16;117(16):4183–4196. doi: 10.1021/jp3018259

Figure 3.

Figure 3

Conformational dynamics of TAR-cTAR mismatch2 DNA duplexes in 2μM NC and in buffer. (A) SM-FRET trajectories (obtained in the image scanning mode) of 158 molecules found in a 30 μm × 30 μm region and the corresponding molecularly-averaged FRET trajectory. The dual dye-labeled TAR-cTAR mismatch2 DNA duplexes were immobilized on a coverslip. During time periods I and II, 2μM NC and buffer were flowed into the reaction chamber, respectively. (B) FRET histograms of all spectroscopic occurrences (upper panel) and time-averaged FRET (lower panel) of the DNA duplex molecules in 2μM NC and buffer. Donor, acceptor and the corresponding FRET trajectory (obtained in the individual trajectory mode) collected on one representative molecule in 2μM NC (C) and in buffer (D) with a bin time of 10 ms. (E) The ensemble FRET histograms obtained from FRET trajectories of 72 molecules in 2μM NC with a bin time τB of 2 ms, 10 ms, 50 ms, and 250 ms. (F) The ensemble FRET autocorrelation obtained from FRET trajectories of the 72 molecules with a time resolution of 1 ms. (G) The ensemble FRET histograms obtained from FRET trajectories of 60 molecules in buffer with a bin time τB of 2 ms, 10 ms, 50 ms, and 250 ms. (H) The ensemble FRET autocorrelation obtained from FRET trajectories of the 60 molecules with a time resolution of 1 ms.