Simulative and Experimental Characterization of a pH-Dependent Clamp-like DNA Triple-Helix Nanoswitch Federico Iacovelli Andrea Idili Alessandro Benincasa Davide Mariottini Alessio Ottaviani Mattia Falconi Francesco Ricci Alessandro Desideri 10.1021/jacs.6b11470.s001 https://acs.figshare.com/articles/journal_contribution/Simulative_and_Experimental_Characterization_of_a_pH-Dependent_Clamp-like_DNA_Triple-Helix_Nanoswitch/4829137 Here we couple experimental and simulative techniques to characterize the structural/dynamical behavior of a pH-triggered switching mechanism based on the formation of a parallel DNA triple helix. Fluorescent data demonstrate the ability of this structure to reversibly switch between two states upon pH changes. Two accelerated, half microsecond, MD simulations of the system having protonated or unprotonated cytosines, mimicking the pH 5.0 and 8.0 conditions, highlight the importance of the Hoogsteen interactions in stabilizing the system, finely depicting the time-dependent disruption of the hydrogen bond network. Urea-unfolding experiments and MM/GBSA calculations converge in indicating a stabilization energy at pH 5.0, 2-fold higher than that observed at pH 8.0. These results validate the pH-controlled behavior of the designed structure and suggest that simulative approaches can be successfully coupled with experimental data to characterize responsive DNA-based nanodevices. 2017-04-02 00:00:00 Experimental Characterization pH 8.0. unprotonated cytosines half microsecond pH 5.0 DNA-based nanodevices reversibly switch pH-Dependent Clamp-like DNA Triple-Helix Nanoswitch Fluorescent data simulative approaches stabilization energy pH-controlled behavior time-dependent disruption hydrogen bond network Urea-unfolding experiments Hoogsteen interactions MM MD simulations simulative techniques pH changes 8.0 conditions