4.8 Article

Simulative and Experimental Characterization of a pH-Dependent Clamp-like DNA Triple-Helix Nanoswitch

期刊

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
卷 139, 期 15, 页码 5321-5329

出版社

AMER CHEMICAL SOC
DOI: 10.1021/jacs.6b11470

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资金

  1. Associazione Italiana per la Ricerca sul Cancro, AIRC [14420]
  2. European Research Council, ERC [336493]
  3. Italian Ministry of University and Research (Project of National Interest PRIN CTAYSY)
  4. NVIDIA Corporation [K40C]

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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 nano devices.

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