A Surface-Bound, pH-controlled DNA Molecular Motor: Computational and Experimental Characterizations.

Opportunely designed synthetic DNA molecules can spontaneously self-assemble into stable nanosized structures of desired shape, and can then assume a large variety of conformations in response to external stimuli [1]. By controlling both the structure and its conformations, its thus possible to obtain functional dynamic nano-structures capable of performing work in the nanoscale. We describe the computational and experimental characterization of a previously reported [2] nanomotor based on the controlled formation and breakdown of an intramolecular DNA triple-helix, and suggest its potential applications. The DNA molecular motor object of this report is driven by a fast and clean mechanism, based on the pH-dependent formation and breakdown of a CT-motif DNA triplehelix [3]. The repeated cycling of the pH between opportune values causes the adduct to intermittently assume a folded or open state, as experimentally confirmed by means of UV, CD and fluorescence spectroscopy, as well as an electrophoretic mobility shift assay. By means of silane chemistry, the nanomotor was then covalently anchored on glass surfaces, allowing for single-molecule fluorescence characterizations of its static and dynamic behaviour. This also confirmed that the smooth functioning of the nanomotor is possible in conditions that could hamper the performance of other DNA nanomotors, i.e. in sterically hindered contexts such as at surfaces, and suggesting that it might also work in other systems where diffusion is dominant and the mobility of the species involved in the cycling is critical, e.g. in nano-sized pores. A computational model of the nanomotor was created, that permitted the individuation of the intermediates occurring during the motors opening and closing events. [1] a) C. M. Niemeyer, M. Adler, Angew. Chem, Int. Ed. 2002, 41, 3779; b) B. Samorì, G. Zuccheri, Angew. Chem, Int. Ed. 2005, 44, 1166. [2] M. Brucale, G. Zuccheri, B. Samorì, Org. Biomol. Chem. 2005, 3, 575. [3] G. Felsenfeld, D. R. Davies, A. Rich, J. Am. Chem. Soc. 1957, 79, 2023.