Probing the conformational states of a pH-sensitive DNA origami zipper via label-free electrochemical methods

Williamson, Paul and Ijas, Heini and Shen, Boxuan and Corrigan, Damion and Linko, Veikko (2021) Probing the conformational states of a pH-sensitive DNA origami zipper via label-free electrochemical methods. Langmuir, 37 (25). pp. 7801-7809. ISSN 0743-7463 (https://doi.org/10.1021/acs.langmuir.1c01110)

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Abstract

DNA origami structures represent an exciting class of materials for use in a wide range of biotechnological applications. This study reports the design, production and characterisation of a DNA origami 'zipper' structure, which contains nine pH-responsive DNA locks. Each lock consists of two parts that are attached to the zipper's opposite arms; a DNA hairpin and a single-stranded DNA that are able to form a DNA triplex through Hoogsteen base pairing. The sequences of the locks were selected in a way that the zipper adopted a closed configuration at pH 6.5 and an open state at pH 8.0 (transition pKa 7.6). By adding thiol groups, it was possible to immobilise the zipper structure onto gold surfaces. The immobilisation process was characterised electrochemically to confirm successful adsorption of the zipper. The open and closed states were then probed electrochemically using differential pulse voltammetry and electrochemical impedance spectroscopy with both solution based redox agents and redox active DNA intercalators. It was found that after immobilisation, the open or closed state of the zipper in different pH regimes could be determined by electrochemical interrogation. These findings pave the way for development of DNA origami-based pH sensing and other pH-responsive sensing and release strategies for zipper-functionalised gold surfaces.

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