Electronic Actuation of Surface-Immobilized, pH-Responsive DNA Nanoswitches

Abstract

Dynamic DNA machines exploit the specificity of base pairing and/or sensitivity to the local environment to control the reversible switching of DNA constructs between conformational states. One such example are pH-sensitive DNA nanoswitches that can be actuated by proton-mediated Hoogsteen interactions within a DNA triplex domain. To date, studies of pH-sensitive DNA nanoswitches have largely focused on DNA machines that are freely diffusing in the solution phase. For many applications, it is advantageous to integrate these dynamic DNA machines with solid-state devices, requiring immobilization on surfaces. Here, we explore the switching of a pH-sensitive DNA triplex immobilized on a surface as a dense, 2-dimensional DNA monolayer. DNA nanoswitches were assembled onto surfaces via thiol chemistry and pH-controlled conformational switching of the constructs examined using quartz crystal microbalance with dissipation monitoring (QCM-D). These QCM-D experiments indicate that despite the high density of DNA within the monolayer (1012 molecules/cm2), pH-switching between open and closed states is retained following immobilization. Moreover, conformational switching of DNA constructs within the monolayer remains highly reversible and repeatable, with negligible reduction in switching efficiency observed over 20 switching cycles. DNA switching experiments were also performed in the solution phase using single-molecular Forster resonance energy transfer (smFRET) and circular dichroism (CD) techniques to confirm their pH responsitivity. Finally, we demonstrate electrically driven, localised, and addressable switching of the DNA triplex by employing electrochemical reduction and oxidation of water at an electrode surface, further demonstrating the potential of the technology for surface-immobilized dynamic DNA machines. This study not only provides insight into the actuation of DNA machines on-surface but also supports the development of new technologies such as hybrid electronic-DNA technologies able to store and process information using both molecular and electronic inputs.