A Surface‐Bound DNA Switch Driven by a Chemical Oscillator

Abstract

The fabrication of autonomously moving molecular structures is one of the central challenges in the field of DNA nanodevices.[1] Some of the concepts introduced recently to achieve this goal rely on the sequence-dependent catalytic action of DNA-modifying enzymes such as restriction endonucleases or nicking enzymes [2] while others use the catalytic power of DNA itself by incorporating DNA enzyme sequences into DNA devices.[3] Both approaches have also been used to realize autonomous molecular computers.[4] Another strategy is based on controlled inhibition of DNA hybridization by formation of secondary structure and its acceleration by catalytic DNA strands.[5] These concepts were developed for the autonomous operation of DNA devices fueled by DNA hybridization. A different approach was recently taken by our research group [6] and we could show that the pH-sensitive conformational transition of a cytosinerich DNA strand between a random conformation and the socalled "i motif" could be driven by the oscillating proton concentration generated by a chemical oscillator. In such a system, the temporal succession of the states of the DNA devices is determined by a nonlinear dynamical system rather than by an external operator. We report here how this system can be significantly improved by attaching the DNA conformational switches to a solid substrate. This attachment allows us to operate the chemical oscillator in a continuous flow stirred tank reactor (CSTR) into which a glass chip supporting the DNA devices is placed. In principle, the surface-bound DNA structures can undergo an infinite number of autonomous conformational switching events in this configuration.We showed recently how proton-fueled DNA devices can be driven by an oscillating chemical reaction [6] by using a variant of the Landolt reaction to periodically change the pH value in a continuously fed reactor. To retain the DNA switches within the reaction solution, a reactor without an outlet had to be used. In such a configuration, one cannot reach a steady state since the continuous influx of reaction solution means the average concentrations of the reactants vary. As a result, this dynamic chemical system is driven out of its oscillatory region, thus causing the oscillations to die away after a few periods.To overcome this limitation in the present work we operated the oscillator in a CSTR with two inlets and one outlet. In principle, an infinite number of homogeneous pH oscillations can be generated by using a continuous filling combined with the simultaneous removal of waste materials. However, the DNA devices had to be attached to a solid substrate to prevent loss of the DNA through the reactors outlet. For these experiments, we used thiol-modified, fluorescently labeled DNA switches bound to an ultrathin transparent gold layer on a glass substrate. This allowed a firm covalent attachment of the DNA to the surface while at the same time energy transfer between the fluorophores and the gold layer [7] could be used to characterize the conformational...

DNA-based switchable devices and materials

“…The reported examples are mostly operated by adding chemicals or fuel DNA molecules that are easily realized in bulk systems, but not under nanoscale. In 2005, Leidl et al [32] reported autonomous switching of DNA motor and surface optical signals for several times using an improved pH oscillator system. In 2007, Liu et al [33] reported a light-driven method, enabling non-contact driving of the i-motif DNA motor for the first time.…”

Nukleinsäure‐basierte molekulare Werkzeuge

“…Der i-Motiv-Schalter reagiert auf pH-Oszillationen sogar dann mit großer Reversibilität, wenn er auf einer Oberfläche immobilisiert wird. [124] Diese beiden Studien waren wichtige Vorstufen für die Entwicklung eines i-Motiv-DNA-Schalters, der reversibel auf den pH-Wert der Umgebung innerhalb einer lebenden Zelle reagiert, wenn er auf einer biologischen Oberfläche -nämlich an der Innenseite einer endosomalen Membranangelagert ist (siehe Abschnitt 7). [121] Verschiedene i-Motiv-Schalter überführen die chemische ¾nderung des pH-Werts in andere messbare ¾nderungen der Eigenschaften der betrachteten Anordnung.…”

From DNA nanotechnology to synthetic biology

“…In more nanotechnology-oriented work along these lines, it has been previously shown that reaction-diffusion systems can be used to produce microand even nanoscale patterns (Grzybowski et al, 2005). In the context of DNA nanotechnology it was demonstrated that chemical oscillators can drive DNA conformational changes (Liedl et al, 2006).…”