We demonstrate here the rational design of purely entropic domains as a versatile approach to achieve control of the input/output response of synthetic molecular receptors. To do so and to highlight the versatility and generality of this approach, we have rationally re-engineered two model DNA-based receptors: a clamp-like DNA-based switch that recognizes a specific DNA sequence and an ATPbinding aptamer. We show that, by varying the length of the linker domain that connects the two recognition portions of these receptors, it is possible to finely control their affinity for their specific ligand. Through mathematical modeling and thermodynamic characterization, we also demonstrate for both systems that entropy changes associated with changes in linker length are responsible for affinity modulation and that the linker we have designed behaves as a disordered random-coil polymer. The approach also allows us to regulate the ligand concentration range at which the receptors respond and show optimal specificity. Given these attributes, the use of purely entropic domains appears as a versatile and general approach to finely control the activity of synthetic receptors in a highly predictable and controlled fashion.

The rational regulation of the pK a of an ionizable group in a synthetic device could be achieved by controlling the entropy of the linker connecting the hydrogen bond forming domains. We demonstrate this by designing a set of pH-responsive synthetic DNA-based nanoswitches that share the same hydrogen bond forming domains but differ in the length of the linker. The observed acidic constant (pK a) of these pH-dependent nanoswitches is linearly dependent on the entropic cost associated with loop formation and is gradually shifted to more basic pH values when the length of the linker domain is reduced. Through mathematical modeling and thermodynamic characterization we demonstrate that the modulation of the observed pK a is due to a purely entropic contribution. This approach represents a very versatile strategy to rationally modulate the pK a of synthetic devices in a highly predictable and accurate way.

We demonstrate here the use of 2-(4-chlorophenyl)-2-cyanopropanoic acid (CPA) and nitroacetic acid (NAA) as convenient chemical fuels to drive the dissipative operation of DNA-based nanodevices. Addition of either of the...

Here we report the rational design of a synthetic molecular nanodevice that is directly inspired from hemoglobin, a highly evolved protein whose oxygen-carrying activity is finely regulated by a sophisticated network of control mechanisms. Inspired by the impressive performance of hemoglobin we have designed and engineered in vitro a synthetic DNA-based nanodevice containing up to four interacting binding sites that, like hemoglobin, can load and release a cargo over narrow concentration ranges, and whose affinity can be finely controlled via both allosteric effectors and environmental cues like pH and temperature. As the first example of a synthetic DNA nanodevice that undergoes a complex network of nature-inspired control mechanisms, this represents an important step toward the use of similar nanodevices for diagnostic and drug-delivery applications.

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 nanodevices. ■ INTRODUCTIONDNA nanotechnology allows us to design and engineer smart nanomaterials and nanodevices using synthetic DNA sequences. 1−6 For example, current methodologies and synthetic strategies, such as DNA tiles, origami, or supramolecular assembly, allowed the production of complex nanostructures of different shapes and dimensions. 7−11 The unparalleled versatility of these approaches allows precise positioning of molecule-responsive switching elements in specific locations of DNA nanostructures, leading to the construction of more complex functional nanodevices. 12−14 Similarly, enzyme−DNA nanostructures have been demonstrated to enhance enzyme catalytic activity and stability. 15 DNA motifs that rely on noncanonical DNA interactions, such as G-quadruplex, triplex, i-motif, hairpin, and aptamers, can be used to design such nanodevices due to their dynamic-responsive behavior toward chemical and environmental stimuli. 16,17 These responsive units often respond to specific chemical inputs through a bindinginduced conformational change mechanism that leads to a measurable output or function. The efficiency of this class of responsive nanodevices strongly depends on the designed structure-switching mechanism that controls their activity or functionality. Therefore, there is an urgent need to understand the energies involved in these responsive systems and the relationship between their structure and dynamics. 16 Among such functional DNA nanodevices, those based on the triple-helix motif are attracting interest for their strong and programmable pH dependence. 18−20 By rationally incorporating triplex-forming portions into DNA nanodevices, it is possible to trigger conformational changes and functions using pH as a chemical input. 21−24 Despite the fair amount of knowledge of the basic design principles and mechanism of action of triplex-based nanodevices, no reports describing the connection between their structural and dynamical properties are available. Toward this aim, simulative approaches represent valuable tools to shed ...