Molecular switches that change their conformation upon target binding offer powerful capabilities for biotechnology and synthetic biology. Aptamers are useful as molecular switches because they offer excellent binding properties, undergo reversible folding, and can be engineered into many nanostructures. Unfortunately, the thermodynamic and kinetic properties of the aptamer switches developed to date are intrinsically coupled, such that high temporal resolution can only be achieved at the cost of lower sensitivity or high background. Here, we describe a design strategy that decouples and enables independent control over the thermodynamics and kinetics of aptamer switches. Starting from a single aptamer, we create an array of aptamer switches with effective dissociation constants ranging from 10 μM to 40 mM and binding kinetics ranging from 170 ms to 3 s. Our strategy is broadly applicable to other aptamers, enabling the development of switches suitable for a diverse range of biotechnology applications.

DNA nanotubes hold great potential as drug delivery vehicles and as programmable templates for the organization of materials and biomolecules. Existing methods for their construction produce assemblies that are entirely double-stranded and rigid, and thus have limited intrinsic dynamic character, or they rely on chemically modified and ligated DNA structures. Here, we report a simple and efficient synthesis of DNA nanotubes from 11 short unmodified strands, and the study of their dynamic behavior by atomic force microscopy and in situ single molecule fluorescence microscopy. This method allows the programmable introduction of DNA structural changes within the repeat units of the tubes. We generate and study fully double-stranded nanotubes, and convert them to nanotubes with one, two and three single-stranded sides, using strand displacement strategies. The nanotubes can be reversibly switched between these forms without compromising their stability and micron-scale lengths. We then site-specifically introduce DNA strands that shorten two sides of the nanotubes, while keeping the length of the third side. The nanotubes undergo bending with increased length mismatch between their sides, until the distortion is significant enough to shorten them, as measured by AFM and single-molecule fluorescence photobleaching experiments. The method presented here produces dynamic and robust nanotubes that can potentially behave as actuators, and allows their site-specific addressability while using a minimal number of component strands.

specific and strong recognition of molecular targets (i.e., aptamers), catalyze biochemical reactions (i.e., ribozymes), or form sophisticated and dynamic "smart materials" or even 3D constructs (i.e., DNA origami). [2] There is particular interest in the use of nucleic acids for the construction of molecular switches, which undergo a function-altering structural change in response to an external stimulus. [3] Many such examples exist in nature, where switches enable organisms to sense physiological changes and selectively control biological functions in response. For example, riboswitches exist naturally as domains within messenger RNA (mRNA) transcripts that can bind to specific metabolites with high specificity in order to stabilize a secondary structure that prevents subsequent translation. [4] Synthetic, engineered molecular switches based on nucleic acids can achieve even greater diversity of function. Such designs make use of aptamersnucleic acid-based affinity reagents isolated via an in vitro process of systematic evolution by exponential enrichment (SELEX), in which DNA or RNA sequences with specific ligand binding are isolated from a large pool of random sequences. [5] Aptamers have proven to be robust recognition elements due to their thermal stability, ease of synthesis, and capacity to undergo ready modification with a broad array of functional groups. Importantly, traditional selection methods can be expanded upon by innovative engineering techniques to enable the incorporation of additional functions that further extend the utility of aptamers. Aptamers can adopt various 2-and 3-D structures such as duplexes, hairpins, and G-quadruplexes, and the inducible formation and disruption of these configurations can be exploited to enable complex functions besides simple biosensing. Consequently, aptamers have been incorporated into many intricate configurations, such as logic gates and dynamic nanomachines. Various research groups have also described aptamer-based switches that undergo conformational changes in response to triggers such as shifts in pH, stimulation with light, or the presence of a specific ligand. [6] Although still a relatively young area of research, these efforts could prove highly useful for materials research-conferring even greater and more selective control over devices based on functionalized nucleic acids. Aptamers are becoming increasingly integrated with various organic and inorganic molecules in order to control the assembly and operation of novel functional Although RNA and DNA are best known for their capacity to encode biological information, it has become increasingly clear over the past few decades that these biomolecules are also capable of performing other complex functions, such as molecular recognition (e.g., aptamers) and catalysis (e.g., ribozymes). Building on these foundations, researchers have begun to exploit the predictable base-pairing properties of RNA and DNA in order to utilize nucleic acids as functional materials that can undergo a molecular "switching" ...

DNA nanotubes have great potential as nanoscale scaffolds for the organization of materials and the templation of nanowires and as drug delivery vehicles. Current methods for making DNA nanotubes either rely on a tile-based step-growth polymerization mechanism or use a large number of component strands and long annealing times. Step-growth polymerization gives little control over length, is sensitive to stoichiometry, and is slow to generate long products. Here, we present a design strategy for DNA nanotubes that uses an alternative, more controlled growth mechanism, while using just five unmodified component strands and a long enzymatically produced backbone. These tubes form rapidly at room temperature and have numerous, orthogonal sites available for the programmable incorporation of arrays of cargo along their length. As a proof-of-concept, cyanine dyes were organized into two distinct patterns by inclusion into these DNA nanotubes.