December 08, 2011

DNA-based switchable devices and materials

Nature Asia - Other than carrying the code of life, in the past three decades, DNA has played an important role in weaving two- and even three-dimensional nanostructures by taking advantage of its programmable sequences and precise recognition properties. The highly specific base-pairing interactions of DNA molecules not only allow for the building of static DNA nanostructures, but also enable the construction of machine-like devices capable of responding to external stimuli, such as pH, small molecules, light, electricity, and temperature, thus performing tasks otherwise beyond our reach. This review summarizes DNA-based switchable devices and materials, particularly where the responsiveness of DNA is caused by changes in secondary structures, and more importantly, where such stimuli-responsive processes are reversible. This review covers DNA-based devices and materials from smart surfaces and responsive nanopores/nanochannels to DNA hydrogels, which are expected to be designed with even more intelligence in the future.

Schematic figure of the working cycle of i-motif DNA motors. At acidic pH, strand X folds into the closed i-motif structure. When the pH is raised to 8.0, strand X unfolds and is captured by hybridization to Y to form an extended duplex structure. Adapted from Ref. 19 (© 2003 Wiley-VCH).

DNA was used to fabricate nanostructures from two-dimensional DNA nanostructures to three-dimensional curved nanostructures, as complex as spheres, ellipsoids, and flasks utilizing DNA origami techniques. DNA was also designed for the construction of molecular devices or machines that can generate nanoscale movement. Besides static nanostructures, DNA could be applied to self-assembled structures or integrated within other functional systems, utilizing properties of DNA such as specific recognition, chain-exchange reactions, specific enzyme reactions and secondary structure transformation to enable precise control of motion at the molecular level or change properties at the macro scale. Such responsive and switchable properties allow molecular machine-like devices to be built. Several aspects of this field have been reviewed by Seeman, Liu and Liu, Simmel and co-workers, Bath and Turberfield and Willner and co-workers in the past several years. The present review focuses on DNA-based devices and smart materials that can respond to external stimuli, resulting in conformational changes to DNA structures at the nanoscale and detectable changes in properties such as volume, wettability at the macroscopic scale or transduction of force to move objects. This responsiveness is recoverable on removal of the external stimulus. DNA-based devices are introduced relating to smart surfaces and nanopores/nanochannels, while DNA-based smart materials are related to newly developed pure and hybrid DNA hydrogels. Figure 1 shows a typical example of a DNA device or motor. In 2003, Liu and Balasubramanian proposed a pH-driven molecular motor system that is strong and swift. It comprises a 21mer ssDNA sequence X containing four stretches of three cytosines and a 17mer single-stranded DNA sequence Y, which is partially complementary to X. At pH 5, via the formation of C·CH+ base-pairs, sequence X folds into a compact 4-stranded i-motif structure with the 3’ and 5’ ends close to each other, representing the closed state of the motor. Changing the pH to 8 results in X unfolding and forming an extended DNA duplex structure XY, corresponding to the open state of the motor. These two states, compact and extended, can be reversibly switched by changing the pH. Each stroke of the motor results in an output of a 5-nm linear movement that finishes in less than 1 s. Moreover, the estimated opening/closing force outputs exceed 10 pN. The i-motif structure has thus seen wide use for constructing responsive DNA devices and materials. We hope this summary will benefit the application of smart devices and materials, allowing the development of new strategies for constructing new types of responsive systems and providing more precise and controllable DNA-based building blocks.

The ability to undergo environment-stimulated conformational transitions has made DNA a popular stimulus-responsive element for creating smart devices and materials, and the response mechanism has also expanded from well-known chain exchange reactions and enzyme restriction reactions to pH changes, small molecules and even light and electrical signals. We believe that the excellent adaptability of DNA, with inspiration from all the reported strategies and further developments in material science and nanotechnology, will enable even more exciting smart systems in the future and will greatly benefit the invention of portable medical devices. Owing to its biocompatibility, DNA-based smart materials, particularly pure DNA hydrogels, will play increasingly important roles in implantable materials and controllable drug/gene delivery systems. In the meantime, many challenges remain in this emerging field, such as how the reliability of DNA smart devices and materials can be improved, and how DNA smart devices can be made to more efficiently convert energy into work. New tools and strategies are also needed to measure the output force of DNA machine directly at the single molecule level. These studies will benefit not only chemistry and materials science, but also lead to advances in physics, biology and medical research.

Smart surfaces based on DNA

A smart surface is a surface that can change its properties or enable certain functions in reaction to external stimuli. Its responsiveness normally results from the functional molecules modified onto the surface. Well-established methods of modifying DNA at the 3’ and 5’ ends have been widely used to make DNA-based functional surfaces like gene chips for sensing purpose. However, ‘smart’ surfaces based on DNA have long been a challenge, due to the difficulties of achieving reversibility. In the case of adjusting surface properties, a densely packing (monolayer) of DNA and functional groups and synchronization of the movement of all components are necessary, requiring DNA structures sufficiently robust to undergo a predesigned performance. As we described previously, the DNA i-motif is a clean, quick, reliable and efficient molecular motor, exhibiting clear advantages over other examples and providing many possibilities to facilitate smart surfaces based on DNA.

DNA responsive nanopore/nanochannel

Nanopores and nanochannels have attracted much attention for a long time because of their importance in biological activities. To understand the transportation mechanism and behavior of ions, biomolecules in the pore/channel and polymer and inorganic nanopores/nanochannels have been created. To confer on these nanopores/nanochannels stimuli-responsive properties to mimic their natural models, polymers, peptides and DNA have been modified onto the inner surface of nanopores/nanochannels. Among these studies, DNA has been demonstrated as an outstanding molecule to create an intelligent nanopore/nanochannel because of the clear transformation of secondary structure.

Other DNA-responsive nanodevices

Pure DNA Hydrogels

Pure DNA hydrogels with (a) pH responsiveness and (b) heat and enzymatic dual responsiveness. (a) A Y-shaped DNA nanostructure is formed from three single-stranded DNAs with two functional domains: an interlocking i-motif domain containing two cytosine-rich stretches (marked in black); and a domain for formation of the double-stranded Y shape (marked in red, green, and blue).

Hybrid DNA hydrogel

Just a small portion of DNA is needed to achieve hydrogel responsiveness, in which the DNA normally acts as a responsive component and is present as a crosslinker

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