DNA machines

However, although countless examples of fluorescence or electrochemical labels have been demonstrated as signal-generating components of aptamer-based sensors, the specific nucleic acid structure of these novel binders has so far not been used sufficiently to improve the sensitivities, and thus the detection limit, of sensorial approaches. A combination of aptamers and DNA machines might take the field to new heights. 

DNA machines are now understood to be assemblies of nucleic acids which upon outside stimulation undergo a series of structural permutations which are predesigned in their respective sequences (Beissenhirtz and Willner, 2006). These reactions are powered by outside fuel molecules, often nucleic acids themselves, which are converted into accumulating waste, much like gasoline-driven macroscopic machines in our daily life. Exhaustion of one of the fuel components brings the system to a stop. Figure 4.5 shows the general mode of operation of most DNA machines. 

Figure 4.5 General operation mode of DNA machines exemplified by the catalytic scission of a substrate DNA strand. In the absence of the fuel-analyte molecule (blue), the DNA machine is inactive (1). Binding of the fuel and subsequent hybridization start the machine s operations (2), in this case a catalytical DNA cleavage reaction (3). Release of waste products due to reduced base pairing resets the machine to its starting configuration (1) and begins the next round of action. Note that different examples of machines performing a vast array of actions other than DNA cutting are shown. (See insert for color representation.)...

After scission of the mutant DNA, the FokFDNA assembly remains intact as a FokI cutter unit, which can hybridize to a signaling hairpin containing a fluorophore-quencher pair at its end. This hairpin structure acts as the fuel for the DNA machine. After hybridization, the FokI cutter unit cleaves the hybridized fuel molecule, and upon its spontaneous release the waste product diffuses away. 

Another example of a DNA machine that can easily be triggered by the actions of an aptamer is based on the isothermal strand displacement amplification (Weiz-mann et al., 2006b). In this case, a single-stranded DNA track contains three distinct domains domain I for the binding of a primer DNA to start replication domain II, which can, upon dnplex formation, be recognized by a nicking endonuclease (which cuts one strand of a double-stranded structure) and domain... 

In these sensors the primer sequence is locked inside a hairpin DNA, which in the absence of viral nucleic acids (the analyte) remains closed and thus prohibits binding of the primer to the DNA machine track. Only in the presence of the... 

Figure 4.8 DNA machine based on strand displacement amplification. The track consists of a primer binding sequence (black, I), a nicking recognition sequence (green, II), and a template for the product DNA (blue, IE). (1) Binding of the primer starts replication of the entire track by a DNA polymerase. (2) The fully replicated duplex is nicked on the newly formed strand by the nicking enzyme, regenerating the primer site...

The DNA machines described in this work, particularly those that start a catalytic process upon exposme to their target molecules, may offer new approaches to the design of clever biosensorial strategies which due to their catalytic nature may improve sensitivities for sensors based on the interaction of aptamers with their respective targets. 

Weizmann, Y., Beissenhirtz, M. K., Cheglakov, Z., Nowarski, R., Kotler, M., Willner, I. (2006b). A virus spotlighted by an autonomous DNA machine. Angew Chem Int Ed Engl 45, 7384-7388. 

Figure 4.5 General operation mode of DNA machines exemplified by the catalytic scission of a substrate DNA strand. (See text for full description.)...

Controlled molecular motion was achieved in several synthetic systems,including DNA machines that use a conformational change of the double helix to develop torque, and propeller-like molecules that can be rotated in a specific direction on a molecular axle by a sequence of chemical transformations. The hybridization and dissociation of DNA strands was also used to make DNA motors that extend and contract like pistons in response to DNA "fuel." One such device, unlike many artificial molecular motors, is capable of free ranning rather than requiring intervention at different points in the duty cycle. ... 

Lu CH, Willner B, Willner I. DNA nanotechnology from sensing and DNA machines to drug-delivery systems. ACS Nano 2013 7 8320-32. 

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