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Photonically controlled DNA nanomachines

With wavelength tuning of the light source, the action of a DNA-based nanomachine is accelerated as much as ten times and achieves a repeatable operation with high transition efficiency.
1 September 2009, SPIE Newsroom. DOI: 10.1117/2.1200908.1780

Not only is DNA the blueprint for life, it is also one of the most flexible materials used in nanotechnology. DNA-based nanomachines offer many advantages for manipulating materials and information effectively at the nanoscale, including fabrication flexibility, technical availability, and unique biomolecular affinities. A strand of DNA is composed of four building blocks—the chemical bases A, C, G, and T—and demonstrates Watson-Crick complementarity (G always binds to C, and A always binds to T), which can be used in both construction of stable nanoscale structures and directed movement of the constructs.1,2 Although such DNA-based nanomachines have many potential capabilities, development of effective structures and operation methods still requires considerable research efforts and progress.

A variety of functional nanomachines consisting of DNA molecules have been demonstrated previously.2,3 Good examples are DNA walkers4 (which can move across a scaffold made of DNA) and DNA tweezers,5 which open or close in response to fuel DNAs (small DNA strands that function as a source of energy). However, injection of fuel DNAs changes the state of the solution surrounding the machines and could possibly cause unexpected reactions. Under these conditions, it is also difficult to control individual machines within a localized region. To address these problems, we have explored the possibility of controlling DNA tweezers using light signals in the absence of fuel DNA.

Our DNA tweezers are constructed using four individual DNA strands, one of which is combined with a photoisomerizing molecule, azobenzene (see Figure 1).6 This allows control of the DNA binding power by light signals instead of fuel DNA. As a result, we can drive the DNA tweezers within a focused region under continuously stable conditions (see Figure 1). The tweezers open when exposed to UV irradiation and close under visible light, owing to photoisomerization of the azobenzene. The state of the tweezers is detected by measuring the fluorescence-resonance energy-transfer signal. The fluorescence intensity from the open state is higher than that from tweezers that are closed.

Figure 1. Schematic diagram of photonically controlled DNA tweezers. The tweezers consist of unmodified DNA strands A, B, and C, and a ‘hook’ strand H, which is modified with azobenzene in a region binding with strand C.

We used a spectrofluorometer (JASCO, FP-6200) to drive the tweezers, because this enables fine tuning of the irradiation wavelength under stable temperature conditions. The fluorescence spectra measured after irradiating with UV light (wavelength peak: 340nm, bandwidth: 20nm) followed by visible light (wavelength peak: 440nm, bandwidth: 20nm) are shown in Figure 2. The results demonstrate that the state of the tweezers could be controlled through optical input.

Figure 2. Fluorescence spectra obtained when irradiating the tweezers with UV and visible light in sequence.

Figure 3 shows a time sequence of the transition ratio as it changes from the closed to the open state during UV irradiation. By tuning the wavelength and spectral width of the control lights, we successfully increased the reaction speed of this nanomachine to ten times that demonstrated in previous experiments,7 which used a UV lamp (Philips TL6w08, peak wavelength: 365nm) as the light source. Although 10min of irradiation was required when using the UV lamp, the required irradiation time was no more than one minute using the spectrofluorometer. This indicates that the fine tuning of the irradiation wavelength was effective at accelerating the behavior of the photonically controlled DNA tweezers.

Figure 3. Time course of the transition ratio from the closed to the open state during UV irradiation using a spectrofluorometer and a UV lamp.

Transitions of the tweezers between open and closed states were induced repeatedly. The fluorescence intensity measured during the operation is shown in Figure 4. The intensity increased following a 1min UV exposure and decreased after irradiation with visible light. The transition ratio was measured at approximately 25–28% during repeated operations, which indicates little decrease in efficiency. The transition speed was estimated at approximately 100 transitions/s in a volume of 1μm3. Thus, the wavelength tuning was also effective at improving the transition ratio.

Figure 4. Fluorescence intensity measured during repeated operations.

Our experimental results demonstrate that photonically controlled DNA tweezers were driven in response to optical signals and that no less than ten repetitions of transition cycles were achieved. A patterned optical signal will enable us to achieve parallel and space-variant control of spatially distributed nanotweezers. Furthermore, tuning the wavelength and spectral bandwidth was effective at improving the operation speed and transition efficiency of the machines. Our future goals include the construction of a functional nanoscale processor that executes specific processes in response to UV irradiation.

Yusuke Ogura, Takahiro Nishimura, Jun Tanida
Graduate School of Information Science and Technology
Osaka University
Suita, Japan

Yusuke Ogura received his PhD in applied physics from Osaka University in 2002. He is an associate professor in the Department of Information and Physical Sciences. His research interests include photonic DNA computing, diffractive optics, and optical manipulation.