We have proposed the concept of photonic DNA computing, which utilizes light and DNA, as a new evolution of parallel computing technology. The scheme has potential for achieving ingenious information processing by use of the properties of light including spatial parallelism and visibility, and the nature of DNA such as reaction parallelism and capability for autonomous reactions. We are developing optical techniques to realize this idea. An important example is the parallel optical manipulation technique that uses vertical-cavity surface-emitting laser (VCSEL) array sources. One can generate various optical field distributions by directly modulating the optical outputs of individual VCSELs, and it is possible to achieve manipulation of microscopic objects without physical contact based on compact hardware and a simple control method. We demonstrated parallel translation and fabrication of a stacked structure of microscopic particles, on the surfaces of which a lot of DNA molecules are bound. A method for reactions of DNA using an optical technique has also being developed. The method is based on control of the temperature of a local small volume of a DNA solution, which is put on a substrate coated with light-absorbing material, by irradiating with laser beams. We irradiated the substrate or a bead, on which DNA molecules were attached by hybridization, and succeeded in detaching DNA from the substrate or the bead. These techniques are expected to contribute miniaturization and weight-reduction of information systems for computing, genome analyses, and other applications.
We are studying on photonic DNA computing, in which the nature of light and DNA is effectively utilized, as a new computing technique. In the scheme, computation is performed by manipulating DNA with chemical reactions at nano-scale and control of light at micro-scale. As a fundamental operation, translation of DNA molecules from a position to another one is important. This paper describes some experimental results on translation of DNA molecules. A DNA cluster is fabricated by making hybridization of anti-tag DNA and data DNA that is complementary to the anti-tag DNA. The translation method consists of three steps; (i) attaching data DNA to beads (fabricating DNA clusters), (ii) translation of DNA clusters, and (iii) detaching the data DNA from the beads. We confirmed that VCSEL array optical manipulation is applicable to step (ii). For steps (i) and (iii), hairpin DNA is used to achieve two stable states of DNA. The experimental results demonstrated that attaching data DNA to a bead and detaching the DNA from the bead is possible by laser irradiation with an appropriated irradiation schedule. These results show effectiveness of the optical technique for controlling DNA molecules locally.
We developed a new type of optical manipulation technique by using a VCSEL array, which we call VCSEL array trapping. Flexible manipulation of small objects is achieved by controlling the spatial and the temporal intensity distribution generated by the VCSEL array sources. We have previously demonstrated parallel translation and non-mechanical translation of microparticles by controlling the emission distribution of the VCSEL array as the light source. Furthermore, we found that a stacked structure when using 2x2 VCSEL beams can be fabricated. In this report, we clarify the stacking process and the conditions for stacking the maximum number microparticles in order to apply this stacking method to three-dimensional structure fabrication. As an experimental result, we confirmed that the stacked structure was lifted up from the sample stage and fabricated without the space between the microparticles. The stacked structure depended on the microparticle size, the beam waist position, and the spot pitch. Furthermore, we investigate the difference of stacking processes when using 2x2 beams and a single beam. As a result, we found that the structure can be fabricated with lower optical power than when using a single beam. This fact indicates that 2x2-beam illumination is particularly effective for stacking micro objects without damage caused by heat.
DNA computing is an interesting computational paradigm utilizing reactive nature of DNA. The DNA computing realizes massively parallel computation because a large number of DNAs are processed in parallel. However, the computational functionality is restricted by the number of DNA molecules and DNA reactions that can be employed. As a new computational scheme, we are studying optically assisted DNA computing, which utilizes flexibility in generating light fields and parallelism of DNA reactions. Toward the goal, we experimentally verified methods for translating DNA molecules and controlling DNA reactions locally by using optical techniques. An optical manipulation method with VCSEL array sources is applied to translate DNA. We succeeded to translate two DNA clusters, which consisted of many DNA molecules attached to particles, in different directions simultaneously by switching the emission pattern of the VCSEL array. The reaction of DNA is controlled by irradiating with a laser beam. Experimental results demonstrated that double stranded DNAs, which were immobilized to the surface of a particle or a substrate, were denaturated at a resolution of several micrometer. The methods make possible to deal with a set of DNAs selectively and are useful in executing flexible operations for computing.