Study on hairpin DNA molecular device for autonomous molecular computer

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DNA-based computing is a new computational paradigm that realizes an autonomous and parallel computation by employing DNA molecular reactions. In contrast to a computation on an electronic computer, DNAC can be used to solve biological problems such as gene expression profiling and gene network regulation by using the algorithm of molecular computing because DNAC has a direct interface with biological molecules. A hairpin DNA molecule, which forms a hairpin structure by intra-base pairing, is an effective DNA nano-device for DNAC. For instance, a whiplash PCR system, which is a promising architecture for DNAC, employs recursive and self-catalytic polymerization reactions of hairpin DNA molecules. The rate of hairpin structure formation does not depend on the concentration of hairpin DNA molecules because the hairpin structure formation is an intra-molecular reaction. In massively parallel DNAC, the concentration of DNA molecules that represent individual programs and data is very low. Therefore, the concentration-independent rate of hairpin formation is extremely effective in massively parallel DNAC. In this study the static and kinetic characteristics of structural transition of hairpin DNA molecules were investigated. New hairpin DNA nano devices for DNAC were then developed based on the characteristics of hairpin DNA molecules as well as optimization and extension of the whiplash PCR system. A new architecture for an autonomous DNAC using hairpin DNA molecules as effective computational components was also developed.