Study on hairpin DNA molecular device for autonomous molecular computer

DNA计算是利用DNA分子反应实现自主并行计算的一种新的计算范式。与电子计算机上的计算不同，DNAC可以通过分子计算的算法来解决基因表达谱和基因网络调控等生物学问题，因为DNAC与生物分子有直接的接口。发夹DNA分子通过碱基内配对形成发夹结构，是一种有效的DNA纳米器件。例如，Whiplash PCR系统，这是DNAC的一个很有前途的体系结构，使用发夹DNA分子的递归和自催化聚合反应。发夹结构的形成速度不依赖于发夹DNA分子的浓度，因为发夹结构的形成是分子内的反应。在大规模并行的DNAC中，代表单个程序和数据的DNA分子的浓度非常低。因此，在大规模平行的DNAC中，与浓度无关的发夹形成速率是非常有效的。本文研究了发夹状DNA分子结构转变的静态和动力学特征。在此基础上，根据发夹DNA分子的特点，并对Whiplash聚合酶链式反应体系进行了优化和扩展，开发了适用于DNAC的新型发夹DNA纳米器件。还开发了一种以发夹DNA分子作为有效计算组件的自主DNAC的新体系结构。

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.