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The Study of Molecular Computing and Nanotechnology Based on DNA Self-Assembly

Author: QianZuoZuo
Tutor: HeLin
School: Shanghai Jiaotong University
Course: Biochemistry and Molecular Biology
Keywords: DNA computing molecular computing DNA self-assembly DNA addition DNA origami
CLC: TP301
Type: PhD thesis
Year: 2007
Downloads: 557
Quote: 1
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Abstract


Compared to conventional top-down routines of shaping, bottom-up self-assembly for constructing shapes (especially nanoscale shapes) is undoubtedly an important method. The accumulated knowledge and technology on DNA and the coding capacity of DNA itself have made DNA self-assembly the most promising self-assembly technology. In 1989, Seeman first proposed a DNA branched junction as the basic self-assembly unit. In 1994, Adleman first solved a mathematic combination problem (Hamiltonian path problem) by 1-D linear DNA self-assembly, which demonstrated the latent of DNA molecule for computation, and thus opened the new research field of DNA computing (also called molecular computing). In this decade, the potential of DNA self-assembly has been widely developed in the fields of molecular computing, biophysics, nanotechnology and so on. This paper mainly focuses on molecular computing and nanotechnology based on DNA self-assembly:First part introduces the basic knowledge of DNA molecule and research background of DNA computing and DNA self-assembly. Basic knowledge of DNA molecule involves the structure property, manipulation and detection of DNA. The detection of DNA includes not only conventional technologies but also newly-developed technologies such as E-DNA Chip and AFM. Research background of DNA computing mainly describes two classical examples. One example is the work of Adleman and another is a SAT problem solved by DNA hairpins, both of which employ the self-assembly of DNA. Research background of DNA self-assembly mostly introduces three kinds of classical DNA self-assembly units (DX tile, TX tile and 4×4 tile) and recommends a new technology, DNA origami invented by Rothemund in 2006, which is a great breakthrough in the field of DNA self-assembly.Second part interprets the study of molecular computation based on DNA self-assembly. First, a DNA algorithm was presented which adds two nonnegative binary integers using 1-D linear self-assembly. For the addition of two binary n-bit integers, this algorithm requires constant experimental steps rather than growing with n. This approach has the benefit of greater experimental simplicity when compared with previous DNA addition algorithms. Then, a DNA adder prototype was constructed based on linear DNA self-assembly addition algorithm. Combining with MEMS technology, the output of this adder prototype was electronic signal of E-DNA Chip. And software was writtern to debug the prototype. Finally, the present level of DNA computer was compared with the electronic computer history, as an interesting reflection and prospect of DNA computing.Third part presents the study of nanotechnology based on DNA self-assembly. First, a DNA nanostructure of analogic China map was created. This structure, with roughly 150nm in diameter and a spatial resolution of 6 nm, was constructed by folding DNA strand. The picture observed by AFM was almost identical with the designed shape. The DNA origami technology was employed in the construction of this shape, which has proved the capability of constructing almost any complicated nanoscale shape enabled by DNA origami, and provided novel bottom-up approach for constructing nanostructures. Then, a subsequential study was carried out as an application of DNA origami: molecular electronic circuit constructed by DNA origami combining with DNA metallization. We tried a shape of inductor, one of the most fundamental electronic components, and made the width less than 20nm. A scheme of DNA metallization was also discussed. Fourth part summarizes the studies involved in this paper and provides some perspective of the research in the future.

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