核酸逻辑门的分子计算模型研究

发布时间：2018-04-27 21:23

本文选题：核酸逻辑门 + 链置换　；参考：《陕西师范大学》2013年硕士论文

【摘要】：第一台通用型电子计算机的发明距今已经有60多年的历史,电子计算机的迅速发展深刻地改变了人类的生活。但电子计算机由于自身的限制,一直以来无法很好的解决一些比如“解决方法的时间赶不上问题规模的扩展速度”之类的计算问题,这使得科学家开始寻求下一代计算机。分子计算机由于其使用的化学和生物材料尺度极小而成为下一代计算机的“宠儿”。分子计算是分子计算机的基础。分子计算的研究属于一个交叉领域,需要分子生物学,系统生物学,有机化学,材料科学,计算机科学,电子电气工程等多领域的科学家共同研究。集成电路是以硅元件为基础的数字逻辑的组合。核酸分子,特别是脱氧核糖核酸(DNA)分子已经成为纳米技术和生化环路上一种优良的工程材料。核酸分子由于其自然的生物特性,体内条件下能支持在技术上的应用,体外条件下易化学合成方便进行实验,Watson-Crick互补原则能够预测分子行为,这些优点使得核酸分子成为分子计算领域一种有力的工具,长远来看可能是硅元件的一种替代物。本论文是基于体外条件下对核酸分子逻辑门的研究。其分子逻辑门是指利用核酸分子在体外条件下重现数字逻辑的过程,构建出的具有良好通用性的基础元件。这大大增加了分子“电路”扩大的可操作性。具体工作如下： (1)主要论述分子计算在经典分子计算模型、图灵分子计算模型、分子逻辑门计算模型3个方面不同领域的科学家门开展的工作研究,分子计算及其理论的分子计算机快速发展必然离不开多学科相互交叉的发展,虽然到目前极少有大规模人工构建的分子“电路”(逻辑门在101-1000个)产生,建立类似于硅电子学这种复杂性可靠性的分子“电路”更为遥远,但可以看出一旦可靠的设计规则被科学家们建立,研究者就可以通过控制纳米级的器件从而在体外环境中合成分子“电路”,这将与体内的分子“电路”相互连接,这将可能推动人工智能,脑机接口等领域的发展研究。 (2)电子电路以硅逻辑门作为基础,通常的8种用于电子器件之中：分别是OR, AND, XOR, INH, NOT, NOR, NAND, XNOR门；分子“电路”则需要以分子逻辑门作为基础,分子生物学的中心法则解释了DNA, RNA,蛋白质之间的关系。本文详细阐述了体外条件下的DNA为核心的分子逻辑门的8种类型,并讨论了更复杂的组件,DNA分子建立的加法器(其中包括半加器,半减器,全加器)和SR锁存器,这证明了利用DNA分子构建基础逻辑门是完全可以的。但是,从电子电路考虑来看,这仍然显得不足,首先,分子逻辑门是多种多样的,其输入输出格式并不完全统一,这为下一步进行级联反应甚至扩大分子“电路”提供了障碍,科学家们仍然需要找寻通用性更好的基本逻辑元件。 (3)DNA链置换技术目前是科学家们在分子“电路”研究领域的“明星”,它被科学家用于动态纳米技术的研究要早于分子“电路”。肽核酸(PNA)是一种人工合成的分子,是核酸分子的类似物。本文通过PNA,基于链置换技术的基本原理,构建了两种链置换领域的新的逻辑门——禁门(INH)和隐含门(Implication),这将为已经达到大规模的链置换式的分子“电路”加入新的逻辑运算模型,为获得更大规模的分子“电路”提供一种基础门的选择。 (4)分子信标和纳米金技术是目前是发展比较成熟的领域,但是在很长时间里研究工作中是独立开展的,最近几年,一些科学研究者开始结合两个领域在分子计算领域做出了一些工作。本文构建了一种新的基于分子信标的核酸逻辑与门和或门模型,以寡核苷酸链作为输入信号,荧光检测作为输出信号,并用更为灵敏的猝灭剂纳米金替代了传统的猝灭剂有机染料,提出与门使用双色纳米尺度的分子信标,区别于或门的单色分子信标。同时本文通过引入分支迁移的原理,提出了一种新型的分子“半减器”模型,这种分子“电路”中比较复杂的逻辑组件将为下一步的小型或者更大规模的纳米金型的分子“电路”提供重要的支持。
[Abstract]:The first universal electronic computer has been invented for more than 60 years, and the rapid development of electronic computers has profoundly changed the life of human beings. However, because of their own limitations, electronic computers have not been able to solve the problems such as "the time of solving the problem of the scale of the problem." This makes scientists start to seek the next generation of computers. Molecular computers are the "favourite" of the next generation computer because of their small scale of chemical and biological materials. Molecular computing is the basis of molecular computers. Molecular computing studies belong to a cross field, requiring molecular biology, systems biology, and organic matter. An integrated circuit is a combination of digital logic based on silicon elements. Nucleic acids, especially DNA molecules, have become an excellent engineering material for nanotechnology and biochemical circuits. Naturally, the biological characteristics, in vivo conditions can support the application of technology, in vitro, easy chemical synthesis is convenient to carry out experiments, Watson-Crick complementary principle can predict molecular behavior, these advantages make nucleic acid molecules become a powerful tool in the field of molecular computing, in the long term it may be a substitute for silicon components.
This paper is based on the study of nucleic acid molecular logic gate in vitro. Its molecular logic gate is the process of using nucleic acid molecules to reproduce digital logic under the conditions of in vitro, and constructs a basic element with good generality. This greatly increases the operability of the molecular "circuit" enlargement. The specific work is as follows:
(1) we mainly discuss the work of molecular computing in the classical molecular computing model, the Turing molecular calculation model, the molecular logic gate calculation model in 3 fields, and the rapid development of molecular computing and the molecular computer of the molecular computing. The artificially constructed molecular "circuit" (logic gate is 101-1000) is produced, and it is far more distant to establish a molecular "circuit" similar to the complexity of silicon electronics, but it can be seen that once the reliable design rules are established by scientists, researchers can synthesize molecules in the external environment by controlling the nano scale devices. "Circuit", which will be interconnected with the molecular "circuit" in the body, will promote the development of artificial intelligence, brain computer interface and other fields.
(2) the electronic circuit is based on the logic gate of silicon, the 8 commonly used in electronic devices: OR, AND, XOR, INH, NOT, NOR, NAND, XNOR gate. The molecular "circuit" needs to be based on the molecular logic gate, and the central rule of molecular biology explains the relationship between DNA, RNA, and protein. The DNA is the core of the 8 types of molecular logic gates and discusses the more complex components, the addition of the DNA molecules (including half adder, semi subtracer, full adder) and the SR latch, which proves that it is completely possible to construct the basic logic gate using the DNA molecule. Molecular logic gates are diverse, and their input and output formats are not completely unified, which provides obstacles to the next cascade of cascading reactions or even the expansion of molecular "circuits", and scientists still need to find the basic logic elements that have better generality.
(3) DNA chain replacement technology is currently the "Star" of scientists in the field of molecular "circuit" research. It has been used by scientists to study dynamic nanotechnology earlier than molecular "circuit". Peptide nucleic acid (PNA) is a synthetic molecule, a analogue of nucleic acid molecules. This article is constructed by PNA, based on the basic principle of chain replacement technology. Two new logic gates in the field of chain permutation, INH and Implication, will be added to the new logical operation model for the molecular "circuit" that has reached a large chain permutation and provide a basic gate for a larger molecular "circuit".
(4) the molecular beacon and nanoscale technology are now a relatively mature field, but in a long time the research work is carried out independently. In the last few years, some scientific researchers have made some work in the field of molecular computing combined with two fields. This paper constructs a new type of nucleic acid logic and gate based on molecular beacons. And or gate model, the oligonucleotide chain is used as the input signal, the fluorescence detection is used as the output signal, and the more sensitive quencher nanoscale gold is used to replace the traditional quenching agent organic dye. The molecular beacon, which is different from the monochromatic molecular beacon, is put forward, which is different from the monochromatic molecular beacon at the gate, and the principle of branch migration is introduced. A novel molecular "semi subtracer" model is proposed. The complex logical components in the molecular "circuit" will provide important support for the next small or larger scale nanoscale molecular "circuit".

【学位授予单位】：陕西师范大学
【学位级别】：硕士
【学位授予年份】：2013
【分类号】：Q523;TP338

【参考文献】