本文選題：核酸邏輯門 + 鏈置換��； 參考：《陜西師范大學(xué)》2013年碩士論文

【摘要】：第一臺通用型電子計(jì)算機(jī)的發(fā)明距今已經(jīng)有60多年的歷史,電子計(jì)算機(jī)的迅速發(fā)展深刻地改變了人類的生活。但電子計(jì)算機(jī)由于自身的限制,一直以來無法很好的解決一些比如“解決方法的時(shí)間趕不上問題規(guī)模的擴(kuò)展速度”之類的計(jì)算問題,這使得科學(xué)家開始尋求下一代計(jì)算機(jī)。分子計(jì)算機(jī)由于其使用的化學(xué)和生物材料尺度極小而成為下一代計(jì)算機(jī)的“寵兒”。分子計(jì)算是分子計(jì)算機(jī)的基礎(chǔ)。分子計(jì)算的研究屬于一個(gè)交叉領(lǐng)域,需要分子生物學(xué),系統(tǒng)生物學(xué),有機(jī)化學(xué),材料科學(xué),計(jì)算機(jī)科學(xué),電子電氣工程等多領(lǐng)域的科學(xué)家共同研究。集成電路是以硅元件為基礎(chǔ)的數(shù)字邏輯的組合。核酸分子,特別是脫氧核糖核酸(DNA)分子已經(jīng)成為納米技術(shù)和生化環(huán)路上一種優(yōu)良的工程材料。核酸分子由于其自然的生物特性,體內(nèi)條件下能支持在技術(shù)上的應(yīng)用,體外條件下易化學(xué)合成方便進(jìn)行實(shí)驗(yàn),Watson-Crick互補(bǔ)原則能夠預(yù)測分子行為,這些優(yōu)點(diǎn)使得核酸分子成為分子計(jì)算領(lǐng)域一種有力的工具,長遠(yuǎn)來看可能是硅元件的一種替代物。 本論文是基于體外條件下對核酸分子邏輯門的研究。其分子邏輯門是指利用核酸分子在體外條件下重現(xiàn)數(shù)字邏輯的過程,構(gòu)建出的具有良好通用性的基礎(chǔ)元件。這大大增加了分子“電路”擴(kuò)大的可操作性。具體工作如下： (1)主要論述分子計(jì)算在經(jīng)典分子計(jì)算模型、圖靈分子計(jì)算模型、分子邏輯門計(jì)算模型3個(gè)方面不同領(lǐng)域的科學(xué)家門開展的工作研究,分子計(jì)算及其理論的分子計(jì)算機(jī)快速發(fā)展必然離不開多學(xué)科相互交叉的發(fā)展,雖然到目前極少有大規(guī)模人工構(gòu)建的分子“電路”(邏輯門在101-1000個(gè))產(chǎn)生,建立類似于硅電子學(xué)這種復(fù)雜性可靠性的分子“電路”更為遙遠(yuǎn),但可以看出一旦可靠的設(shè)計(jì)規(guī)則被科學(xué)家們建立,研究者就可以通過控制納米級的器件從而在體外環(huán)境中合成分子“電路”,這將與體內(nèi)的分子“電路”相互連接,這將可能推動(dòng)人工智能,腦機(jī)接口等領(lǐng)域的發(fā)展研究。 (2)電子電路以硅邏輯門作為基礎(chǔ),通常的8種用于電子器件之中：分別是OR, AND, XOR, INH, NOT, NOR, NAND, XNOR門；分子“電路”則需要以分子邏輯門作為基礎(chǔ),分子生物學(xué)的中心法則解釋了DNA, RNA,蛋白質(zhì)之間的關(guān)系。本文詳細(xì)闡述了體外條件下的DNA為核心的分子邏輯門的8種類型,并討論了更復(fù)雜的組件,DNA分子建立的加法器(其中包括半加器,半減器,全加器)和SR鎖存器,這證明了利用DNA分子構(gòu)建基礎(chǔ)邏輯門是完全可以的。但是,從電子電路考慮來看,這仍然顯得不足,首先,分子邏輯門是多種多樣的,其輸入輸出格式并不完全統(tǒng)一,這為下一步進(jìn)行級聯(lián)反應(yīng)甚至擴(kuò)大分子“電路”提供了障礙,科學(xué)家們?nèi)匀恍枰覍ねㄓ眯愿玫幕具壿嬙?(3)DNA鏈置換技術(shù)目前是科學(xué)家們在分子“電路”研究領(lǐng)域的“明星”,它被科學(xué)家用于動(dòng)態(tài)納米技術(shù)的研究要早于分子“電路”。肽核酸(PNA)是一種人工合成的分子,是核酸分子的類似物。本文通過PNA,基于鏈置換技術(shù)的基本原理,構(gòu)建了兩種鏈置換領(lǐng)域的新的邏輯門——禁門(INH)和隱含門(Implication),這將為已經(jīng)達(dá)到大規(guī)模的鏈置換式的分子“電路”加入新的邏輯運(yùn)算模型,為獲得更大規(guī)模的分子“電路”提供一種基礎(chǔ)門的選擇。 (4)分子信標(biāo)和納米金技術(shù)是目前是發(fā)展比較成熟的領(lǐng)域,但是在很長時(shí)間里研究工作中是獨(dú)立開展的,最近幾年,一些科學(xué)研究者開始結(jié)合兩個(gè)領(lǐng)域在分子計(jì)算領(lǐng)域做出了一些工作。本文構(gòu)建了一種新的基于分子信標(biāo)的核酸邏輯與門和或門模型,以寡核苷酸鏈作為輸入信號,熒光檢測作為輸出信號,并用更為靈敏的猝滅劑納米金替代了傳統(tǒng)的猝滅劑有機(jī)染料,提出與門使用雙色納米尺度的分子信標(biāo),區(qū)別于或門的單色分子信標(biāo)。同時(shí)本文通過引入分支遷移的原理,提出了一種新型的分子“半減器”模型,這種分子“電路”中比較復(fù)雜的邏輯組件將為下一步的小型或者更大規(guī)模的納米金型的分子“電路”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".

【學(xué)位授予單位】：陜西師范大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2013
【分類號】：Q523;TP338

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