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Applied Research On DNA Self-assembly Model In Biosensor Design

Posted on:2015-02-16Degree:DoctorType:Dissertation
Country:ChinaCandidate:J YangFull Text:PDF
GTID:1108330470476016Subject:Environmental Engineering
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This paper takes the self-assembly molecular beacons as the core, the biosensor design as the main study object to improve the performance of the biosensor. Study the application of the model in the NP problem and its complexity. And study exploratory of its application in biosensor probe design, analyze the improvement of the sensor sensitivity and response time.This paper focuses on the monitoring of drinking water sources combining the advantages of nano gold and magnetic particles to design biosensors for the detection of pathogens and viruses in water. The main detection principle of the biosensor is the self-assembly technology of DNA molecules. Therefore, the paper first introduces the techniques of DNA molecular self-assembly, and gives the computational model of DNA self-assembly on combinatorial optimization problems, and demonstrates the enormous parallelism of DNA computing.The main contents are as follows:Firstly, we analyze "hairpin" unique structure of the molecular beacon, and give DNA computing model of maximum matching problem by using the high sensitivity, specific combination, quick response, fluorescently labeled and so on. Using fluorescent labels of molecular beacons stems, we can visually observe complete biochemical reactions. When the hairpin turns on, the fluorescence enhances, but when all the hairpins are opened, the fluorescence is not changed. It shows this reaction time has been finished completely, and we can go on to the next step. In addition, the complexity of the model is associated with the degree of the vertices. Theoretical analysis shows that there is the undirected graph of m vertices and n arcs, which calculates its maximum matching by using molecular beacon. Use the model to analyze the complexity of the algorithm. Encoding and biological complexity of the encoding operation, and with only the vertices and arcs increases to increase, and its complexity is (?) (n2).Secondly, the paper analyzes currently used DNA tile, it has some shortage of complex structure, difficult to fluorescent labels and so on. We design molecular beacons tile by using molecular beacons advantages. It has simple structure which can be fluorescently labeled, and in the reading solution by means of fluorescence spectroscopy, etc. to help analyze and reduce the biochemical operations in the calculation process. It has strong specific binding and fast response, etc. to a certain extent reduce the error rate calculation solution. Using molecular beacons tile to give the maximum matching computational model of graph G Setting the arcs of G be mapped to binary combinations before calculating. If i-th bit of an n-bit binary number is set to 1, it represents the corresponding i-th arc in M rather than in E-M. If it was set to 0, it represents the corresponding i-th edge is not in M rather than in the E-M (M is arcs set).Using self-assembly algorithm finds all the matching from combinations 2n of G, and then finds the maximum matching. For molecular beacons calculation model, this algorithm reduces the complexity from (?)(n2) to (?)(n).Using self-assembly model to solve the dislocation permutation problem in combinatorial optimization, we provide all the arrangement, and then verify whether every arrangement is full derangement by using of parallelism of biochemical reaction, last use fluorescence spectrometer to read result. Later the paper puts forward self-assembly model of integer linear programming problem, builds multiplication, addition and compares subsystem to solve the problem, then reads solution making use of the fluorescently labeled and some other molecular biotechnology operations. Fortunately, the self-assembly model also solves the 3-satisfiability problem, using fluorescent labeling methods and self-assembled modules for simultaneous determination of each sentence. Then, make every sentence be true that is solution of the problem means this formula is satisfiable.On the complexity of the self-assembly of molecular beacons were analyzed separately from model calculations and spatial complexity, we can know that the computational complexity and space complexity are all constant or linear function of problem size n. From solving these NP problems, the model fully embodies the advantages of self-assembled molecular beacon models. The next step is that we will study the versatility of this model and test it.In summary, this paper is based on the advantages of their unique structure which combines advantages of the nano-gold and magnetic nano-particles to design a DNA biosensor for detecting a pathogen (e.g., E. coli). Using the characteristics of the probe of locked nucleic acid (LNA), peptide nucleic acid (PNA), the DNA nano structure and combining the advantages of nano-gold and magnetic nano-particles, the paper respectively design several DNA biosensors for the detection of virus in water. These several DNA biosensors theoretically shorten the response time, improve the sensitivity and make a step for achieving the real-time monitoring of the environment...
Keywords/Search Tags:DNA biosensor, environmental monitoring, molecular beacon self-assembly, maximum matching problem, integer linear programming, the dislocation arrangement, satisfiability problem
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