Research On The Construction Of DNA Circuit For Data Backtracking And Single Nucleotide Variants Smart Identification

Based on DNA nanomaterials,researchers designed a variety of DNA strand displacement reaction mechanisms.Based on different reaction mechanisms they constructed functional circuits that can perform logic judgment,information protection,reuse,signal amplification,and nucleic acid detection.These functional circuits have been widely used in their respective fields.Despite this,the functional circuits have not been able to meet all research needs.There are still some unresolved issues.First,the existing DNA function circuit cannot trace back the data output in the middle of the circuit.Second,the single nucleotide variant(SNV)detection circuit cannot identify multiple homologous DNAs at once.Around these problems,this paper proposes two DNA functional circuits for data backtracking and SNV intelligent identification.Nupack software is used to simulate and test the designed circuit using,cross-check the hybridization properties and anti-interference ability of DNA molecules in the circuit,design and select the base sequence that meets the experimental design.Native-PAGE and fluorescence spectrum experiment are used to verify the operation process and results of the circuit.The main thesis is consisted of the following parts:Chapter 2: Similar to the silicon-based computing system,the DNA computing system is also difficult to avoid the transmission of erroneous data during the data transmission process.It will seriously affect the reliability of the results of conventional logic calculations.In order to solve this problem,we integrate data redundancy programming idea into the design of DNA logic circuits to construct functional circuits that can perform data backtracking.According to the redundancy idea,the redundant module equivalent to the calculation module is constructed on the logic gate unit of the circuit.Thus,the redundant reporting module is equivalent to the information of the reporting strand when reporting the redundant strand,thereby recording the state of the previous logic gate.According to the comparison between the information reported by the redundant reporting module and the truth table,the reliability of the final circuit calculation result can be verified.The backtracking function can also help find the error position of the circuit when the calculation result is wrong,thereby improving the circuit design.Chapter 3: There are multiple homologous oligonucleotide strands in an organism with only one base difference from each other,which has different biological significance.If identify each nucleotide based on traditional methods,an equal number of DNA labeled probes have to be designed,which causes unnecessary manual checks and increases the complexity of the system.In order to solve this problem,we try to apply the combinational logic judgment function of DNA logic circuits to the SNV identification,enabling analysis of each input.We designed a 4-to-2 encoder circuit with molecular diagnostics function,which can accurately identify SNV sites in four homologous oligonucleotides.First,according to the differential information of four homologous oligo-nucleotides,two 2-to-1 encoders have been constructed with the molecular information as the input.And then,two 2-to-1 encoders have been assembled to fabricate a 4-to-2 encoder,which converts the DNA molecular information into four different combinations of fluorescent signals.Therefore,based on the one-to-one correspondence between input and output,we have realized the smart identification of SNV on a domain level from four homologous strands with one test instead of four,greatly enhancing the identification efficiency.