The Chinese Postman Problem Based on Molecular Beacon Strand Displacement

With the help of the special structure of the molecular beacon, a solution model of the Chinese postman problem is established by using the DNA strand displacement reaction principle. First, the problem is mapped into an undirected weighting graph. Then the vertex and arc of the graph are coded according to the coding principle. Secondly, structure probe, and make use of stand displacement to find solutions to satisfy the problem. Finally, the optimum solution was extracted by gel electrophoresis. The model has high sensitivity, specificity, and the lower error rate. The solution reaction can be carried out at normal temperature. The model calculation shows that the complexity of the problem can be reduced by using the molecular beacon strand displacement reaction to solve the Chinese postman problem.

[1]  Yuriy Brun Arithmetic computation in the tile assembly model: Addition and multiplication , 2007, Theor. Comput. Sci..

[2]  J. SantaLucia,et al.  A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Lulu Qian,et al.  Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components , 2017, Nature Communications.

[4]  E. Winfree,et al.  Algorithmic Self-Assembly of DNA Sierpinski Triangles , 2004, PLoS biology.

[5]  Aby K. George,et al.  DNA strand displacement-based logic inverter gate design , 2017 .

[6]  Yuriy Brun Nondeterministic polynomial time factoring in the tile assembly model , 2008, Theor. Comput. Sci..

[7]  Yuriy Brun Solving NP-complete problems in the tile assembly model , 2008, Theor. Comput. Sci..

[8]  Bernard Yurke,et al.  Using DNA to Power Nanostructures , 2003, Genetic Programming and Evolvable Machines.

[9]  Brian M. Frezza,et al.  Modular multi-level circuits from immobilized DNA-based logic gates. , 2007, Journal of the American Chemical Society.

[10]  Arun Richard Chandrasekaran,et al.  DNA origami and biotechnology applications: a perspective , 2016 .

[11]  Jing Yang,et al.  The Working Operation Problem Based on Probe Machine Model , 2016, BIC-TA.

[12]  Luca Cardelli,et al.  Design and analysis of DNA strand displacement devices using probabilistic model checking , 2012, Journal of The Royal Society Interface.

[13]  G. Seelig,et al.  Enzyme-Free Nucleic Acid Logic Circuits , 2022 .

[14]  Thomas H LaBean,et al.  Stepwise self-assembly of DNA tile lattices using dsDNA bridges. , 2008, Journal of the American Chemical Society.

[15]  Jing Yang,et al.  Molecular logic computing model based on DNA self-assembly strand branch migration , 2013 .

[16]  C. P. Chandran Prediction and simulation on DNA strand displacement for the analysis of DNA nanotechnology , 2016 .

[17]  P. Cochat,et al.  Et al , 2008, Archives de pediatrie : organe officiel de la Societe francaise de pediatrie.

[18]  Guangzhao Cui,et al.  Fluorescence Resonance Energy Transfer-Based Photonic Circuits Using Single-Stranded Tile Self-Assembly and DNA Strand Displacement. , 2017, Journal of nanoscience and nanotechnology.

[19]  Lulu Qian,et al.  Supporting Online Material Materials and Methods Figs. S1 to S6 Tables S1 to S4 References and Notes Scaling up Digital Circuit Computation with Dna Strand Displacement Cascades , 2022 .

[20]  Jehoshua Bruck,et al.  Neural network computation with DNA strand displacement cascades , 2011, Nature.

[21]  Jin Xu,et al.  Probe Machine , 2015, IEEE Transactions on Neural Networks and Learning Systems.

[22]  Qiang Zhang,et al.  Logic Calculation Based on Two-Domain DNA Strand Displacement , 2017, ISNN.

[23]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.