Molecular Computing And Applications Based On Strand Displacement

Traditional silicon-based computers face two major bottlenecks in terms of solving complex large-scale computing problems: chip manufacturing process limitations and computation power.DNA computing makes full use of the ultra-high-density information storage capacity of DNA molecules and the high parallelism of storage-computing integration.It has the potential to overcome the above-mentioned bottlenecks,and is especially suitable for the representation of graph-structured data and the solution of graph computing problems.DNA strand displacement is one of the important techniques of DNA computing,which has the characteristics of programmability,accuracy,spontaneity and sensitivity.In recent years,it has been widely used to construct molecular circuits for complex functions such as handwriting recognition and NP-complete problem.However,as the scale of the molecular circuit increases and the number of cascades grows,the leakage problem becomes an urgent issue that needs to be addressed.In order to overcome the leakage problem and achieve more complex functional applications,this thesis designs a domino AND computational system and a DNA computational system for cancer analysis based on DNA strand displacement.The main aspects are as follows.To solve the leakage problem caused by cascading between logic gates,Domino logic gates are driven by long chains and powered by toehold domains,enabling multi-level cascading.Drawing inspiration from the gravitational potential energy transfer of dominoes,this thesis proposes the domino rule,which adjusts the sequence based on melting temperature and free energy,and improves the scalability,stability and robustness of logic gates.A multiparallelism molecular circuit is constructed based on domino logic gates,enabling the solution of decision problems using tic-tac-toe as an example.Biomarkers were obtained by analyzing the Cancer Genome Atlas(TCGA)data set including mi RNA and clinical features,using bioinformatics methods such as limma analysis and WGCNA.A DNA calculation system for cancer analysis was designed using biomarkers as input and fluorescence report results as output according to the winner-take-all principle.The system has the advantages of faster and easier operation compared with traditional methods.It is beneficial to explore rapid and accurate cancer diagnostic techniques toward inexpensive,non-invasive and rapid disease screening,categorization and progress detection.