Construction And Biomedical Applications Of Intelligent DNA Molecular Machine

DNA has been widely used in the construction of molecular computation systems due to its powerful parallel computing capability and super-high storage capacity.On the other hand,attributed to its unprecedented spatial addressability and sequence programmability,DNA has been used as highly versatile building blocks for constructing various nanostructures with precisely controlled sizes and shapes.Intelligent DNA molecular machines can be developed by combining DNA nanostructures with DNA molecular computation.In this thesis,by integrating DNA computing modules into DNA nanostructures,three functional DNA molecular machines have been constructed and applied to the biomedical field,including cancer cell recognition and bioimaging,protein function regulation and molecular diagnosis.The major contents are as follows:(1)We engineered an aptamer and DNA displacement reaction-based molecular machine that can drive the assembly of gold nanoparticles in response to epithelial cell adhesion molecule(EpCAM)on cancer cell membranes.The dynamic system consisted of a core nanoparticle and small satellite nanoparticles.With the modifications of different DNA hairpin strands and swing arm strands partially hybridized with an aptamer that specifically recognizes EpCAM,the two separated particles can dynamically assemble into a core-satellite assembly in response to EpCAM proteins on the cell membrane surface.The assembly of nanoparticles driven by DNA molecular machine generated plasmonic coupled hot spots for surface-enhanced Raman scattering(SERS)for sensitively capturing the dynamic shape change of nanoassembly in cellular environment.Thus this DNA molecular machine can identify cancer cells by targeting overexpressed cancer cell biomarkers.(2)Molecular machines that are able to autonomously perform their functions based on a concentration-triggered threshold control inspire a more efficient and safer strategy for future personalized medicine.Herein,we constructed an intelligent DNA molecular machine for autonomous blood anticoagulation in human plasma.The DNA molecular machine comprises a barrel-shaped DNA nanostructure as the framework and molecular reaction cascades embedded as the computing core.This molecular machine can intelligently sense the concentration of thrombin in the local environment and trigger an autonomous anticoagulation when excess thrombin is present.The triggering concentration of thrombin at which the molecular machine responds can be tuned arbitrarily to avoid possible side effects induced by excess thrombin.This makes the molecular machine useful for autonomous anticoagulation in various medical scenarios.(3)We constructed a DNA molecular machine for molecular diagnosis,which can be used to analyse miRNA profiles in clinical serum samples and accurately differentiate non-small cell lung cancer(NSCLC)and healthy individuals from their serum samples at a molecular level.The DNA molecular machine comprises molecular reaction cascades embedded as the computing core and a two-dimensional DNA origami as the framework.We simplified the mathematical operations of the in silico-trained classifier into multiplication,summation and subtraction,and DNA molecular machine implemented the calculations at a molecular level.The DNA molecular machine can be applied to analyse miRNA profiles in clinical serum samples and realize rapid and accurate cancer diagnosis.We envision that the DNA molecular machine will inspire more clinical applications towards inexpensive,non-invasive and routine early cancer screening and classification,as well as monitoring cancer recurrence.