Design and Application of On-chip DNA Hybridization Probe and DNA-directed Assembly of Gold Nanoparticles

Author:Zhou Xiang

Supervisor:liang hao jun


Degree Year:2018





As the carrier of genetic information,DNA plays an important genetic role in living systems.Owing to the specificity and predictability of Watson-Crick base pairing,DNA has proved its importance in the fields of biology and biotechnology,such as isothermal amplifications,microarrays and oligonucleotide hybridization probe.In chapter two,we investigated the influence of the toehold strategy of on-chip DNA hybridization probe on the discrimination of single nucleotide polymorphism using dual polarization interferometry.Through adjusting the toehold length,the toehold strategies of on-chip toehold exchange probe were thoroughly optimized.For the "6/5" probe,an optimal discrimination factor of 78%against the spurious target was achieved.Moreover,the ability of the on-chip probe in SNP discrimination was significantly enhanced compared to its pure solution counterpart.This simple and rapid detection method for SNP discrimination based on the on-chip toehold exchange probe will show great potential in disease diagnosis.On the other hand,owing to its sequence-specific binding property and programmability,DNA has also emerged as a versatile and powerful material in the field of nanotechnology and nanoscale engineering.As a kind of DNA nanomaterials,spherical nucleic acid(SNA)-nanoparticle conjugates have been applied for biosensing,gene regulation and material manufacturing based on its excellent and specific properties.In chapter three,we designed and prepared photoresponsive SNA conjugates by inserting photocleavable linker into the recognition sequence of SNAs which can block the reactivity of system temporally until specific UV light(~365 nm)is introduced.The photoresponsive SNAs realized a temporal regulation of self-assembly reaction circuit and a spatial selectivity of microRNA release in cell population,respectively.As a polyvalent nanoparticle whose external DNA molecules carry information in their sequence,SNA-nanoparticle conjugates are typical "programmable atom-equivalents".Like atoms,SNAs are treated as building blocks that can be assembled into highly ordered materials,but unlike atoms,the interaction between SNAs particles even the equilibrium crystal structures can be programmed by DNA sequence.Although promising in thermodynamics,unfortunately,due to the kinetic barriers on its way to the most stable state during assembly,it always traps in some metastable states.In order to control the kinetic pathway,the temperature of assembly system is always adjusted by an annealing process.However,the steep dependence of the attractive strength between SNAs particles on temperature challenges the control of programing SNAs into a particular structure of equilibrium phases and their temperature-dependent transitions.In chapter four,we proposed a new approach to control the kinetic pathway by omitting the annealing step.Through constructing a time-dependent interaction system in a two-layer fashion,the interaction between SNAs particles can be tuned to increase slowly.As a result,SNAs have been programmed into face-centred-cubic and body-centred-cubic crystal structures.We hope SNAs can be further programmed into the sophisticated materials with more complex phase bebaviors by intergrating time-dependent interaction schemes.