DNA Dynamic Assembly Induced By The Non-classical Hydrogen Bond

A series of dynamic DNA devices could be rationally constructed by using toehold-mediated DNA strand displacement reaction(TSDR).A small molecule,cyanuric acid,could reprogramme the assembly of poly(adenine)(poly(A))into stable fibres by the non-classical hydrogen bond.Here,we construct a new dynamic assembly model for micro RNA typing and DNA tetrahedron assembly,which is toehold-mediated DNA strand displacement reaction induced by the formation of the non-classical hydrogen bond between the poly(A)and cyanuric acid.We intend to make the DNA dynamic assembly happen and improve its yield and rate by optimizing the reaction conditions,the concentration of the reactants and the length of the oligonucleotide.While optimizing the reaction conditions,we find the yield and the rate of the reaction reaches the maximum at a pH value of 4.5,10 mmol·L-1 Mg2+ and room temperature(25 °C),which means the fluorescence intensity of the system increases the most.While optimizing the concentration of the reactants,we find when the initial concentration of the oligonucleotide is 1 ?mol·L-1,the yield and the rate of the reaction could reach the maximum at 500 ?mol·L-1 cyanuric acid.While optimizing the length of the oligonucleotide,we find when two bases are added into the head of the model,the yield of the reaction could reach the maximum.The experimental results are characterized using atomic force microscope,polyacrylamide gel electrophoresis,emission spectrum,circular dichroism spectra and melting curve apart from the fluorescence intensity.This model assembles quickly than the Watson-Crick bond induced strand displacement,and the rate of strand displacement can be tuned by a variety of external and internal factors.If we would like to make a distinction between micro RNA let-7a and let-7c by this DNA model,we should replace the protector strand by the let-7a or let-7c and make it happen at the optimum conditions.From the results,we find the rate and degree of the decrease of the fluorescence intensity are different at different target strands,which means this model could be used for micro RNA typing.This model could also be used for DNA tetrahedron assembly,which means it has ability for building nanostructure.