Construction Of Dynamic DNA Origami Structures For In Situ PH Monitoring Studies

Probing the subtle variation of localized pH is crucial toward progress in exploring and understanding chemical reactions and physiological processes for wide fields of electrocatalysis,biochemical engineering,cell biology,and biomedicine.As a programmable material,DNA has good biocompatibility and spatial addressing ability,and plays an important role in biosensor,drug delivery and molecular machine construction.Among them,DNA origami,as an epoch-making DNA self-assembly technology,can control the construction of a variety of complex static and dynamic nanostructures.Its conformational changes and nano-precision positioning functions provide unparalleled spatial resolution for the detection of biochemical reactions and the study of single molecule interactions.Under this background,a dynamic DNA origami structure is designed and constructed in this paper.With three-stranded nucleic acid as the recognition unit,the conformational changes of DNA origami can be directly monitored by transmission electron microscope,and the pH gradient around single-arm carbon nanotubes can be successfully drawn.This in-situ measurement method is expected to accurately detect the subtle changes of local pH at the nanometer resolution,which provides a basis for further study of chemical and biological reaction processes and mechanisms in vivo and in vitro.It mainly includes the following contents:(1)A three-dimensional DNA origami structure is successfully designed by using ca DNAno software.In this chapter,the design principle of DNA origami and the basic operation of ca DNAno software are introduced in detail,and the V-shaped DNA origami is designed successfully by using this software.Compared with manual drawing,the use of ca DNAno greatly reduces the workload of designing DNA origami structure and reduces the error rate in the design process.(2)A highly stable dynamic DNA origami structure is constructed.By simulating the motion mechanism of a natural machine,a dynamic and accurately assembled V-shaped DNA origami is successfully constructed by a simple "one-pot method".At the same time,the DNA origami structure maintained high stability under simulated biological conditions(high salt concentration,molecular crowding and weak acid conditions).The combination of kinetic mechanism and DNA origami is of great significance for the construction of molecular motors,drug delivery,biosensors and plasma.(3)An in-situ DNA monitoring method based on dynamic pH origami structure was developed.Through the combination of DNA origami and transmission electron microscopy,using triple-stranded nucleic acid as a recognition probe,the conformational changes of local DNA origami were directly revealed by the conformational changes of visible pH origami.In addition,different target molecules are identified by changing the viscous end modification of the staple chain.Unlike spectroscopic pH sensors,our molecular nanocaliper provides high spatial resolution and stable response with the help of TEM.(4)The pH gradient near single-walled carbon nanotubes was successfully revealed by using dynamic DNA origami structure.We have developed a dynamic DNA origami probe.With the help of high-resolution imaging analysis of transmission electron microscope,it is found that the pH gradient boundary near carbon nanotubes can reach 200 nm.This in situ measurement of local pH changes provides a basis for further study of chemical and biological processes and mechanisms in vivo and in vitro.