Precise Control And Application Of Reconfigurable DNA Origami Domino Array

The field of DNA nanotechnology uses DNA molecules as the basic building blocks to assemble artificial structural motifs and to connect them together.Structural DNA nanotechnology offers a robust programmable platform for diverse nanoscale shapes that can be used in constructing custom nanoshapes and exquisite patterns.The dynamic DNA nanotechnology can further realize the dynamic manipulation and regulation of assembled molecules and nanomaterials,and has been widely used in plasma sensors,nanophotonic devices,catalysis,structural biology and other fields.This research is mainly based on the controllably conformational transformation of the reconfigurable DNA origami domino array(DODA).It is used as a platform for nano-scale controllable molecular manipulation,and its dynamic modification is used to rearrange the assembled primitives in space,and explore its use in information storage.It is expected to provide new methods and platforms for exploring energy conversion,biomolecular interaction and regulation mechanisms at the nanoscale.The main content of the research includes the following four parts:1.Design,Preparation and Characterization of Reconfigurable DODAFirst,I designed and synthesized a reconfigurable DODA nanostructure.Unlike the static DNA origami nanostructure,the conformation of the reconfigurable DODA nanostructure is variable,that is,after adding the trigger DNA strands,DODA can transform from one stable conformation("Before" DODA)to another stable conformation("After" DODA).The conformational transformation of DODA is longrange and controllable.In addition,the conformational transformation of the reconfigurable DODA is also affected by the number and position of the boundary DNA strands,temperature and formamide concentration.Then I systematically explored the influence of these parameters on the efficiency of conformational transformation of DODA nanostructures,the obtained optimal conditions have effectively improved the efficiency of its conformation transformation.This work laid the foundation for subsequent applications.2.Information Coding in Reconfigurable DODADNA nanostructures with programmable nanoscale patterns has been achieved in the past decades,and molecular information coding(MIC)on those designed nanostructures has gained increasing attention for information security.However,exerting steganography and cryptography synchronously on DNA nanostructures still remains a challenge to guarantee more security approach for MIC.In this part,we demonstrated MIC in a reconfigurable DNA origami domino array(DODA),which can reconfigure intrinsic patterns but keep the DODA outline the same for steganography.When a set of keys(DNA strands)are added,the cryptographic data(e.g.Numbers “0-9”)can be translated into visible patterns within DODA.More complex cryptography with ASCII nanocodes definition within programmable 6×6 lattice is demonstrated to ensure the versatility of MIC in the DODA.3.Proximity-induced Pattern Operations in Reconfigurable DODAMolecular patterns with nanoscale precision have been used to mimic complex molecular networks.One key challenge in molecular patterns is to perform active pattern operations in controllable systems to fully imitate their complex dynamic behaviors.In this part,we present a reconfigurable DNA origami domino array based dynamic pattern operation(DODA DPO)system to perform proximity-induced molecular control for complex pattern operations.The activatable platform of reconfigurable DODA endows a spontaneous cascade of stacking conformational transformation from the “Before” to “After” conformation by a set of “trigger” DNA strands.The conformational transformation further brings the operational pattern units into close proximity to undergo DNA strand displacement cascades to accomplish three different pattern operations of “Writing”,“Erasing” and “Shifting”.Our results also demonstrate the reconfigurable DODA DPO system provides a useful basis to study vari-ous molecular control analysis in a fully programmable and controllable fashion.4.Controlling the self-assembly of biocatalytic architectures in reconfigurable DODAMolecular self-assembly in biological system is regulated by spatially confined molecular mechanisms.Researchers are increasingly seeking to mimic biology’s approaches in an effort to enhance control over self-assembly processes.One key challenge is to reconstitute and reprogram to fully imitate their complex dynamic behaviors to achieve similar complexity in the laboratory.Here,we present a reconfigurable DNA origami domino array-based(DODA)system to control and regulate self-assembly reactions.The DODA-based system performs controllable and regulable self-assembly process for the assembling reactants compared to the free system.The platform of reconfigurable DODA endows a spontaneous cascade of stacking conformational transformation from “2D narrow(2D-N)” to “2D wide(2DW)”,then to “3D narrow(3D-N)”,final to “3D wide(3D-W)” conformations by distinct“trigger” DNA strands.The conformational transformation not only regulates the assembling reactants into close proximity to undergo self-assembly reactions,but also spatially isolates the reactants to disassemble.This work also demonstrates the reconfigurable DODA-based system provides a useful basis to study various molecular control analyses in a fully programmable and controllable fashion.