DNA Self-assembly Based On Small Circular DNAs To Create 1D And 2D Nanostructures

DNA being a nanoscale molecule serving as a complete store-house of genetic information can be fabricated into geometrically fine nanostructures in one-(1D),two-(2D)and three-(3D)dimensions via bottom-up self-assembly of designed nucleotides with specified length.In 1982,Nadrian C.Seeman and his colleagues pioneered the field of DNA nanotechnology after taking the specific programmability of DNA under their consideration to construct a variety of nanostructures,nanofabrication and nanodevices.In fact,the construction of highly ordered and complex geometric structures and periodic arrays has been made possible merely due to distinct characteristics of DNA such as its nanoscale size,distinct base-pairing,excellent predictability and programmability.Also the advent of synthetic oligonucleotides has fast-tracked the self assembly of the complex nanoarchitecture.DNA nanotubes as an important component class in nanomachine can potentially template the growth of nanowires,act as drug delivery vehicles and molecular motors.In particular,drug delivery vehicles based on DNA are a promising class of biodegradable and biocompatible drug nanocarriers.Their size,shapes,and ligand-targeting are more precisely tunable than any of the currently available nanomaterials.The parallelogram framework yielding 2D arrays based on rigid DNA triangle tiles with Holliday junction at vertices are of promising importance on the ground of their usage,for example,for probing cooperative effects in ligand binding,for investigating proximity effect between proteins or other macromolecules and for the evaluation of their organizational power to position the target site.The parallelograms can further be implemented to construct sophisticated biomimetic nanostructures.The designed 2D DNA arrays can be used to manipulate signals for gene regulation as well as gene expression,as nano-medicine carrier and target specific drug release.DNA lattices could serve as a support for biological particles,for example protein complexes or viruses,for TEM imaging.In this dissertation,experiments rendered small circular DNA molecules as tiny building blocks to construct 1D and 2D nanostructures.This presents an endeavor to make the small circular oligonucleotides a new family member of DNA nanotechnology.The small circular DNA molecules(<100-nt)were assembled into 1D nanotubes and 2D crystalline arrays,described as follows.1.The 5'-phosphorylated linear DNA strand was circularized with the help of a splint strand in the presence of T4 DNA Ligase.The small circular DNA strands with designed lengths of 48-,50-,and 52-nt,are directed to self-assemble into four types of nanotubes after hybridization with complementary staple strands,following the folding strategy with each double crossover(DX)at 2.5 turns.Much smaller DNA circles such as the 32-nt ring were also tried to grow nanotubes.2.We used small circularized DNA molecules of different lengths(?84-nt)as core strands,and successfully synthesized two dimensional(2D)arrays consisting of lozenge framework based on Mao's DNA tensegrity triangle tiles with four-arm junctions(Holliday junctions)at all vertices.Due to the intrinsic curvature of the triangle tile and the consecutive tile alignment,the 2D arrays are organized in the form of nanotubes.Two kinds of triangle tiles with equilateral side lengths of 1.5 and 2.5 full helical turns are connected by sticky ended cohesion of duplex with a length of 2.5 helical turns respectively.They were observed as parallel lozenge tiling lattices by high resolution AFM images,where the former has a unit cell of internal angles of 60° and side length of 13.6 nM,and the latter has the similar geometrical type of unit cells but with the side length of 17.0 nm.Modification of the triangle tile with infinitesimal side length disturbance and insertion of one T(thymine nucleotide)single stranded loop at every vertex of the triangle has also been tested.