Insights into the Structure and Energy of DNA Nanoassemblies

Abstract

Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.

Design, Mechanical Properties, and Dynamics of Synthetic DNA Filaments

“…Briefly, the main difference between a tile-based and a scaffold-based (or origami) approach is the following: whereas in the former method all strands hybridize to one another, in the latter method all strands hybridize to distinct regions of the same scaffold sequence. 22 The consequence is that the selfassembly of tile-based structures requires careful control of the stoichiometry ratio and purity of the component strands to be successful. This results in lengthy and error-prone procedures, but�once optimal conditions are found�few sequences are sufficient to obtain very long filaments.…”

Molecular Dynamic Studies of Dye–Dye and Dye–DNA Interactions Governing Excitonic Coupling in Squaraine Aggregates Templated by DNA Holliday Junctions

“…DNA nanotechnology has recently demonstrated that it is a useful tool for the assembly of nanoscale structures. It can control dye-dye distances with sub-nanoscale control of distances necessary to produce excitonic coupling in dye aggregates covalently templated (or scaffolded) by DNA [ 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. The construction of complex DNA scaffolds is facilitated by the programmable self-assembly method enabled by Watson–Crick–Franklin base pairing rules [ 34 , 35 ].…”

“…The construction of complex DNA scaffolds is facilitated by the programmable self-assembly method enabled by Watson–Crick–Franklin base pairing rules [ 34 , 35 ]. More complex DNA scaffolds can be used to create molecular aggregates [ 23 , 36 , 37 , 38 ]. The four-arm DNA Holliday Junction (HJ) is an example [ 37 , 38 , 39 ].…”

Analysis of Selected Variants of DRD2 and ANKK1 Genes in Combat Athletes

“…To be more precise, the DRD2 gene and rs1076560 polymorphism. Human DNA (deoxyribonucleic acid) is composed of two polynucleotide chains composed of simpler monomeric units called nucleotides [5,6]. Each nucleotide is composed of one of four nitrogen-containing nucleobases, which are cytosine (C), guanine (G), adenine (A) or thymine (T).…”