Nucleic Acid Nanostructures and Topology

Abstract

Three aesthetically pleasing topological target structures resulting from DNA nanotechnology (from top to bottom): a cube, Borromean rings, and a truncated octahedron.These molecules are constructed by applying the assembly methods of biotechnology to stable branched DNA molecules.1. Introduction DNA NanotechnologyThe term ªnanotechnologyº has become a word encountered frequently in chemistry. There are many interpretations to this word, but the most visible goal of nanotechnology is to establish the same level of control over the manipulation and assembly of real molecules and molecular groupings that molecular graphics has over the manipulation and assembly of molecular models. There have been two key inspirations for this approach to very ambitious chemistry: The first was Feynmans famous talk, entitled ªTheres Plenty of Room at the Bottomº.[1] He suggested that it would be possible to make machines that could make replicas of themselves on a somewhat smaller scale; the ultimate application of this procedure would be very tiny factories that could be packed densely. The second inspiration has been our growing knowledge of the ways that biological systems arrange their structural components, primarily by self-assembly on a supramolecular scale; hence, this second approach to nanotechnology is biomimetic. Feynmans approach has engendered the ªtop-downº methodology, best exemplified today by molecular assemblies that have been arranged by using scanning probe microscopes.[2] By contrast, biomimetic nanotechnology is ªbottom-upº, in that individual components are designed to assume particular tertiary structures, and ultimately to self-assemble into quaternary structures and arrays.Top-down nanotechnology is characterized at this stage by elegance and by the ability to deal with substances of largely arbitrary composition. Its key limitation is its lack of parallelism; only small numbers of objects can be assembled at once. The bottom-up approach has a number of drawbacks, but it has the primary advantage of enormous parallelism; even chemistry done with a picomole of material results in more than 100 billion copies of the product species. Biomimetic nanotechnology cannot make use conveniently of intervention by the scanning probe microscopist; hence it has an additional burden, the design of molecules that fold correctly and reliably into their proper shapes. We understand this type of design best in those systems composed of biological macromolecules. This is a very restricted set of species, and their behavior is largely limited to aqueous systems. Nevertheless, we have better control over the folding of nucleic acids and, to a lesser extent, proteins than over most other polymers on the nanoscale. The design of a protein and accurate prediction of protein folding remain key challenges in the area, although striking progress is being made. [3] Nucleic acids are much simpler, and therefore we have a much better grasp of their folding. Here, we will dwell on nucleic acid nanotechnology, primarily DNA nanotechnolo...

Topological constraints in nucleic acid hybridization kinetics

“…Intertwining of strands is a common occurrence in nucleic acid structures, as stacking interactions between adjacent base pairs ensure that the strands wrap around each other in a helical fashion. This phenomenon has been exploited by Seeman and co-workers (7) to design structures with knotted and linked topologies that employ both the right-handed helicity of B-DNA and the left-handed helicity of Z-DNA.…”

Programmable motion of DNA origami mechanisms

“…Amino acid polymers exhibit well-defined and complex dynamics in natural systems and have been assembled into designed structures including nanotubes, sheets, and networks (10)(11)(12), although the complexity of interactions that govern amino acid folding make designing complex geometries extremely challenging. DNA nanotechnology, on the other hand, has exploited well-understood assembly properties of DNA to create a variety of increasingly complex designed nanostructures (13)(14)(15).…”

DNA Branch Migration Reactions Through Photocontrollable Toehold Formation

“…Branch migration describes the ability of a DNA strand partially paired with its complement in a duplex to extend its pairing by displacing the resident strand with which it is homologous. Extending this concept to DNA nanotechnology, 2,3 Yurke et al constructed a type of dynamic DNA-fueled molecular machine, 4 which they termed as “toehold-mediated DNA strand displacement”. In this machine, a single-stranded DNA in a double-stranded complex is displaced by another single-stranded DNA with the help of a short sequence of contiguous bases called a “toehold”, and today this concept prevails in dynamic DNA nanostructures 5–7 worldwide.…”