New motifs in DNA nanotechnology

Abstract

Recently, we have invested a great deal of effort to construct molecular building blocks from unusual DNA motifs. DNA is an extremely favorable construction medium. The sticky-ended association of DNA molecules occurs with high specificity, and it results in the formation of B-DNA, whose structure is well known. The use of stable-branched DNA molecules permits one to make stick-figures. We have used this strategy to construct a covalently closed DNA molecule whose helix axes have the connectivity of a cube, and a second molecule, whose helix axes have the connectivity of a truncated octahedron. In addition to branching topology, DNA also yields control of linking topology, because double helical half-turns of B-DNA or Z-DNA can be equated, respectively, with negative or positive crossings in topological objects. Consequently, we have been able to use DNA to make trefoil knots of both signs and figure of 8 knots. By making RNA knots, we have discovered the existence of an RNA topoisomerase. DNA-based topological control has also led to the construction of Borromean rings, which could be used in DNA-based computing applications. The key feature previously lacking in DNA construction has been a rigid molecule. We have discovered that DNA double crossover molecules can provide this capability. We have incorporated these components in DNA assemblies that use this rigidity to achieve control on the geometrical level, as well as on the topological level. Some of these involve double crossover molecules, and others involve double crossovers associated with geometrical figures, such as triangles and deltahedra.

Electron self-trapping on a nanocircle

“…Amongst them one finds the cyclic biological macromolecules, such as intact DNA from most prokaryotes and viruses, mitochondria plasmid DNA [2,3,4], cyclic DNA macroarrays used for the systematic screening of gene expression [5,6,7]. Large circular single stranded RNAs form genomic material of viroids [8,9].…”

Fabrication of Positively Patterned Conducting Polymer Microstructures via One‐Step Electrodeposition

“…[1] Traditionally, the construction of patterned conducting polymer structures is achieved through photolithography, [2] electron-beam (e-beam) writing, [3] screen printing, [4] or ink-jet printing, [5] as has been reviewed by several authors. [6] However, these methods may either cause damage to the conducting polymer layer or involve high costs, while new opportunities in nano-/microscale fabrication require new types of patterning technology.…”

Rational Design of DNA Nanoarchitectures

“…[19] For example, single building blocks might be assembled and purified in individual reactions before they are combined to produce the final architecture. A most crucial step in the entire process is that the structural integrity, connectivity, and possibly also the conformation of the resulting supramolecular network need to be characterized by using biochemical methods, such as electrophoresis of reporter strands (Figure 2), [20] restriction analysis, or fragmentation assays, [21] or nowadays by microscopic techniques, such as atomic force microscopy (AFM), [22] transmission electron microscopy (TEM), or cryoelectron microscopy. [23] 3.…”