Rational Engineering of Dynamic DNA Systems

Abstract

Opening time: A method for the systematic and automatable design of DNA hybridization networks was recently introduced, which was based on the catalytic opening of metastable hairpin loops (see scheme). This technique has various applications in nanobiotechnology, such as the stepwise self‐assembly of DNA scaffolds and the engineering of dynamic DNA devices.

From DNA Nanotechnology to Material Systems Engineering

“…From its very beginning, the genesis of DNA nanotechnology was intrinsically tied to the development of mathematical models and computational algorithms, be it to design complex DNA nanostructures using computer‐aided methods or to exploit DNA assembly and amplification in DNA computation to process information . Both approaches include dynamic DNA systems, in which reversible transition mechanisms between various stable or metastable states, such as secondary structure conformations, are implemented by means of hybridization, strand‐displacement, cleavage or other processes . This can be utilized, on the one hand, for dynamic scaffolds, such as the reconfigurable plasmonic metamolecule, shown in Figure C.…”

Functionalized DNA Nanostructures for Nanomedicine

“…Reports of such nanomachines date back to 1999 when Seeman and coworkers built a DX tileÀbased device containing a double-stranded d(CG) 10 linker [41] that was converted from B-DNA to left-handed Z-DNA at high ionic conditions. Since then various other DNA nanomachines have been reported, including DNA tweezers driven by hybridization of complementary strands, [42,43] catalytic DNA, [43,44] G-rich quadruplexes, [45,46] and i-motifs. [47,48] In recent years there has been a great deal of interest in DNA computing, with reports of the construction of a series of DNA logic gates and higher-order DNA circuits [49][50][51][52][53] that produce output signals based on various inputs (usually DNA strands).…”

“…a) Nanomechanical device based on the B-Z transition of DNA. [41] b) Illustration of a DNA nanotweezer driven by various environmental stimuli (hybridization of complementary DNA, [42,43] catalytic DNA, [44] changes in pH, [47,48] and ion concentration [45,46] ). c) Representative DNA logic gate.…”

Nucleic acid-based nanoengineering: novel structures for biomedical applications

“…An optimized device was further developed by Seelig et al [132], where they introduced a DNA catalyst strand and a fuel strand with a kinetically trapped metastable configuration. With improved understanding of the metastable states of DNA structures, scientists were able to build more complex systems with higher rates of catalysis [133,134]. Apart from these examples, there are numerous other DNA nanodevices that have relied primarily on hybridization-induced actuation, such as the single-stranded nanomotor relying on the formation of a G-rich quadruplex [135], and molecular gears with a pair of DNA nanocircles that were 6.5 nm in diameter [136].…”