Tile-based modeling of DNA self-assembly for two graph families with appended paths (Q6102107): Difference between revisions

In 1974, twenty one years after the famous discovery of the structure of the DNA by Watson and Crick, N. Taniguchi, professor of the Tokyo Science University, introduced the term ``nanotechnology'' [\textit{N. Taniguchi}, ``On the basic concept of `nano-technology''', in: Proceedings of the International Conference on Production Engineering. 26--29 (1974)] for describing the engineering of materials at an atomic level. Three years later, at another corner of the Earth, Nadrian (Ned) C. Seeman (1945--2021) was appointed, after earning his PhD in biochemistry at the University of Chicago followed by postdoctoral work first at Columbia University and, then, with the legendary crystallographer A. Rich at the M.I.T. on the structure of large biological molecules. Istvan and Balazs Hargittai dubbed him the pioneer of DNA nanotechnology: [\textit{I. Hargittai} and \textit{B. Hargittai}, Struct. Chem. 33, 631--633 (2022; \url{doi:10.1007/s11224-022-01894-3})]. While not especially successful in various Projects there, Seeman stumbled upon the concept of the so called Holliday junction which caught his imagination. It is worth saying, though, that Seeman's motto was next (1995) ``Just because we can't do it doesn't mean we can't think about doing it''. Recall that Holliday junction was described by the molecular biologist Robin Holliday in 1964. It is a branched nucleic acid structure that joins four double stranded arms. Playing with its model led Seeman to develop his life motif, constructing three-dimensional DNA structures, and he became a nano-architect, inventing DNA nanotechnology in an attempt to better the crystallization process [\textit{E. Winfree} et al., Nature 394, 539--544 (1998; \url{doi:10.1038/28998})]. A key technology of DNA nanotechnology became in the early 2000s DNA-nanostructure self-assembling of some specially designed DNA strands -- the so called target structures. The latter can mathematically be represented as discrete graphs. In this case one can use the Ellis-Monaghan model of a k-armed branched junction molecule that is a molecule of DNA consisting of a center point with extending arms (see Figure 1). Self-assembling of branched molecules of DNA into nanostructures via a complementary cohesive base-pairing is the theme of the present work under review. Its aim is to minimize the number of different types of branched junction molecules necessary to assemble certain target structures. For this purpose this work represents target structures as discrete graphs and branched DNA molecules as vertices with half-edges and presents the minimum numbers of required branched molecule and cohesive-end types under three levels of restrictive conditions for the tadpole and lollipop graph families which represent cycle and complete graphs with a path appended via a single cut-vertex. Three general lemmas regarding these vertex-induced path subgraphs are derived. A summary of the results of three different theoretical lab scenarios is given in Table 3. These results may be helpful in future studies on graphs with path subgraphs appended via a single cut-vertex.