Self-replication of DNA rings

Abstract

Biology provides numerous examples of self-replicating machines, but artificially engineering such complex systems remains a formidable challenge. In particular, although simple artificial self-replicating systems including wooden blocks, magnetic systems, modular robots and synthetic molecular systems have been devised, such kinematic self-replicators are rare compared with examples of theoretical cellular self-replication. One of the principal reasons for this is the amount of complexity that arises when you try to incorporate self-replication into a physical medium. In this regard, DNA is a prime candidate material for constructing self-replicating systems due to its ability to self-assemble through molecular recognition. Here, we show that DNA T-motifs, which self-assemble into ring structures, can be designed to self-replicate through toehold-mediated strand displacement reactions. The inherent design of these rings allows the population dynamics of the systems to be controlled. We also analyse the replication scheme within a universal framework of self-replication and derive a quantitative metric of the self-replicability of the rings.

Colloquium : Toward living matter with colloidal particles

“…The chemical energy stored in the nucleic acid bonds can be released during a reaction, pushing it out of equilibrium. Such reactions are the foundation of self-replicating RNA (Lincoln and Joyce, 2009) and DNA systems (Kim et al, 2015).…”

Proliferating droplets formed via prebiotic polymerisation: the missing link between chemistry and biology on the origin of life

“…Renewed interest in the role of CDs in the origin of life has been generated by the novel studies of Mann and co-workers, who have demonstrated cellular life-like features such as communication 11 and predator-prey interactions 12 in populations of CDs. As is the case with CD formation, autocatalytic self-reproduction is a crucial property of protocells that proliferate steadily 13 and has been demonstrated for supramolecular structures such as DNA origami rafts 14,15 , lipid micelles [16][17][18] , and lipid vesicles [19][20][21] in an aqueous medium. Previous studies of the fusion and division of molecular assemblies without self-reproduction have reported the importance of non-equilibrium states [22][23][24] .…”

Kinetic Trans-Assembly of DNA Nanostructures

“…[28][29][30] The other impetus behind DNA nanotechnology has been the desire to create dynamic systems, in which DNA assemblies no longer remain static but change their form, carry out functions, or both. Examples of this type include autonomous walkers, [31][32][33] molecular motors and robots, [34][35][36][37][38][39] and self-replicators 40 . The central mechanism underlying a large portion of these works is toehold-mediated strand displacement reactions, 41,42 where an invading DNA strand latches onto a short single-stranded toehold domain of a partially double-stranded DNA molecule and undergoes branch migration, displacing one or more of the incumbent strands which can further participate in downstream reactions.…”