Mutations in artificial self-replicating tiles: A step toward Darwinian evolution

Abstract

Artificial self-replication and exponential growth holds the promise of gaining a better understanding of fundamental processes in nature but also of evolving new materials and devices with useful properties. A system of DNA origami dimers has been shown to exhibit exponential growth and selection. Here we introduce mutation and growth advantages to study the possibility of Darwinian-like evolution. We seed and grow one dimer species, AB, from A and B monomers that doubles in each cycle. A similar species from C and D monomers can replicate at a controlled growth rate of two or four per cycle but is unseeded. Introducing a small mutation rate so that AB parents infrequently template CD offspring we show experimentally that the CD species can take over the system in approximately six generations in an advantageous environment. This demonstration opens the door to the use of evolution in materials design.

Recent Advances in DNA Origami-Engineered Nanomaterials and Applications

“…(C) Mutations on the self-replicating system based on cross-tile origami. Reproduced with permission from ref . Copyright 2021 National Academy of Sciences.…”

“…The development of error-prone replication systems enables directed evolution, which can be utilized to obtain offspring with desired properties. In order to mimic the evolution, the Chaikin group introduced mutations in the artificial self-replication tiles (Figure C) . In the replication system based on origami cross-tiles, the dimer AB seeds templated the tile assembly of monomer tiles A and B.…”

Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex

“…Structural prediction, no matter how accurate it is, lacks specific details on interatomic interactions, which is the domain of quantum mechanics [ 50 , 51 ]. Prominent British Science writer Philip Ball [ 52 ] pointed out that, in fact, subjects such as replication, mutation, and selection are still not much explored at the level of single molecules or amino acids (AAs) [ 53 ].…”

Direct visualization of floppy two-dimensional DNA origami using cryogenic electron microscopy

“…We postulate they will be floppy in solution owing to their softness and flexibility, which may affect their intermolecular properties and interactions. Conventional imaging techniques, such as atomic force microscopy (AFM) and negatively stained transmission electron microscopy (TEM), have been widely used to investigate DNA origami ( Douglas et al., 2009a ; Han et al., 2011 ; Ke et al., 2012a , 2014 ; Liu et al., 2011 ; Rothemund, 2006 ; Wei et al., 2012 ; Woo and Rothemund, 2011 ; Yang et al., 2012 ; Zhou et al., 2021 ). However, these techniques require the deposition of 2D origami tiles onto a flat surface.…”