DNA nanotechnology: understanding and optimisation through simulation

Abstract

DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA nanotechnology, highlighting the need for a more detailed understanding of the key processes, both in terms of theoretical modelling and experimental characterisation. I then consider coarse-grained models of DNA, mesoscale descriptions that have the potential to provide great insight into the operation of DNA nanotechnology if they are well designed. In particular, I discuss a number of nanotechnological systems that have been studied with oxDNA, a recently developed coarse-grained model, highlighting the subtle interplay of kinetic, thermodynamic and mechanical factors that can determine behaviour. Finally, new results highlighting the importance of mechanical tension in the operation of a two-footed walker are presented, demonstrating that recovery from an unintended 'overstepped' configuration can be accelerated by three to four orders of magnitude by application of a moderate tension to the walker's track. More generally, the walker illustrates the possibility of biasing strand-displacement processes to affect the overall rate.

Rational design of hidden thermodynamic driving through DNA mismatch repair

“…oxDNA has previously been applied to a number of systems in which displacement is important. 19,[23][24][25] Here, we use the sequence-dependent parameterisation of Sulc et. al.…”

Nanoestructuras inusuales de ácidos nucleicos basados en ADN G-cuádruple

“…Como se puede ver en la Figura 3 efectivamente no se observan bandas con movilidades que correspondan a especies tipo (C2) 3 SQ1A. En la linea 2 se observan claramente dos bandas de mayor movilidad, la más rápida correspondería a la cadena simple y la siguiente muy posiblemente a una especie G-cuádruple del tipo (SQ1B) 4 . Esta línea 2 nos puede servir de guía para interpretar las otras bandas.…”

“…Ensambles inusuales de ácidos nucleicos, nanofibras, G-cuádruple, nanoestructuras inusuales. lares/nanosistemas capaces de realizar funciones complejas integrando múltiples componentes como es en el caso de toda nuestra tecnología basada en la estrategia tradicional top-down es aún un desafío tecnológico muy importante [1,4]. Las principales limitaciones son la capacidad de diseñar sistemas que sin una inversión importante de energía o de manipulación excesiva puedan ensamblarse por sí mismos en un sistema capaz de realizar una función compleja.…”

Multiscale simulation of DNA

“…Recent developments have expanded the accuracy of CG methods, especially for B-DNA, as extensively reviewed in a series of excellent articles by the groups of Levitt [119], Papoian [120], Marrink [121] and Noid [122] among others, and a book chapter by Leonarski and Trylska [123]. We will limit ourselves here to the latest (from 2013) advances in particle-based CG methods, both those oriented towards the study of DNA in biological context [124•-133], and those designed for nanocomposites (see the recent revisions of Yingling et al [134] and Ouldridge [135] [142] have been used in both fields. Despite the particle-based CG models reviewed here, it is worth to note the effort done by the community to build models at the interface of atomistic and coarse grain modeling, like the ones based on the flexibility of DNA bases considered as independent interacting rigid bodies where the ground state and the stiffness matrixes are taken from MD simulations [143,144], or the works done by Rohs and coworkers that used atomistic MC (Monte Carlo) simulations to derive a method for high-throughput DNA shape predictions [145][146][147].…”

“…Most of the successful CG models use from 2 (oxDNA [135][136][137][138], and Aksim nti v's m d l [148]), or 3 (3SPN [131][132][133]139,140], BioModi [149]), to eight beads per nucleotide (see Figure 2, and Table 1 for more details). However, coarser models with five beads per base-pair step (four nucleotides), or even a single bead per nucleotide have emerged [126,127].…”