DNA dynamics and computation based on toehold-free strand displacement

Abstract

We present a simple and effective scheme of a dynamic switch for DNA nanostructures. Under such a framework of toehold-free strand displacement, blocking strands at an excess amount are applied to displace the complementation of specific segments of paired duplexes. The functional mechanism of the scheme is illustrated by modelling the base pairing kinetics of competing strands on a target strand. Simulation reveals the unique properties of toehold-free strand displacement in equilibrium control, which can be leveraged for information processing. Based on the controllable dynamics in the binding of preformed DNA nanostructures, a multi-input-multi-output (MIMO) Boolean function is controlled by the presence of the blockers. In conclusion, we implement two MIMO Boolean functions (one with 4-bit input and 2-bit output, and the other with 16-bit input and 8-bit output) to showcase the controllable dynamics.

DNA Walkers for Biosensing Development

“…[ 36 , 37 ] Strand displacement reactions‐based methods are employed for driving DNA walkers effectively due to the high controllability and programmability of DNA self‐assembled nanostructures. [ 38 , 39 ] DNA strands displacement reactions are accomplished by the competition of hybridization and de‐hybridization, which promotes the kinetic and thermodynamics equilibrium through the hybridization between the walking strand and the substrate strand or the fuel strand. [ 40 ] The exposed toehold of walking strand is accessible to integrating with downstream reaction.…”

Thermal Effects on Optical Chirality and Associated Symmetry Properties

“…As biological materials, double-helix (double-strand) DNAs (deoxyribo nucleic acids) are the most notable twisted structure [17]. The geometry of a DNA is characterized by a pair of parameters: the diameter and the pitch of a helix [18], [19].…”

Programmable mismatch-fueled high-efficiency DNA signal amplifier

“…7,8 Remarkably, in the development of dynamic DNA nanostructural chemistry, the catalytic multiple-arm DNA junction assembly (CMDJA) 9,10 as a exible and ideal basic building block for DNA structural nanotechnology [11][12][13][14][15] has attracted increasing attention. Compared to the branched DNA obtained by conventional annealing approaches with tedious temperature control, 16,17 the isothermal CMDJA was obtained simply by relying on the base-pairing principle, in which the self-assembly can be well controlled by catalysts. Nevertheless, the CMDJA has also suffered from multiple-step reactions and weak driving forces, resulting in inherent time-consuming and suboptimal kinetic and thermodynamic properties, which further limits its deeper exploitation and wider application.…”