Principles and Applications of Nucleic Acid Strand Displacement Reactions

Abstract

Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNAbased nanomachine et al. Nature 2000, 406, 605−608). Since then, toeholdmediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287−294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.

Understanding DNA interactions in crowded environments with a coarse-grained model

“…The invader strand (shown in red) will displace the incumbent strand (green) from the substrate strand (yellow) through a 6-nt toehold and then a branch migration process for 10-nt. Strand displacement processes are of great importance in active nucleic acid nanotechnology 6,57 and are likely involved in several processes in biology 58 . To study how crowders affect the strand displacement reaction, we conducted both VMMC and FFS simulation for the strand displacement process to extract the thermodynamic and kinetic features of the reaction.…”

Create Nanoscale Patterns with DNA Origami

“…DNA origami‐based dynamic systems expand the dynamic range to ≈100 nm with higher design complexity. The driving force of the dynamic nanomachines usually arises from DNA hybridization, strand displacement, or external stimuli such as electricity, pH, light, magnetic field, etc. For example, Castro and co‐workers reported the construction of complicated and reversible DNA robots by implementing the design principles of macroscopic mechanical machines .…”

Engineering Cell‐Surface Receptors with DNA Nanotechnology for Cell Manipulation

“…Toehold‐mediated DNA strand displacement is the strategy most commonly used to achieve dynamic control. In this molecular process, two strands with partial or full complementarity hybridize to each other and displace one or more prehybridized strands, leading to the addition of toeholds (Figure C, ii) . Continuous dynamic characteristics can be scaled up by combining multiple DNA‐strand‐exchange reactions.…”