Toehold-mediated strand displacement (TMSD) - one of the most applied reactions of dynamic DNA nanotechnology - involves the displacement of an "incumbent" strand bound to a complementary strand by an "invader" strand, which is supported by a short, single-stranded sequence - the toehold - to which the invader can bind to initiate the displacement reaction.
The kinetics of TMSD is known to vary exponentially with the toehold length and under ideal conditions saturates for toeholds above ~ 8 nucleotides. However, in a biological context, such reactions have to take place in the presence of other DNA or RNA strands that might interact with invader and toehold, which slows down the reaction.
We addressed this issue by studying TMSD reactions in the presence of pools of random sequences and characterized the impact of different strand lengths and binding positions. Using various machine-learning approaches, we derived rules to predict the impact of interfering strands, and we also investigated strategies to make TMSD robust against interactions with random sequences.
T. Mayer, L. Oesinghaus, F. C. Simmel, Toehold-Mediated Strand Displacement in Random Sequence Pools. J. Am. Chem. Soc. 145, 634-644 (2023).
https://pubs.acs.org/doi/full/10.1021/jacs.2c11208