# First passage time study of DNA strand displacement

Source: [First passage time study of DNA strand displacement](<https://www.sota2.com/research/paper/68fa3f171e209131ce8eaa72>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-25T02:12:28.536Z

Authors: D. W. Bo Broadwater, Jr., Alexander W. Cook, Harold D. Kim

Published: 2020-05-21T22:14:52.000Z

## Abstract

DNA strand displacement, where a single-stranded nucleic acid invades a DNA duplex, is pervasive in genomic processes and DNA engineering applications. The kinetics of strand displacement have been studied in bulk; however, the kinetics of the underlying strand exchange were obfuscated by a slow bimolecular association step. Here, we use a novel single-molecule Fluorescence Resonance Energy Transfer (smFRET) approach termed the "fission" assay to obtain the full distribution of first passage times of unimolecular strand displacement. At a frame time of 4.4 ms, the first passage time distribution for a 14-nt displacement domain exhibited a nearly monotonic decay with little delay. Among the eight different sequences we tested, the mean displacement time was on average 35 ms and varied by up to a factor of 13. The measured displacement kinetics also varied between complementary invaders and between RNA and DNA invaders of the same base sequence except for T$\\rightarrow$U substitution. However, displacement times were largely insensitive to the monovalent salt concentration in the range of 0.25 M to 1 M. Using a one-dimensional random walk model, we infer that the single-step displacement time is in the range of $\\sim 30 \\mu s$ to $\\sim 300 \\mu s$ depending on the base identity. The framework presented here is broadly applicable to the kinetic analysis of multistep processes investigated at the single-molecule level.

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## Original sources and implementation

[Original paper](<https://arxiv.org/abs/2005.10925>)

[PDF](<https://arxiv.org/pdf/2005.10925.pdf>)