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• W3026169136 abstract "DNA strand displacement, in which 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 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-nucleotide 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 → U substitution. However, displacement times were largely insensitive to the monovalent salt concentration in the range of 0.25–1 M. Using a one-dimensional random walk model, we infer that the single-step displacement time is in the range of ∼30–300 μs, 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." @default.
• W3026169136 created "2020-05-29" @default.
• W3026169136 creator A5043697995 @default.
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• W3026169136 date "2021-06-01" @default.
• W3026169136 modified "2023-10-17" @default.
• W3026169136 title "First passage time study of DNA strand displacement" @default.
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• W3026169136 doi "https://doi.org/10.1016/j.bpj.2021.01.043" @default.
• W3026169136 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/8390875" @default.
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