Weak tension accelerates hybridization and dehybridization of short oligonucleotides

TL;DR

This study demonstrates that weak tension (2-6 pN) accelerates both hybridization and dehybridization of short DNA oligonucleotides, revealing the extended nature of the transition state and challenging traditional models.

Contribution

Developed a DNA bow assay combined with single-molecule FRET to measure how weak tension influences DNA hybridization kinetics, providing new insights into DNA mechanics.

Findings

Both hybridization and dehybridization rates increase with tension.

The transition state of DNA duplex formation is more extended than expected.

Standard worm-like chain models do not explain low-force DNA kinetics.

Abstract

The hybridization and dehybridization of DNA subject to tension is relevant to fundamental genetic processes and to the design of DNA-based mechanobiology assays. While strong tension accelerates DNA melting and decelerates DNA annealing, the effects of tension weaker than 5 pN are less clear. In this study, we developed a DNA bow assay, which uses the bending rigidity of double-stranded DNA (dsDNA) to exert weak tension on a single-stranded DNA (ssDNA) target in the range of 2 pN to 6 pN. Combining this assay with single-molecule FRET, we measured the hybridization and dehybridization kinetics between a 15 nt ssDNA under tension and a 8-9 nt oligo, and found that both the hybridization and dehybridization rates monotonically increase with tension for various nucleotide sequences tested. These findings suggest that the nucleated duplex in its transition state is more extended than the pure dsDNA or ssDNA counterpart. Our simulations using the coarse-grained oxDNA2 model indicate that the increased extension of the transition state is due to exclusion interactions between unpaired ssDNA regions in close proximity to one another. This study highlights an example where the ideal worm-like chain models fail to explain the kinetic behavior of DNA in the low force regime.