DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization

Abstract

The effect of secondary structure on DNA duplex formation is poorly understood. Using oxDNA, a nucleotide level coarse-grained model of DNA, we study how hairpins influence the rate and reaction pathways of DNA hybridzation. We compare to experimental systems studied by Gao et al. (1) and find that 3-base pair hairpins reduce the hybridization rate by a factor of 2, and 4-base pair hairpins by a factor of 10, compared to DNA with limited secondary structure, which is in good agreement with experiments. By contrast, melting rates are accelerated by factors of ∼100 and ∼2000. This surprisingly large speed-up occurs because hairpins form during the melting process, and significantly lower the free energy barrier for dissociation. These results should assist experimentalists in designing sequences to be used in DNA nanotechnology, by putting limits on the suppression of hybridization reaction rates through the use of hairpins and offering the possibility of deliberately increasing dissociation rates by incorporating hairpins into single strands.

Characterizing the bending and flexibility induced by bulges in DNA duplexes

“…47 Moreover, applications to study the fundamental biophysics of DNA, including the kinetics of hybridization, 48,49 toehold-mediated strand displacement, 50 the response to mechanical stress such as the over-stretching transition of dsDNA under tension, 51 the formation of cruciform structures under negative twist, 52 and the role of topology in the formation of kissing hairpin complexes, 53 have confirmed the robustness of the model. Furthermore, the model has proved useful in providing physical insight into the action of DNA nanodevices, such as nanotweezers 54 and walkers, 55,56 and is starting to be applied to characterize large DNA nanostructures.…”

Recent Progress towards Chemically-Specific Coarse-Grained Simulation Models with Consistent Dynamical Properties

“…However, there are cases where chemically-specific CG models for biomolecules are capable of generating rates and pathways of structure formation that are consistent with experimental measurements. For example, the OxDNA model [171]-a two-site per nucleotide model for DNA parametrized to reproduce the melting temperatures of short duplexesgenerates relative rates of duplex hybridization [172,173], strand displacement [174], and hairpin formation [175] that appear directly comparable to experiments. Apparently, the melting-curvebased parametrization probes the dominant energetic driving forces (i.e., base pairing interactions) for a whole range of larger-scale structure formation.…”

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

“…This treatment is sufficient to obtain good agreement with experimental data on the structural, mechanical, and especially the thermodynamic properties of single-and double-stranded DNA. Consequently, the model has provided key insights into many different processes relevant to DNA nanotechnology [32][33][34][35][36][37][38][39][40] and biophysics [41][42][43][44][45] and importantly has also been shown to provide direct agreement with experimentally measured properties on a range of systems including DNA overstretching, 45 a two-footed DNA walker, 35 and toehold-mediated strand displacement. 39,46 Despite these achievements, there are some areas where oxDNA can be improved.…”