Probing the elastic limit of DNA bending

TL;DR

This study investigates the limits of DNA bending elasticity by measuring loop stability at various lengths, revealing a transition from elastic to softening behavior around 60-100 base pairs, with magnesium influencing this transition.

Contribution

The paper provides experimental evidence for a bending regime transition in dsDNA and validates the kinkable worm-like chain model against empirical data.

Findings

Identified a critical loop size of ~60-100 bp where DNA softening occurs.

Magnesium ions shift the softening transition to larger loop sizes.

Results align with the kinkable worm-like chain model predictions.

Abstract

Many structures inside the cell such as nucleosomes and protein-mediated DNA loops contain sharply bent double-stranded (ds) DNA. Therefore, the energetics of strong dsDNA bending constitutes an essential part of cellular thermodynamics. Although the thermomechanical behavior of long dsDNA is well described by the worm-like chain (WLC) model, the length limit of such elastic behavior remains controversial. To investigate the energetics of strong dsDNA bending, we measured the opening rate of small dsDNA loops with contour lengths of 40-200 bp using Fluorescence Resonance Energy Transfer (FRET). From the measured relationship of loop stability to loop size, we observed a transition between two separate bending regimes at a critical loop size below 100 bp. Above this loop size, the loop lifetime decreased with decreasing loop size in a manner consistent with an elastic bending stress. Below the critical loop size, however, the loop lifetime became less sensitive to loop size, indicative of softening of the double helix. The critical loop size was measured to be ~60 bp with sodium only and ~100 bp with 5 mM magnesium, which suggests that magnesium facilitates the softening transition. We show that our results are in quantitative agreement with the kinkable worm-like chain model. Furthermore, the model parameters constrained by our data can reproduce previously measured J factors between 50 and 200 bp. Our work provides powerful means to study dsDNA bending in the strong bending regime.