Probing the elastic limit of DNA bending

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.

References in corpus (8)

• Exact theory of kinkable elastic polymers
• A generalized theory of semiflexible polymers
• Concentration and Length Dependence of DNA Looping in Transcriptional Regulation
• From mechanical folding trajectories to intrinsic energy landscapes of biopolymers
• Distribution Functions, Loop Formation Probabilities and Force-Extension Relations in a Model for Short Double-Stranded DNA Molecules
• DNA flexibility on short length scales probed by atomic force microscopy
• Protein-Mediated DNA Loops: Effects of Protein Bridge Size and Kinks
• Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA

Cited by in corpus (23)

• A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
• Coarse-grained modelling of strong DNA bending II: Cyclization
• Modulation of DNA loop lifetimes by the free energy of loop formation
• Revisiting the anomalous bending elasticity of sharply bent DNA
• Strongly bent double-stranded DNA: reconciling theory and experiment
• J-factors of short DNA molecules
• End-to-end distance and contour length distribution functions of DNA helices
• Twist-bend coupling, twist waves and the shape of DNA loops
• Flexibility of short DNA helices under mechanical stretching
• DNA size in confined environments
• Base-pair mismatch can destabilize small DNA loops through cooperative kinking
• Extreme bendability of DNA double helix due to bending asymmetry
• Base pair fluctuations in helical models for nucleic acids
• Twisting short dsDNA with applied tension
• Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"
• Twist-stretch profiles of DNA chains
• First-passage probability: a test for DNA Hamiltonian parameters
• Stretching DNA in hard-wall potential channels
• Mesoscopic helical models for DNA
• Rigidity of Melting DNA
• Twist-stretch relations in nucleic acids
• Force distribution in a semiflexible loop
• Statistical method for A-RNA and B-DNA