Measuring Energetics of Sharp DNA Bending from Breakage Kinetics of Small DNA Loops

Abstract

Double-stranded DNA (dsDNA) can undergo diverse modes of conformational changes inside a cell. Among them, dsDNA bending is closely associated with genome packaging and gene regulation, and therefore a consistent polymer model of dsDNA bending is essential for quantitative description of genome-related processes. The behavior of dsDNA at large length scales can be well described as a worm-like chain whose bending energy depends quadratically on curvature. However, many studies on dsDNA bending at short length scales have produced results contradictory to the worm-like chain model. Here we show that the free energy of a dsDNA loop as short as 60 bp in contour length can be well described by the wormlike chain model. We measured the breakage rates of small dsDNA loop stabilized by sticky ends using Fluorescence Resonance Energy Transfer (FRET). We found that the breakage rate vs. loop length relationship to be in good agreement with the worm-like chain model, but not with an alternative model which predicts superflexible behavior at short length scales. Furthermore, we found that energetics of dsDNA begins to deviate from the worm-like chain model below 60 bp. Our result pushes the lower limit of the worm-like chain regime of dsDNA down to 60 bp, and suggests that dsDNA undergoes structural transitions below this length.