DNA Bending Stiffness on Small Length Scales

Bending properties of short (15–90 bp), double-stranded DNA fragments are quantified using fluorescence resonance energy transfer and small angle x-ray scattering. Results from both types of measurements indicate that short double-stranded DNA fragments exhibit surprisingly high flexibility. These observations are discussed in terms of base-pair-level length fluctuations originating from dynamic features of Watson-Crick base pairs.

Figure 1

${\sigma }_m^2$ of short DNA fragments, 15–21 bp, versus DNA contour length. Measurements were performed at room temperature in aqueous solutions containing 10 mM Tris-HCl, 500 mM NaCl, 1 mM EDTA, pH 8.0.

Figure 2

Plot of $\ln \mathbf{(}I(q)\mathbf{)}$ vs $q^2$ for 16 and 89 bp dsDNA.

Figure 3

Simulated persistence length ($L_p$) calculated as a function of nucleotide flipout probability ($P_{\mathrm{fl}}$) using Monte Carlo simulation with a 30° kink angle per flipped-out base [13].