Scaling exponents and probability distributions of DNA end-to-end distance

Abstract

Correlation length exponent $\nu$ for long linear DNA molecules was determined by direct measurement of the average end-to-end distance as a function of the contour length $s$ by means of atomic force microscopy (AFM). Linear DNA, up to 48'502 base pairs (bp), was irreversibly deposited from a solution onto silanized mica and imaged in air. Under the adsorption conditions used, the DNA is trapped onto the surface without any two-dimensional equilibration. The measured exponent is $\nu = 0.589 \pm 0.006$, in agreement with the theoretical 3D value of $\nu = 0.5880 \pm 0.0010$. The persistence length $\ell_p$ of DNA was estimated to be 44$\pm$3 nm, in agreement with the literature values. The distribution of the end-to-end distances for a given contour length $s$ and the exponents characterizing the distribution were determined for different $s$. For $s$ smaller or comparable to $\ell_p$, a delta function like distribution was observed, while for larger $s$, a probability distribution of the type $x^{d-1}x^g e^{-bx^\delta}$ was observed with $g=0.33\pm0.22$ and $\delta=2.58\pm0.76$. These values are compared to the theoretical exponents for Self-Avoiding Walk (SAW): namely $g=\frac{\gamma-1}{\nu}$ and $\delta=(1-\nu)^{-1}$. So for $d=2$, $g\approx0.44$ and $\delta=4$, while for $d=3$, $g\approx0.33$ and $\delta\approx2.5$. The derived entropic exponent $\gamma$ is $\gamma=1.194\pm0.129$. The present data indicate that the DNA behaves on large length scales like a 3 dimensional SAW.