Short-fragment Na-DNA dilute aqueous solutions: fundamental length scales and screening

TL;DR

This study uses dielectric spectroscopy to identify and analyze fundamental length scales in short-fragment Na-DNA solutions, revealing how these scales depend on salt concentration and DNA conformation.

Contribution

It provides new insights into the length scales and screening effects in short-fragment Na-DNA solutions, differing from long genomic DNA behavior.

Findings

High-frequency mode length scales relate to DNA separation at low salt.

Low-frequency mode corresponds to DNA contour length.

Salt concentration influences length scales and denaturation phenomena.

Abstract

Dielectric spectroscopy is used to investigate fundamental length scales of 146 bp short-fragment (nucleosomal) dilute Na-DNA solutions. Two relaxation modes are detected: the high- and the low-frequency mode. Dependence of the corresponding length scales on the DNA and on the (uni-valent) salt concentration is studied in detail, being different from the case of long, genomic DNA, investigated before. In low added salt regime, the length scale of the high-frequency mode scales as the average separation between DNAs, though it is smaller in absolute magnitude, whereas the length scale of the low-frequency mode is equal to the contour length of DNA. These fundamental length scales in low added salt regime do not depend on whether DNA is in a double stranded or single stranded form. On the other hand, with increasing added salt, the characteristic length scale of low-frequency mode diminishes at low DNA concentrations probably due to dynamical formation of denaturation bubbles and/or fraying in the vicinity of DNA denaturation threshold.