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

¹  Institut za fiziku - HR-10001 Zagreb, Croatia
²  Rudjer Bošković Institute - HR-10001 Zagreb, Croatia
³  Laboratoire de Physique des Solides, Université Paris Sud - F-91405 Orsay, France
⁴  Department of Physics, University of Ljubljana - SI-1000 Ljubljana, Slovenia
⁵  J. Stefan Institute - SI-1000 Ljubljana, Slovenia
⁶  Laboratory of Physical and Structural Biology, NICHD, National Institutes of Health - Bethesda, MD 20892, USA

Corresponding author: stomic@ifs.hr

Received: 20 July 2007
Accepted: 28 January 2008

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 the 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.