Issue
EPL
Volume 81, Number 6, March 2008
Article Number 68003
Number of page(s) 5
Section Interdisciplinary Physics and Related Areas of Science and Technology
DOI http://dx.doi.org/10.1209/0295-5075/81/68003
Published online 25 February 2008
EPL, 81 (2008) 68003
DOI: 10.1209/0295-5075/81/68003

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

S. Tomic1, S. Dolanski Babic1, T. Ivek1, T. Vuletic1, S. Krca2, F. Livolant3 and R. Podgornik4, 5, 6

1  Institut za fiziku - HR-10001 Zagreb, Croatia
2  Rudjer Boskovic 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

stomic@ifs.hr

received 20 July 2007; accepted in final form 28 January 2008; published March 2008
published online 25 February 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.

PACS
87.15.H- - Dynamics of biomolecules.
82.39.Pj - Nucleic acids, DNA and RNA bases.
77.22.Gm - Dielectric loss and relaxation.

© EPLA 2008