Biopolym. Cell. 2006; 22(1):18-28.
http://dx.doi.org/10.7124/bc.000716
Structure and Function of Biopolymers
Compaction of supercoiled DNA on modified aminomica
1, 2Limanskaya O. Y., 1Limanskaya L. O., 1, 3Lymunskii O. P.
  1. Mechnikov Institute of Microbiology and Immunology NAMS of Ukraine
    14, Pushkinska Str., Kharkiv, Ukraine, 61057
  2. Institute of Experimental and Clinical Veterinary Medicine, UAAS
    83, Pushkinska Str., Kharkov, Ukraine, 61023
  3. Laboratory of Plasma Membrane and Nuclear Signaling Graduate school of Biostudies, Kyoto University
    Yoshida-Konoecho, Sakyo-ku, Kyoto, Japan 606-8501

Abstract

Stages of compaction of single molecules of supercoiled DNA pGEMEX, immobilized on modified aminomica, were visualized using atomic force microscopy. At the increase of the level of its compaction the length of molecule superhelix axis of the first order is decreased from ~580 nm down to ~370 nm with further formation of the superhelix axis of the second and third order with the length of ~260 nm and ~140 nm which makes ~20 % and ~10 % of outline length of the relaxed molecule respectively. Compaction of single molecules is completed with the formation of minitoroids, whose diameter is ~50 nm, and spheric conformation molecules. The model of possible conformational transitions of supercoiled DNA in vitro in the absence of proteins has been suggested. Compaction of supercoiled DNA molecules up to minitoroid level was shown to be caused by high surface charge density of aminomica on which DNA molecules were immobilized.
Keywords: supercoiled DNA, atomic force microscopy, aminomica, DNA compactization, minitoroid, spheroid
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