Compaction of Single Supercoiled DNA Molecules Adsorbed onto Amino Mica

L. A. Limanskayaa and A. P. Limanskiia,b,#

# Phone: (38)-057 7001-708; fax: (38)-057 7003-410; e-mail:
a Mechnikov Institute of Microbiology and Immunology, Academy of Medical Sciences of Ukraine, ul. Pushkinskaya 14/16, Kharkov, 61057 Ukraine
b Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan

Received December 16, 2005; in final form, March 24, 2006

Abstract: A model of possible conformational transitions of supercoiled DNA in vitro in the absence of proteins under the conditions of increasing degree of compaction was developed. A 3993-bp pGEMEX supercoiled DNA immobilized on various substrates (freshly cleaved mica, standard amino mica, and modified amino mica with a hydrophobicity higher than that of standard amino mica) was visualized by atomic force microscopy in air. On the modified amino mica, which has an increased density of surface positive charges, single molecules with an extremely high degree of compaction were visualized in addition to plectonemic DNA molecules. As the degree of DNA supercoiling increased, the length of the first-order superhelical axis of molecules decreased from 570 to 370 nm, followed by the formation of second- and third-order superhelical axes about 280 and 140 nm long, respectively. The compaction of molecules ends with the formation of minitoroids about 50 nm in diameter and molecules of spherical shape. It was shown that the compaction of single supercoiled DNA molecules immobilized on amino mica to the level of minitoroids and spheroids is due to the shielding of mutually repulsing negatively charged phosphate groups of DNA by positively charged amino groups of the amino mica, which has a high charge density of its surface.

Key words: amino mica, atomic force microscopy (AFM), DNA compaction, supercoiled DNA, toroid

Russian Journal of Bioorganic Chemistry 2006, 32 (5):444-459