Biopolym. Cell. 2006; 22(1):18-28.
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


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


[1] Kim J, Yoshimura SH, Hizume K, Ohniwa RL, Ishihama A, Takeyasu K. Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy. Nucleic Acids Res. 2004;32(6):1982-92.
[2] Hizume K, Yoshimura SH, Maruyama H, Kim J, Wada H, Takeyasu K. Chromatin reconstitution: development of a salt-dialysis method monitored by nano-technology. Arch Histol Cytol. 2002;65(5):405-13.
[3] Gonz?lez-Huici V, Salas M, Hermoso JM. Genome wide, supercoiling-dependent in vivo binding of a viral protein involved in DNA replication and transcriptional control. Nucleic Acids Res. 2004;32(8):2306-14.
[4] Yoshimura SH, Hizume K, Murakami A, Sutani T, Takeyasu K, Yanagida M. Condensin architecture and interaction with DNA: regulatory non-SMC subunits bind to the head of SMC heterodimer. Curr Biol. 2002;12(6):508-13.
[5] Kimura K, Rybenkov VV, Crisona NJ, Hirano T, Cozzarelli NR. 13S condensin actively reconfigures DNA by introducing global positive writhe: implications for chromosome condensation. Cell. 1999;98(2):239-48.
[6] Sato MH, Ura K, Hohmura KI, Tokumasu F, Yoshimura SH, Hanaoka F, Takeyasu K. Atomic force microscopy sees nucleosome positioning and histone H1-induced compaction in reconstituted chromatin. FEBS Lett. 1999;452(3):267-71.
[7] Golan R, Pietrasanta LI, Hsieh W, Hansma HG. DNA toroids: stages in condensation. Biochemistry. 1999;38(42):14069-76.
[8] Allen MJ, Bradbury EM, Balhorn R. AFM analysis of DNA-protamine complexes bound to mica. Nucleic Acids Res. 1997;25(11):2221-6.
[9] Dunlap DD, Maggi A, Soria MR, Monaco L. Nanoscopic structure of DNA condensed for gene delivery. Nucleic Acids Res. 1997;25(15):3095-101.
[10] Fang Y, Hoh JH. Surface-directed DNA condensation in the absence of soluble multivalent cations. Nucleic Acids Res. 1998;26(2):588-93.
[11] Cherny DI, Jovin TM. Electron and scanning force microscopy studies of alterations in supercoiled DNA tertiary structure. J Mol Biol. 2001;313(2):295-307.
[12] Hud NV, Downing KH. Cryoelectron microscopy of lambda phage DNA condensates in vitreous ice: the fine structure of DNA toroids. Proc Natl Acad Sci U S A. 2001;98(26):14925-30.
[13] Lin Z, Wang C, Feng X, Liu M, Li J, Bai C. The observation of the local ordering characteristics of spermidine-condensed DNA: atomic force microscopy and polarizing microscopy studies. Nucleic Acids Res. 1998;26(13):3228-34.
[14] Limansky AP, Shlyakhtenko LS, Schaus S, Henderson E, Lyubchenko YL. Aminomodified probes for atomic force microscopy. Probe Microscopy. 2002;2(3-4):227-34.
[15] Boles TC, White JH, Cozzarelli NR. Structure of plectonemically supercoiled DNA. J Mol Biol. 1990;213(4):931-51.
[16] Hansma HG, Golan R, Hsieh W, Lollo CP, Mullen-Ley P, Kwoh D. DNA condensation for gene therapy as monitored by atomic force microscopy. Nucleic Acids Res. 1998;26(10):2481-7.
[17] Polianichko AM, Chikhirzhina EV, Andrushchenko VV, Kostyleva EI, Wieser H, Vorob'ev VI. The effect of Ca2+ ions on DNA compaction in the complex with non-histone chromosomal protein HMGB1. Mol Biol (Mosk). 2004;38(4):701-12. Russian.
[18] Sivolob A, Prunell A. Nucleosome conformational flexibility and implications for chromatin dynamics. Philos Trans A Math Phys Eng Sci. 2004;362(1820):1519-47. Review.
[19] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[20] Limanskii A. Atomic force microscopy: visualization of DNA and proteins to measure the strength of intermolecular interactions. Usp Sovrem Biol. 2003; 123(6):531-42.
[21] Shlyakhtenko LS, Gall AA, Weimer JJ, Hawn DD, Lyubchenko YL. Atomic force microscopy imaging of DNA covalently immobilized on a functionalized mica substrate. Biophys J. 1999;77(1):568-76.
[22] Limansky AP. Investigation of aminomodified mica as a substrate for nucleic acids atomic force microscopy. Biopolym Cell. 2001; 17(4):292-7.
[23] Vezenov DV, Noy A, Rozsnyai LF, Lieber CM. Force titrations and ionization state sensitive imaging of functional groups in aqueous solutions by chemical force microscopy. J Am Chem Soc. 1997;119(8):2006-15.
[24] Zhang H, He H-X, Wang J, Mu T, Liu Z-F. Force titration of amino group-terminated self-assembled monolayers using chemical force microscopy. Appl Phys A Mater Sci Process. 1998;66(7):S269-S271.
[25] Lyamichev VI, Mirkin SM, Frank-Kamenetskii MD. Structure of (dG)n.(dC)n under superhelical stress and acid pH. J Biomol Struct Dyn. 1987;5(2):275-82.
[26] Wu A, Li Z, Yu L, Wang H, Wang E. Plasmid DNA network on a mica substrate investigated by atomic force microscopy. Anal Sci. 2001;17(5):583-4.