Biopolym. Cell. 2002; 18(5):401-405.
http://dx.doi.org/10.7124/bc.00061D
Structure and Function of Biopolymers
Study of cruciform structure in supercoiled pUC8 plasmid DNA by atomic force microscopy and computer modelling
1, 2, 3Limansky A. P.
  1. Mechnikov Institute of Microbiology and Immunology AMS of Ukraine
    14, Pushkinska Str., Kharkiv, Ukraine, 61057
  2. Institute of Experimental and Clinical Veterinary Medicine, UAAS
    83, Pushkinska Str., Kharkov, Ukraine, 61023
  3. Department of Microbiology, Arizona State Univesity
    Tempe, AZ 85287-2701 USA

Abstract

The cruciform structure in supercoiled pUCS plasmid DNA immobilized on aminomodified mica in buffer solution after sample drying was imaged by atomic force microscopy (APM). The cruciform structure was formed by 15 nucleotides inverted repeats as shown from AFM images of DNA. The computer modelling has revealed the cruciform structure to be formed by 11 nucleotides hairpins and 4 bases loops. Free energy of the hairpin was determined to be -17.8 kcal/mol.
Full text: (PDF, in Ukrainian)

References

[1] Lilley DM. The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. Proc Natl Acad Sci U S A. 1980;77(11):6468-72.
[2] Vologodskii A. Formation of unusual structures in the supercoiled DNA. Influence of transitions. Mol Biol (Mosk). 1985;19(3):687-92.
[3] Ptashne M. A Genetic Switch: Gene Control and Phage A. Cell Press, Cambridge, MA, and Blackwell Scientific, Palo Alto, CA, 1986. 138 pp.
[4] Shlyakhtenko LS, Hsieh P, Grigoriev M, Potaman VN, Sinden RR, Lyubchenko YL. A cruciform structural transition provides a molecular switch for chromosome structure and dynamics. J Mol Biol. 2000;296(5):1169-73.
[5] Bartok K, Denhardt DT. Site of cleavage of superhelical phiX174 replicative form DNA by the single strand-specific Neurospora crassa endonuclease. J Biol Chem. 1976;251(2):530-5.
[6] Panyutin I, Klishko V, Lyamichev V. Kinetics of cruciform formation and stability of cruciform structure in superhelical DNA. J Biomol Struct Dyn. 1984;1(6):1311-24.
[7] Binnig G, Quate CF, Gerber C. Atomic force microscope. Phys Rev Lett. 1986;56(9):930-933.
[8] Lyubchenko YL, Jacobs BL, Lindsay SM. Atomic force microscopy of reovirus dsRNA: a routine technique for length measurements. Nucleic Acids Res. 1992;20(15):3983-6.
[9] 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.
[10] Brodsky LI, Drachev AL, Leontovich AM. A novel method of multiple sequence alighment of biopolymers (program H-Align of the GenBee package). Biopolym Cell. 1991; 7(1):14-22.
[11] Rychlik W, Spencer WJ, Rhoads RE. Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res. 1990;18(21):6409-12.
[12] Vologodskii AV, Frank-Kamenetskii MD. Theoretical study of cruciform states in superhelical DNAs. FEBS Lett. 1982;143(2):257-60.
[13] Vologodskii AV, Frank-Kamenetskii MD. The relaxation time for a cruciform structure in superhelical DNA. FEBS Lett. 1983;160(1-2):173-6.
[14] Panyutin IG, Lyamichev VI, Lyubchenko YuL. A sharp structural transition in pA03 plasmid DNA caused by increased superhelix density. FEBS Lett. 1982;148(2):297-301.
[15] Sinden RR, Pettijohn DE. Cruciform transitions in DNA. J Biol Chem. 1984;259(10):6593-600.
[16] Haniford DB, Pulleyblank DE. Transition of a cloned d(AT)n-d(AT)n tract to a cruciform in vivo. Nucleic Acids Res. 1985;13(12):4343-63.
[17] Lyamichev V, Panyutin I, Mirkin S. The absence of cruciform structures from pAO3 plasmid DNA in vivo. J Biomol Struct Dyn. 1984;2(2):291-301.
[18] Plueddemann E. P. Silane coupling agents. New York; London: Plenum press, 1991. 438 p.
[19] Lyubchenko YL, Gall AA, Shlyakhtenko LS, Harrington RE, Jacobs BL, Oden PI, Lindsay SM. Atomic force microscopy imaging of double stranded DNA and RNA. J Biomol Struct Dyn. 1992;10(3):589-606.
[20] Golan R, Pietrasanta LI, Hsieh W, Hansma HG. DNA toroids: stages in condensation. Biochemistry. 1999;38(42):14069-76.
[21] Hansma HG. Varieties of imaging with scanning probe microscopes. Proc Natl Acad Sci U S A. 1999;96(26):14678-80.