Atomic force microscopy studies of intercalation‐induced changes in plasmid DNA tertiary structure

Structural transitions in the tertiary structure of plasmid DNA have been investigated using atomic force microscopy. Changes in superhelical stress were induced by ethidium bromide intercalation, and conformational effects monitored by recording topographic images from DNA complexes of various ethi...

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Bibliographic Details
Published in:Journal of microscopy (Oxford) 2000-07, Vol.199 (1), p.68-78
Main Authors: Pope, L. H., Davies, M. C., Laughton, C. A., Roberts, C. J., Tendler, S. J. B., Williams, P. M.
Format: Article
Language:English
Subjects:
AFM
atomic force microscopy
DNA
DNA, Superhelical - chemistry
DNA–intercalator complex
Electrophoresis, Agar Gel
Ethidium - chemistry
ethidium bromide
Intercalating Agents - chemistry
Microscopy, Atomic Force
Nucleic Acid Conformation
Plasmids
plectonemic supercoiling
supercoiled DNA
toroidal supercoiling
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Summary:Structural transitions in the tertiary structure of plasmid DNA have been investigated using atomic force microscopy. Changes in superhelical stress were induced by ethidium bromide intercalation, and conformational effects monitored by recording topographic images from DNA complexes of various ethidium bromide : base pair stoichiometry. Significant changes in the tertiary structure of individual DNA molecules were observed with increasing ethidium bromide concentration. The first distinct conformational transition was from a predominantly relaxed structure to one consisting solely of toroidal supercoils. A further increase in ethidium bromide concentration resulted in the formation of regions of plectonemic supercoiling. The ratio of plectonemic : toroidal supercoiling gradually increased until an extremely tightly interwound structure of solely plectonemic supercoiling was finally adopted. The toroidal form of supercoiling observed in this study is unusual as both atomic force microscopy and electron microscopy techniques have previously shown that plectonemic supercoiling is the predominant form adopted by plasmid DNA.
ISSN:0022-2720
1365-2818
DOI:10.1046/j.1365-2818.2000.00703.x