Imaging of cruciform structure in supercoiled DNA by atomic force microscopy

Alex Limansky

Mechnikov Institute of Microbiology and Immunology of Academy of Medical Sciences,
Pushkinskaya street, 14, Kharkov, 61057, Ukraine

Institute of Experimental and Clinical Veterinary Medicine,
83 Pushkinskaya st., Kharkov 61023, Ukraine

Atomic force microscopy(AFM) was used for imaging of cruciform structure in su-percoiled plasmid pUC8 DNA immobilized on aminomodified mica in buffer solution after sample drying. Cruciform structure dimension was determined from AFM ima-ging and molecular modeling. It was shown from AFM imaging of DNA that cruciform structure was formed by 15 nucleotides inverted repeats. Molecular modeling have revealed that 11 nucleotides hairpins and 4 bases loops have formed cruciform structure. Great potential of AFM for structural studies of supercoiled DNA complexes with key proteins which regulate gene expression and procceses of transcription, replication, recombination.