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Journal of Structural Chemistry

2009 year, number 5


Y. D. Nechipurenko, M. V. Golovkin, D. Y. Nechipurenko, I. A. Il'icheva, L. A. Panchenko, R. V. Polozov, S. L. Grokhovskii
Keywords: ultrasonic cleavage of DNA, conformational heterogeneity of DNA, gel electrophoresis, site specificity, footprinting
Pages: 1045-1052


The site effect (the dependence of the band intensity on the band position of gel) is the key factor that should be taken into account in quantitative analysis of the images of high-resolution electrophoretic gels containing many bands. We developed two procedures for taking this effect into account. The dependence of the relative frequencies of internucleotide bond cleavages on the type of nucleotide, obtained in the analysis of the splitting patterns of DNA fragments under the action of ultrasound or chemical factors, was evaluated by а) using the linearly sliding mean; b) describing the function of the site dependence as a third degree polynomial. The methods lead to similar results. An analysis of the splitting of different sequences, whose total length was more than 20,000 nucleotides, allowed us to determine the relative frequencies of bond cleavages in all 16 dinucleotides found in a DNA sequence. In ultrasonic treatment, the phosphodiester bond, lying between cytosine and guanine, undergoes cleavage more often than the corresponding bonds between other nucleotides in the sequence.