Abstract
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 a) 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.
Similar content being viewed by others
References
S. L. Grokhovskii, Molek. Biol., 40, 317–325 (2006).
S. L. Grokhovskii, I. A. Il’icheva, D. Yu. Nechipurenko, et al., Biofizika, 53, 417–425 (2008).
Yu. D. Nechipurenko, R. V. Polozov, D. Yu. Nechipuenko, et al., “Mathematical models of gene expression regulation: mechanical perturbations in the structure of DNA,” Mathematics. Computer. Education, in: A Collection of Treatises, Vol. 2, G. Yu. Riznichenko (ed.), Regular and Chaotic Dynamics Center, Izhevsk, (2006), pp. 392–402.
Yu. D. Nechipurenko, D. Yu. Nechipurenko, R. V. Polozov, et al., DNA-Based Nanostructures: Changes of Mechanical Properties of DNA Upon Ligand Binding, Nanomaterials for Application in Medicine and Biology (NATO Workshop in Bonn), Springer (2008), pp. 59–67.
J. A. Greenbaum, S. C. J. Parker, and T. D. Tullius, Genome Res., 17, 940–946 (2007).
J. A. Greenbaum, Bo Pang, and T. D. Tullius, ibid., 947–953.
R. Das, A. Laederach, S. M. Pearlman, et al., RNA, 11, 344–354 (2005).
W. P. Tate and G. B. Petersen, Biochem. J., 147, 439–445 (1975).
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text Copyright © 2009 by Yu. D. Nechipurenko, M. V. Golovkin, D. Yu. Nechipurenko, I. A. Il’icheva, L. A. Panchenko, R. V. Polozov, and S. L. Grokhovskii
__________
Translated from Zhurnal Strukturnoi Khimii, Vol. 50, No. 5, pp. 1045–1052, September–October, 2009.
Rights and permissions
About this article
Cite this article
Nechipurenko, Y.D., Golovkin, M.V., Nechipurenko, D.Y. et al. Characteristics of ultrasonic cleavage of DNA. J Struct Chem 50, 1007–1013 (2009). https://doi.org/10.1007/s10947-009-0149-1
Received:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10947-009-0149-1