Earlier we have shown that ultrasound irradiation causes multiple breakages in DNA and cleavage intensities in different positions of sugar-phosphate chains depend on dinucleotide types and the surrounding sequence. The relative intensities of cleavage of the central phosphodiester bond in 16 dinucleotides and 256 tetranucleotides were determined on the data of polyacrylamide gel electrophoresis. We observed a remarkable enhancement of the mean values of the relative intensities of cleavage (cleavage rates) in phosphodiester bonds following deoxycytidine, which diminished in the row of dinucleotides: d(CpG) > d(CpA) > d(CpT) >> d(CpC).The cleavage rates for all pairs of complementary dinucleotides were significantly different from each other. Subsequently, we showed that the frequencies of dinucleotides cleavage of genomic DNA in the process of its fragmentation during NGS sequencing is very close to our cleavage rates, obtained earlier. These differences in cleavage intensity in different positions of DNA sequence may be caused by the differences of local conformational motions, mainly with singularities of pseudorotation of the furanose cycle. Thus, we came to the conclusion that there is a second level of information coding by a DNA molecule - the existence of a “conformational code”. Analysis of a large number of physical and structural characteristics of DNA averaged over representative samples of different species of animals, plants and prokaryotes has shown that the index profiles characterizing DNA cleavage by ultrasound have characteristic properties in the areas that corresponds to region between the TATA box and the beginning of the transcription initiation site (TSS) in multicellular organisms. Since these indices carry information on conformational motions in individual strands of the DNA molecule, it can be asserted that the intensity of the conformational motions of the complementary chains in these regions varies in antiphase along the axis of the double-helix molecule. The most pronounced is this type of index profiles in the regulatory regions of DNA from mammalian cells. The intensity of cleavage of the CpG dinucleotide is also affected by the methylation of the cytosine at the 5-position of the pyrimidine ring. We evaluated the effect of methylation of cytosine on the cleavage of dinucleotides in human tissues, as well on the cleavage of CpG islands in control and cancer tissues (lymphoma and hepatocarcinoma). It turned out that on the sites of methylated CpG-dinucleotide clustering, genomic DNA is cleaved much more often than in similar sites, but with a low level of methylation. Moreover, a difference in the cleavage of CpG islands in cancer and control samples was established, and this is also due to differences in the level of their methylation. Therefore, it is possible to identify the precancerous state of tissues based on an estimate of the cleavage frequencies of CpG islands of different cell lines from DNA fragmentation data in NGS sequencing. The physical and chemical properties of DNA discovered by us can be used, both in theoretical studies and in the diagnostics of diseases.
Local DNA structure and conformation, sequence-specific ultrasonic cleavage, RNA polymerase II promoter sequences, methylation of heterocyclic basis in DNA, epigenetics, cancerogenesis
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