Search of the minimums of energy of interaction between complementary chains of DNA in promoter and coding parts of genes of E. coli

Abstract

By means of computer analysis of nucleotide composition and the energy of interaction between DNA chains in promoter and coding regions of genes of E. coli was studied. It showed an increase in the content of adenine and thymine in the promoter region. There were no significant differences between the genes in the direct and reverse orientation. It was found the minimums in the energy a of the interaction of complementary DNA strands in genes of direct and reverse orientations of the promoter and coding regions are near the positions: -100, -70, - 40, +5, +20, +30. Sites -40, +5 are close to the known consensus sequences of nucleotides in the promoter affecting the activity of the gene. Sites -100, -70, +20, +30, according to our data, also have the energy decrease of the interaction of complementary strands of DNA, suggesting that they have regulatory significance. The interaction energy of the complementary strands of DNA is reduced not only in the promoter but also at the beginning of the coding gene. Growth in the energy of interaction of DNA in the coding region of a gene occurs after the 100th position. The interaction energy of DNA chain interaction is lower in genes of reverse orientation. Differences between direct and reverse sequences are statistically significant in the region from -150 to - 101 and from 1 to 51. Genes in the reverse orientation have the additional energy minims in positions: -140,-120, -25, and +40. In addition, genes with a reverse orientation have a minimum of the energy of interaction between DNA strands in the cite -85, while in the genes with a direct orientation the minimum of energy is in position about -80.