Year: 2025
Type: article
Abstract: We investigated overlapping dispersed repeats (DRs) on the plus and minus DNA strands in 12 bacterial genomes. The use of the iterative procedure method (IP method) without taking into account insertions or deletions of nucleotides allowed speeding up the calculations by several times and increased the number of the identified DRs by 10–20%. Most of the DRs were found in the known bacterial genes. The intersection regions of the bacterial DRs contained reverse complement codons. Calculation of triplet periodicity matrices mt(i,j) (i is the position in the codon and j is the nucleotide) was performed for the intersection regions. Two classes of matrices in which the number of nucleotides was significantly greater than in random sequences were revealed: the first contained mt(1,G), mt(2,A), mt(2,T), and mt(3,C) cells and the second mt(1,G), mt(2,C), mt(3,A), and mt(3,T) cells. These classes included 10 and 2 bacterial genomes, respectively. The reverse complement transformation of the DR intersection regions preserved the cells in both classes, although cyclic matrix shifting to the right by one base was observed in the second class. The reverse complement codons in the DR intersection regions on the plus and minus DNA strands could represent sites of more frequent inversions/transpositions or participate in the formation of secondary/tertiary mRNA structures.
Source: Symmetry
DOI: 10.3390/sym17040549
Author: Eugene Vadimovitch Korotkov
Institution: Russian Academy of Sciences
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,896
OpenAlex ID: W4409197146