Figure 1.
Analysis of direct repeat (DR) motifs in mitochondrial genomes.
Abundance, distribution and free energy of DRs in mtDNA and random DNA sequences (n = 100) with the same base composition (R1) as corresponding mtDNA. (A) Frequency of DR pairs (≥6 bp) in the mtDNA of human, rhesus monkey, mouse and rat. The DR frequency is normalized with respect to the mtDNA length in each species. (B) The distribution of left and right DR sequences in the minor and major arcs of human mtDNA and the mean distribution of DRs in R1 random sequences. (C) DR sizes and DR free energies in human mtDNA and the corresponding R1 random sequences. The lower the free energy of a DR, i.e. the more negative, the more stable is the DNA duplex formed. (D) Distribution of free energies of DNA duplex formed by DRs (≥6 bp) in native mtDNA and random sequences (R1) of human, rhesus monkey, mouse and rat.
Figure 2.
Stem-loop (SL) motifs in human mitochondrial genome.
Abundance and distribution of predicted SL motifs in single-stranded human mtDNA heavy strand major arc. The positions 545 to 10665 correspond to the H-strand sequence from the end of D-loop till the beginning of L-strand origin of replication respectively. The minimum free energy folded structure is depicted in circular form.
Table 1.
Abundance of stem-loop motifs in mtDNA and random DNA sequences.
Figure 3.
Deletion breakpoints and direct repeats.
Distributions of left and right breakpoints of aging-associated mtDNA deletions and of left and right DR motifs from (A) human, (B) rhesus monkey, (C) mouse and (D) rat. Standard deviation (error bars) for the frequency of breakpoints in each bin is calculated based on a binomial distribution.
Figure 4.
Free energy and position wise distribution of the DRs in mtDNA major arc.
Resolution of DR distribution based on DR free energy and position in mtDNA sequence of (A) human, (B) rhesus monkey, (C) mouse and (D) rat. The x- and y- axis values denote the midpoint of each corresponding bin, i.e. a bin centered at 5.5 kb denotes a range from 5 to 6 kb and similarly, a bin centered at −2 kcal/mol has a range between 0 to −4 kcal/mol. (E) The most stable DR motifs in mtDNA major arc are associated with reported common deletions. Left and right breakpoint positions (denoted by open and close braces respectively) of common deletion [18], [27], [28], the flanking DR sequence (highlighted in red) and the calculated DR free energy value in human, rhesus monkey and rat mtDNA.
Table 2.
Role of sequence motifs in mtDNA deletions.
Table 3.
Mitochondrial genome sequence information.