In silico comparative analysis of nuclear and mitochondrial genomes of vertebrates and yeast revealed the distribution of nucleotide sequences that are predisposed to the formation of noncanonical DNA structures, G-quadruplexes, which are closely related to the regulation of expression of a number of genes and are abundant within the hot-spots of double-strand DNA breaks. The obtained data indicate the preferred localization of potential quadruplexes in the noncoding DNA sequences, their evolutionary conservation, and the existence of homology between them in the mitochondrial and nuclear genomes. The relationship between quadruplexes, Pif1 helicase, and genomic instability is discussed.