Recombinogenicity of perfect palindromes and quasipalindromes with short central spacers in vivo

A palindromic sequence in DNA with two identical inverted repeats and no central spacer region is called a perfect palindrome. Otherwise the palindrome is referred to as a quasipalindrome. Both perfect palindromes and quasipalindromes can constitute fragile sites in the genome prone to chromosome breakage which can result in potentially dangerous mutations and rearrangements. Several conditions in humans (such as the Emanuel syndrome) are caused by recombinogenic palindromic sequences in the genome. Palindrome recombinogenicity is caused by their ability to form secondary structures – hairpins in ssDNA and cruciforms in dsDNA. Using yeast Saccharomyces cerevisiae as a model, we compared the recombinogenicity of a perfect palindrome and quasipalindromes with short central spacers (1-10 bp) in vivo. We determined that a spacer as short as 7 bp significantly reduces the recombinogenicity, while a 10 bp spacer can completely stabilize palindromes up to 150 bp long, most likely by disabling cruciform formation. Furthermore, we found that in the absence of Sgs1 helicase the recombinogenicity of a perfect palindrome and of otherwise stable quasipalindrome with a 10 bp spacer is increased by the same factor, indicating that these two sequences have the same probability for hairpin formation in the lagging strand during replication. On the other hand, the absence of Rad27 nuclease (involved in Okazaki fragment maturation) dramatically increases the recombinogenicity of a perfect palindrome, but not a quasipalindrome with a 10 bp spacer. This result indicates that in the case of Rad27 absence the hairpin might form in the relatively short 5’ flap displaced by Pol  during Okazaki fragment synthesis.