Quasi-Palindrome Effects On Dna Sequence Evolution

Quasi-palindromes can be harmful or helpful, but most of this functionality is attributed to the formation of cruciforms. Unfortunately, the general properties a sequence must have to facilitate cruciform formation are poorly understood, as most research has focused on case studies of the unusual secondary structures of a few specific sequences. In this work, we investigate the general sequence properties leading to the formation of cruciforms by exploiting the fact that cruciforms lead to an increased mutation rate. We use evolutionary divergences in protein-coding sequences to calculate the mutation rates in quasi-palindromes with different degrees of self-complementarity. We perform this calculation to test different quasi-palindrome properties, then compare the observed patterns with the expected results. The most promising trials indicate that quasi-palindromes must be 10-30bp long with a self-complementarity at least 94% to form cruciforms, and that nucleotides near the center of the sequence are protected from mutation.