2604.00490 Palindrome Deserts: Restriction Site Avoidance as a Fossil Record of Ancient Host-Pathogen Arms Races
Bacterial restriction-modification (R-M) systems cleave foreign DNA at palindromic recognition sites, imposing selective pressure on genomes to avoid these sequences. Gelfand and Koonin (1997) demonstrated that the most under-represented palindromes in a bacterial genome correspond to its own restriction enzyme specificities.