Homo sapiens DNA Palindromes

DNA palindromes are implicated as a causative agent in cancer formation due to their association with genomic instability and DNA amplification. However, the unique properties of palindromes render them refractory to current methods of analyses including PCR amplification and cloning into bacterial vectors. Consequently, sequencing protocols that are dependent on PCR amplification fail on DNA palindromes. New tools are required for their discovery and characterization. Here we report our analysis of DNA palindromes from MCF-7, a widely used cell line model for estrogen receptor positive breast cancer. We developed a new strategy to identify and clone palindrome junctions by high throughput sequence analysis of DNA isolated by the Genome-wide Analysis of Palindrome Formation technique. We identified 35 palindrome candidates from MCF-7 and have cloned and sequenced 4 of the centers of the palindromes. None of these identified palindromes are present in other published data sets, despite the fact that MCF-7 DNA has been extensively sequenced and breakpoints analyzed, confirming that conventional methods fail on DNA palindromes. Our results provide further support for a correlation between palindromes and gene amplification in cancer, and underscore the importance of developing new tools for identifying and characterizing palindromes