GC-rich DNA sequences block homologous recombination in vitro

The capacity of the RecA protein of Escherichia coli to promote an essential step in homologous recombination, strand transfer, was tested on DNA substrates varying in percentage GC. GC content was determined by a novel method using the polymerase chain reaction. Strand transfer activity is greatly reduced as a function of increasing GC content of the DNA. Some reduction is observed with substrates having a GC percentage similar to that of E. coli. The transfer reaction between sequences adjacent, but not distal, to GC-rich sequences is similarly decreased, suggesting that the structure of RecA-DNA complexes may differ with the GC content of DNA. Our results implicate an important role of DNA sequence in homologous recombination and suggest that many sequences are excluded due to their GC content.