Homologous recombination in bovine papillomavirus shuttlevecter; effect of relative orientation of substrate sequences.

Relative orientation of recombination substrates, neo gene, strongly influenced homologous recombination events in a bovine papillomavirus shuttle vector. Between direct repeats, recombination occurred at a high frequency while between inverted repeats, it was rare. Double strand break near the mutation site increased the recombination frequency between inverted repeats but not between direct repeats. Formation of long heteroduplex as a recombination intermediate may explain this apparently paradoxical phenomenon.