Viability of palindromic DNA is restored by deletions occurring at low but variable frequency in plasmids of Escherichia coli.

Palindromic arrangements of 2 X 400 to 2 X 1517 bp of nucleotide sequences were created by in vitro manipulation of Escherichia coli plasmids. As a consequence of its method of formation, each palindrome possessed at its center the recognition site for a particular restriction endonuclease. Eight out of eight palindromes, having at their centers the recognition sites for BamHI, BglI, BglII, HindIII, PstI, SalI, XhoI, and Xma III, were shown to be inviable when transformed into E. coli. The smallest of these palindromes had a half-length of approx. 400 bp. The lethality of palindromic sequences for their carrier plasmids was circumvented at low frequencies by spontaneous in vivo deletion events which removed the centers of symmetry of the palindromes. The frequencies of such deletions were less than 1% in most cases, but varied significantly both with the palindromic sequence in question and with the surrounding nonpalindromic sequences of the carrier plasmid. We confirmed the viability of a plasmid with a 147-bp palindrome [Bergsma et al., Gene 20 (1982) 157-167] and found that this palindrome (derived from SV40) does not confer viability on the plasmids with long palindromes.