Biological characteristics of palindromic DNA. II.

Abstract

We have prepared plasmids containing various lengths of palindrome. When the palindrome is longer than 184bp, the plasmid can not grow in wild-type Escherichia coli, but a plasmid with a palindrome less than 95bp can. The absolute length of the palindrome determines whether the plasmid can grow or not. Electron microscopy confirmed that the plasmid with palindrome had a relaxed form with cruciform structure. The length of the protruding region is not the same size as the palindrome inserted into the plasmid but the self-annealing length seems to be just enough to make the twisted molecule into the relaxed form. Although plasmids with palindromes longer than 184bp multiply in E. coli recB recC sbcB recF, deletions occur in the palindromes and these deletions seem to occur at a specific site.A plasmid containing a long palindromic sequence has been shown not to multiply in wild-type Escherichia coli (1-4). However, a plasmid with the 73 by palindrome (half-length) derived from SV40 (pSVoriH) can be maintained in wildtype E. coli (5). LEACH and STAHL (6) found that phage ) with a 1.6 kb palindrome could multiply in E, coli recB recC sbcB, suggesting that such a palindrome is degraded by a recombination system in E. coli. In vitro, a plasmid which contains a palindromic structure becomes cruciform when treated with DNA gyrase (7). We studied a plasmid carrying two lactose promoter sequences in palindromic positions (184 by x 2) and found that it could not multiply in wild-type E. coli but could in E. coli recB recC sbcB recF. Structural analysis of the plasmid DNA by agarose gel

Replication strand preference for deletions associated with DNA palindromes

“…Naturally occurring palindromes in E. coli are mostly short (< 40 bp) and generally imperfect. DNA palindromes longer than 150-200 bp cannot be cloned in wild-type E. coli, either the replicon containing the palindrome is so poorly replicated that it is inviable (Warren and Green, 1985;Yoshimura et al, 1986), or the palindrome is so unstable that it suffers partial or complete deletion (Collins, 1981;Hagen and Warren, 1983). These phenomena are interlinked and have been termed inviability and instability respectively.…”

Frequent integration of short homologous DNA tracks during Acinetobacter baylyi transformation and influence of transcription and RecJ and SbcCD DNases

“…The same nucleotide sequences are present in the recipient DNA. There they do not pose a problem, as imperfect palindromes of up to 200 nt are tolerated in bacteria (Warren & Green, 1985;Yoshimura et al, 1986). In the case that they are subject to cleavage by SbcCD, e.g.…”

Flexi Vector Cloning

“…This region of identity acts to inhibit replication by forming of an extensive DNA palindrome when two vectors with substantial sequence identity ligate to each other (22). Therefore, inclusion of a region of either 3′ or 5′ sequence identity of ~100 bp or longer should be included in the design when different vector backbones are customized for use with the Flexi Vector system.…”