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Genetics, Vol 121, 651-658, Copyright © 1989
INVESTIGATIONS |
Palindromy and the Location of Deletion Endpoints in Escherichia coli
K. Weston-Hafer and D. E. Berg
Departments of Microbiology and Immunology and of Genetics, Washington University Medical School, St. Louis, Missouri 63110
The contributions of direct and inverted repeats to deletion formation were studied by characterizing Amp(r) revertants of plasmids with a series of insertion mutations at a specific site in the pBR322 ampicillin resistance (amp) gene. The inserts at this site are palindromic, variable in length, and bracketed by 9- or 10-bp direct repeats of amp sequence. There is an additional direct repeat composed of 4 bp within the insert and 4 bp of adjoining amp sequence. DNA sequencing and colony hybridization of Amp(r) revertants showed that they contained either the parental amp sequence, implying deletion endpoints in the flanking 9- or 10-bp repeats, or a specific 1-bp substitution, implying endpoints in the 4-bp repeats. Although generally direct repeats seem to be used as deletion endpoints with a frequency proportional to their lengths, we found that with uninterrupted palindromes longer than 32 bp, the majority of deletions ended in the 4 bp, not the 9- or 10-bp repeats. This preferential use of the shorter direct repeats associated with palindromes is interpreted according to a DNA synthesis-error model in which hairpin structures formed by intrastrand pairing foster the slippage of nascent strands during DNA synthesis.
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