A model is described for the templated production of frameshift and base-substitution mutations mediated through aberrant DNA structures arising as a consequence of quasi-palindromic DNA sequences. Two general mechanisms are considered. One evokes the formation and processing ofimperfect DNA secondary structures (hairpins) for the production of mutations. The other evokes a "strand switch" during DNA synthesis which, in a manner unique to quasi-palindromic sequences, may be resolved to produce frameshift or base-substitution mutations, or both. It is the unique combination of symmetrical and asymmetrical elements of the quasi-palindromic sequence itself that provides the basis for both models. Through the mechanisms described, the symmetrical elements permit unusually paired DNA substrates, and the asymmetrical elements permit templated insertions, deletions, and base substitutions. The model predicts a class of mutations simultaneously frameshifts and base substitutions-whose sequences can be predicted from a local quasi-palindromic sequence. This prediction appears to be met by a significant fraction (more than 15%) of frameshift mutations in the iso-l-cytochrome c gene of Saccharomyces cerevii'ae.Additions or deletions ofsmall numbers ofDNA bases resulting in frameshift mutations represent a sizable proportion of spontaneous mutations, and their frequency is often increased by mutagenic treatments. Studies of frameshift mutational mechanisms have focused upon the DNA sequences in which frameshift mutations arise. In many genetic systems, frameshift mutation has been correlated with DNA sequences comprised of repeated bases (1-4). This observation, first made in the T4 lysozyme gene, led to the suggestion by Streisinger et aL that repeated sequences mediated additions or deletions by allowing local misalignments of the complementary strands of DNA (1). Such aberrant DNA intermediates, if formed during replication, recombination, or repair, could then be the precursors of frameshift mutations. These repeated DNA sequences may be the simple reiteration of a single base as observed in the lysozyme and rI genes ofT4 (ref. 5; J. E. Owen, D. W. Shulz, A. Taylor, and G. R. Smith, personal communication) but also may be more complex repeats. For example, a frameshift hot spot in the Escherichia coli lad gene is a sequence of three tandem C-T-G-G units (4). Frameshift mutations arising at this site were found to be the addition or deletion of one C-T-G-G unit and, thus, were consistent with the prediction of the Streisinger model. Palindromic sequences in double-stranded DNA molecules have the inherent property ofself-complementarity within each single strand of the DNA. This complementarity permits such sequences to form uniquely paired DNA structures that are impossible in sequences lacking this complementarity; a classical example is the formation ofhairpins or cruciform structures. In quasi-palindromic sequences, where complementarity is imperfect, the formation of the unusual DNA configurations still may ...

A model is presented for deletion mutations whose formation is mediated by palindromic and quasipalindromic DNA sequences. It proposes that the self-complementarity of palindromes allows the formation of DNA secondary structures that serve as deletion intermediates. The structures juxtapose the end points of the deletion and thus direct deletion specificity. While misaligned DNA intermediates that explain deletion termini occurring in repeated DNA sequences have been described, no explanations have been offered for deletion termini occurring in other sequences. The DNA secondary structures whose formation is mediated by palindromic sequences appear to explain many of these. In this paper, secondary-structure intermediates are described for a series of spontaneous deletions of known sequence in the lad gene of Escherichia coli. The model is supported by its failure to predict structures that can juxtapose simulated deletion termini in the lacI gene. We have found a strong association between palindromic sequences and repeated sequences at lacl deletion termini that suggests the joint participation of repeated and palindromic DNA sequences in the formation of some deletions. Sequences of deletions in other organisms also suggest the participation of palindromic DNA sequences in the formation of deletions.Local DNA sequences can strongly influence the frequency of mutation (1). The frequent association of deletion termini with repeated DNA sequences (2-4) suggests that deletion mutations are no exception. The In its simplest form, our model proposes that DNA secondary structures whose formation is potentiated by palindromic or quasipalindromic DNA sequences participate in deletion formation through the juxtaposition of deletion end points. The inherent self-complementarity of palindromic DNA sequences permits the formation of cruciform or hairpin structures in nucleic acids, precisely juxtaposing otherwise distant bases (6). Repeated DNA sequences are not required.The termini of the E. coli lacd deletion S86 cannot be juxtaposed by a misalignment involving repeated sequences. However, the deletion termini are located precisely at the ends of a quasipalindromic DNA sequence that includes the entire deletion. The formation of a DNA hairpin or cruciform structure in the wild-type DNA sequence places the deletion termini immediately adjacent to one another, rather than separated by their normal linear distance of 27 base pairs (Fig. 1A). This structural intermediate would produce the S86 deletion if it served as a substrate for excision or as a template for DNA synthesis (Fig. 1B). The latter process might be mediated by either DNA polymerase or DNA ligase. A ligation across such a hairpin stem might also be responsible for deletions if the hairpin served as a substrate for nucleases that removed aberrantly aligned regions from ordinary double-stranded DNA. Whatever the precise molecular mechanism(s) responsible for the production of deletions from such DNA structures, the prediction of the model is that the ...

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The in vivo production of frameshift and base-substitution mutations predicted as a consequence of the metabolic processing of misaligned quasipalindromic DNA sequences has been confirmed. Spontaneous frameshift mutations of the T4 Wi gene that had been genetically mapped to quasipalindromic DNA sequences were sequenced. Some of the mutant sequences are exactly those predicted by a mutational model based on misaligned quasipalindromes. Furthermore, these sequences are distinct from those predicted by the classical frameshift model based on misaligned repeated sequences. The ilI frameshift mutant sequences reported here result from the deletion of a specific base or bases that would remain looped out should the quasipalindromes assume a hairpin secondary structure. One hairpin predicted not only the deletion of two bases (a frameshift) but the concomitant production of nearby but noncontiguous base substitutions. The substitution of as many as three bases as well as the frameshift were predicted to arise as a consequence of a single mutational event in the palindrome. Two independent examples of the predicted deletion frameshift were found among the small sample of sequenced spontaneous frameshifts examined and both were associated with the predicted transversion and transition base substitutions.Frameshift mutations often result from the addition or deletion of a repeating unit of a repeated DNA sequence. Metabolic processing of misaligned pairing between one of the repeating units and the complement of another is believed to be responsible (1, 2). However, frameshifts can occur in DNA sequences that are not repeated. A consideration of molecular mechanisms responsible for these mutations led to the proposal that some frameshifts occur because of processing of misaligned pairing mediated by quasipalindromes (3-5).Palindromic sequences permit the formation of alternative DNA secondary structures such as DNA hairpins. The action of ordinary DNA metabolism on such structures is predicted to lead to mutation (3, 5). The demonstration of mutations predicted to occur as a consequence of such processing and not by other mutational models would be strong confirmation of the quasipalindrome mutational model and would suggest the occurrence of palindromically mediated misalignments in vivo.Quasipalindromes permit the formation of misaligned structures through the self-complementarity of their palindromic portions and provide templates for base-substitution and frameshift mutations in their nonpalindromic portions (3). Mutations are predicted to result from templated processes that replace bases residing in one half of the hairpin with bases complementary to the other half. The predicted mutations can be readily visualized by examining quasipalindromic DNA sequences in hairpin structures (Fig. 1). Each unpaired base in the stem of the hairpin lacks a complemen-