{"doi":"10.1093/genetics/121.4.651","title":"Palindromy and the location of deletion endpoints in Escherichia coli.","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>The contributions of direct and inverted repeats to deletion formation were studied by characterizing Ampr 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 Ampr 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.</jats:p>","journal":"Genetics","year":1989,"id":589171,"datarank":3.390493882131972,"base_score":3.9318256327243257,"endowment":3.9318256327243257,"self_citation_contribution":0.5897738449086489,"citation_network_contribution":2.800720037223323,"self_endowment_contribution":0.5897738449086489,"citer_contribution":2.800720037223323,"corpus_percentile":null,"corpus_rank":null,"citation_count":50,"citer_count":46,"citers_with_citation_signal":45,"citers_with_endowment":45,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1507392,"name":"D E Berg","orcid":null,"position":1,"is_corresponding":false},{"id":1507391,"name":"K Weston-Hafer","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Palindromy and the location of deletion endpoints in Escherichia coli.","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>The contributions of direct and inverted repeats to deletion formation were studied by characterizing Ampr 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 Ampr 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.</jats:p>","is_dataset_classified":null,"base_score":3.9318256327243257,"endowment":3.9318256327243257,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"2656400","pmcid":"PMC1203650","openalex_id":"https://openalex.org/W2096374018","authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"GM-37138","title":null},{"funder_name":"National Science Foundation","grant_id":"8608193","title":"Mechanism of Spontaneous Deletion Formation"}],"total_grants":2,"fwci":3.2381,"citation_percentile":0.9220217,"influential_citations":0,"citation_trend":[{"year":2014,"count":2},{"year":2017,"count":1}],"oa_status":"bronze","license":"OUP Standard Publication Reuse","oa_locations":[{"url":"https://academic.oup.com/genetics/article-pdf/121/4/651/34457794/genetics0651.pdf","host_type":"journal"},{"url":"https://academic.oup.com/genetics/article-pdf/121/4/651/34457794/genetics0651.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/genetics/article-pdf/121/4/651/34457794/genetics0651.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/genetics/121.4.651","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/2656400","host_type":"repository"},{"url":"https://dx.doi.org/10.1093/genetics/121.4.651","host_type":""}],"fields_of_study":["Bacterial Genetics and Biotechnology","RNA and protein synthesis mechanisms","DNA Repair Mechanisms","0301 basic medicine","0303 health sciences","03 medical and health sciences","Alleles","Chromosome Deletion","Escherichia coli","Models, Genetic","Molecular Sequence Data","Mutation","Repetitive Sequences, Nucleic Acid"],"mesh_terms":["Alleles","Chromosome Deletion","Escherichia coli","Models, Genetic","Molecular Sequence Data","Mutation","Repetitive Sequences, Nucleic Acid"],"keywords":["Direct repeat","Palindrome","Biology","Genetics","Inverted repeat","PBR322","Plasmid","Palindromic sequence","Repeated sequence","DNA","Sequence (biology)","Tandem repeat","Insertion sequence","Gene","Molecular biology","Transposable element","Genome","Models, Genetic","Molecular Sequence Data","Mutation","Escherichia coli","Chromosome Deletion","Alleles","Repetitive Sequences, Nucleic Acid"],"sdg_mappings":[{"sdg_number":3,"sdg_label":"3. 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