{"doi":"10.1186/1472-6750-13-87","title":"Accuracy and efficiency define Bxb1 integrase as the best of fifteen candidate serine recombinases for the integration of DNA into the human genome","abstract":"<jats:title>Abstract</jats:title>\n          <jats:sec>\n            <jats:title>Background</jats:title>\n            <jats:p>Phage-encoded serine integrases, such as φC31 integrase, are widely used for genome engineering. Fifteen such integrases have been described but their utility for genome engineering has not been compared in uniform assays.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Results</jats:title>\n            <jats:p>We have compared fifteen serine integrases for their utility for DNA manipulations in mammalian cells after first demonstrating that all were functional in <jats:italic>E. coli</jats:italic>. Chromosomal recombination reporters were used to show that seven integrases were active on chromosomally integrated DNA in human fibroblasts and mouse embryonic stem cells. Five of the remaining eight enzymes were active on extra-chromosomal substrates thereby demonstrating that the ability to mediate extra-chromosomal recombination is no guide to ability to mediate site-specific recombination on integrated DNA. All the integrases that were active on integrated DNA also promoted DNA integration reactions that were not mediated through conservative site-specific recombination or damaged the recombination sites but the extent of these aberrant reactions varied over at least an order of magnitude. Bxb1 integrase yielded approximately two-fold more recombinants and displayed about two fold less damage to the recombination sites than the next best recombinase; φC31 integrase.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions</jats:title>\n            <jats:p>We conclude that the Bxb1 and φC31 integrases are the reagents of choice for genome engineering in vertebrate cells and that DNA damage repair is a major limitation upon the utility of this class of site-specific recombinase.</jats:p>\n          </jats:sec>","journal":"BMC Biotechnology","year":2013,"id":622171,"datarank":0.7156026936698499,"base_score":4.770684624465665,"endowment":4.770684624465665,"self_citation_contribution":0.7156026936698499,"citation_network_contribution":0.0,"self_endowment_contribution":0.7156026936698499,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":117,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"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":1607341,"name":"Louise Thomas","orcid":null,"position":1,"is_corresponding":false},{"id":978832,"name":"Ben Davies","orcid":"0000-0003-4612-7894","position":2,"is_corresponding":false},{"id":1607343,"name":"Ronald Chalmers","orcid":null,"position":3,"is_corresponding":false},{"id":1607344,"name":"Maggie Smith","orcid":null,"position":4,"is_corresponding":false},{"id":34439,"name":"William Brown","orcid":null,"position":5,"is_corresponding":false},{"id":1607339,"name":"Zhengyao Xu","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Accuracy and efficiency define Bxb1 integrase as the best of fifteen candidate serine recombinases for the integration of DNA into the human genome","abstract":"<jats:title>Abstract</jats:title>\n          <jats:sec>\n            <jats:title>Background</jats:title>\n            <jats:p>Phage-encoded serine integrases, such as φC31 integrase, are widely used for genome engineering. Fifteen such integrases have been described but their utility for genome engineering has not been compared in uniform assays.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Results</jats:title>\n            <jats:p>We have compared fifteen serine integrases for their utility for DNA manipulations in mammalian cells after first demonstrating that all were functional in <jats:italic>E. coli</jats:italic>. Chromosomal recombination reporters were used to show that seven integrases were active on chromosomally integrated DNA in human fibroblasts and mouse embryonic stem cells. Five of the remaining eight enzymes were active on extra-chromosomal substrates thereby demonstrating that the ability to mediate extra-chromosomal recombination is no guide to ability to mediate site-specific recombination on integrated DNA. All the integrases that were active on integrated DNA also promoted DNA integration reactions that were not mediated through conservative site-specific recombination or damaged the recombination sites but the extent of these aberrant reactions varied over at least an order of magnitude. Bxb1 integrase yielded approximately two-fold more recombinants and displayed about two fold less damage to the recombination sites than the next best recombinase; φC31 integrase.</jats:p>\n          </jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions</jats:title>\n            <jats:p>We conclude that the Bxb1 and φC31 integrases are the reagents of choice for genome engineering in vertebrate cells and that DNA damage repair is a major limitation upon the utility of this class of site-specific recombinase.</jats:p>\n          </jats:sec>","is_dataset_classified":null,"base_score":4.770684624465665,"endowment":4.770684624465665,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"24139482","pmcid":"PMC4015280","openalex_id":"https://openalex.org/W2130696033","authors":[],"funders":[{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BB/H005277/1","title":null},{"funder_name":"Wellcome Trust","grant_id":"090532","title":null},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BB/H005447/1","title":null},{"funder_name":"Wellcome Trust","grant_id":"unidentified","title":"unidentified"}],"total_grants":4,"fwci":1.9268,"citation_percentile":0.86138158,"influential_citations":0,"citation_trend":[{"year":2014,"count":2},{"year":2015,"count":5},{"year":2016,"count":7},{"year":2017,"count":11},{"year":2018,"count":4},{"year":2019,"count":7},{"year":2020,"count":8},{"year":2021,"count":9},{"year":2022,"count":7},{"year":2023,"count":9},{"year":2024,"count":24},{"year":2025,"count":13},{"year":2026,"count":11}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://bmcbiotechnol.biomedcentral.com/counter/pdf/10.1186/1472-6750-13-87","host_type":"journal"},{"url":"https://bmcbiotechnol.biomedcentral.com/counter/pdf/10.1186/1472-6750-13-87","host_type":"publisher"},{"url":"https://link.springer.com/content/pdf/10.1186/1472-6750-13-87.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1186/1472-6750-13-87","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/24139482","host_type":"repository"},{"url":"http://hdl.handle.net/2164/3390","host_type":"repository"},{"url":"http://www.biomedcentral.com/1472-6750/13/87","host_type":"repository"},{"url":"http://europepmc.org/articles/PMC4015280","host_type":"repository"},{"url":"https://nottingham-repository.worktribe.com/output/718606","host_type":"repository"},{"url":"https://ora.ox.ac.uk/objects/uuid:b92a48a1-7e9f-4d49-ab9a-c7e936ddd2fe","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4015280","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC4015280","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC4015280?pdf=render","host_type":"Europe_PMC"},{"url":"https://bmcbiotechnol.biomedcentral.com/track/pdf/10.1186/1472-6750-13-87","host_type":""},{"url":"http://dx.doi.org/10.1186/1472-6750-13-87","host_type":""},{"url":"https://nottingham-repository.worktribe.com/file/718606/1/Brown_Accuracy.pdf","host_type":""},{"url":"https://dx.doi.org/10.1186/1472-6750-13-87","host_type":""},{"url":"https://doi.org/https://doi.org/10.1186/1472-6750-13-87","host_type":""}],"fields_of_study":["CRISPR and Genetic Engineering","Biochemical and Molecular Research","Bacterial Genetics and Biotechnology","0301 basic medicine","03 medical and health sciences","0303 health sciences","Amino Acid Sequence","Animals","Attachment Sites, Microbiological","Bacteriophages","Cell Line, Tumor","Cloning, Molecular","DNA","DNA Nucleotidyltransferases","Embryonic Stem Cells","Escherichia coli","Fibrosarcoma","Gene Deletion","Genome, Human","Humans","Integrases","Mice","Molecular Sequence Data","Plasmids","Recombinases","Recombination, Genetic","Serine"],"mesh_terms":["Amino Acid Sequence","Animals","Attachment Sites, Microbiological","Bacteriophages","Cloning, Molecular","DNA","DNA Nucleotidyltransferases","Escherichia coli","Fibrosarcoma","Humans","Molecular Sequence Data","Plasmids","Recombination, Genetic","Serine","Genome, Human","Gene Deletion","Integrases","Recombinases","Cell Line, Tumor","Mice","Embryonic Stem Cells"],"keywords":["Integrases","Recombinase","Integrase","Biology","DNA","Site-specific recombination","Genetics","Genome","Cre-Lox recombination","Homologous recombination","Recombination","Computational biology","Gene","Transgene","prophage","Fibrosarcoma","mammalian-cells","Molecular Sequence Data","610","system","Recombinases","Mice","directionality","Cell Line, Tumor","Escherichia coli","Animals","Humans","Bacteriophages","Amino Acid Sequence","Cloning, Molecular","serine recombinases","Embryonic Stem Cells","Recombination, Genetic","TP901-1","Genome, Human","T","T Technology","streptomyces phage PHI-BT1","PHI-C31 integrase","cassette exchange","Attachment Sites, Microbiological","DNA Nucleotidyltransferases","excision","DNA damage","genome manipulation","Gene Deletion","Biotechnology","Research Article","Plasmids"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-03T18:31:27.501912Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}