{"doi":"10.1093/nar/gkq078","title":"DNA linking number change induced by sequence-specific DNA-binding proteins","abstract":null,"journal":"Nucleic Acids Research","year":2010,"id":616613,"datarank":0.4493598410330987,"base_score":2.995732273553991,"endowment":2.995732273553991,"self_citation_contribution":0.4493598410330987,"citation_network_contribution":0.0,"self_endowment_contribution":0.4493598410330987,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":19,"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":1589836,"name":"Yazhong Xiao","orcid":null,"position":1,"is_corresponding":false},{"id":972024,"name":"Chang Liu","orcid":"0000-0001-7951-4546","position":2,"is_corresponding":false},{"id":827992,"name":"Chenzhong Li","orcid":"0000-0001-8514-7674","position":3,"is_corresponding":false},{"id":471718,"name":"Fenfei Leng","orcid":"0000-0002-9024-1216","position":4,"is_corresponding":false},{"id":366402,"name":"Bo Chen","orcid":"0000-0002-1931-3002","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"DNA linking number change induced by sequence-specific DNA-binding proteins","abstract":"Sequence-specific DNA-binding proteins play a key role in many fundamental biological processes, such as transcription, DNA replication and recombination. Very often, these DNA-binding proteins introduce structural changes to the target DNA-binding sites including DNA bending, twisting or untwisting and wrapping, which in many cases induce a linking number change (Delta Lk) to the DNA-binding site. Due to the lack of a feasible approach, Delta Lk induced by sequence-specific DNA-binding proteins has not been fully explored. In this paper we successfully constructed a series of DNA plasmids that carry many tandem copies of a DNA-binding site for one sequence-specific DNA-binding protein, such as lambda O, LacI, GalR, CRP and AraC. In this case, the protein-induced Delta Lk was greatly amplified and can be measured experimentally. Indeed, not only were we able to simultaneously determine the protein-induced Delta Lk and the DNA-binding constant for lambda O and GalR, but also we demonstrated that the protein-induced Delta Lk is an intrinsic property for these sequence-specific DNA-binding proteins. Our results also showed that protein-mediated DNA looping by AraC and LacI can induce a Delta Lk to the plasmid DNA templates. Furthermore, we demonstrated that the protein-induced Delta Lk does not correlate with the protein-induced DNA bending by the DNA-binding proteins.","is_dataset_classified":null,"base_score":2.995732273553991,"endowment":2.995732273553991,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"20185570","pmcid":"PMC2887952","openalex_id":"https://openalex.org/W2062800010","authors":[],"funders":[{"funder_name":"NICHD NIH HHS","grant_id":"1SC1HD063059-01A1","title":"Mechanisms of Transcription-Coupled DNA Supercoiling"}],"total_grants":1,"fwci":0.6226,"citation_percentile":0.66433249,"influential_citations":0,"citation_trend":[{"year":2012,"count":1},{"year":2013,"count":3},{"year":2014,"count":2},{"year":2015,"count":2},{"year":2016,"count":4},{"year":2017,"count":1},{"year":2018,"count":1},{"year":2019,"count":1},{"year":2020,"count":1},{"year":2021,"count":1},{"year":2024,"count":1}],"oa_status":"gold","license":"cc-by-nc","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/38/11/3643/16764333/gkq078.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/38/11/3643/16764333/gkq078.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/nar/article-pdf/38/11/3643/16764333/gkq078.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkq078","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/20185570","host_type":"repository"},{"url":"https://digitalcommons.fiu.edu/chemistry_fac/24","host_type":"repository"},{"url":"http://nar.oxfordjournals.org/cgi/content/short/38/11/3643","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2887952","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC2887952","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC2887952?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1093/nar/gkq078","host_type":""},{"url":"https://dx.doi.org/10.1093/nar/gkq078","host_type":""},{"url":"https://doi.org/https://doi.org/10.1093/nar/gkq078","host_type":""}],"fields_of_study":["DNA and Nucleic Acid Chemistry","Genomics and Chromatin Dynamics","Advanced biosensing and bioanalysis techniques","0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":["Base Sequence","Binding Sites","Cyclic AMP Receptor Protein","DNA-Binding Proteins","DNA, Circular","Nucleic Acid Conformation","Plasmids","Protein Binding","Repressor Proteins","Viral Proteins","Escherichia coli Proteins","AraC Transcription Factor","Lac Repressors"],"keywords":["HMG-box","Biology","DNA","DNA binding site","DNA supercoil","Replication protein A","Lac repressor","DNA clamp","DNA-binding protein","DNA replication","Molecular biology","Protein–DNA interaction","Single-stranded binding protein","In vitro recombination","Plasmid","Genetics","Transcription factor","Promoter","Peptide sequence","Gene","lac operon","Molecular cloning","RNA","Binding Sites","Cyclic AMP Receptor Protein","Base Sequence","Escherichia coli Proteins","AraC Transcription Factor","DNA-Binding Proteins","Repressor Proteins","Chemistry","Viral Proteins","Lac Repressors","Nucleic Acid Conformation","DNA, Circular","Biomedical Engineering and Bioengineering","Plasmids","Protein Binding"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-02T23:21:17.973986Z","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":[]}