{"doi":"10.1093/nar/24.13.2567","title":"Assessment of major and minor groove DNA interactions by the zinc fingers of Xenopus transcription factor IIIA","abstract":null,"journal":"Nucleic Acids Research","year":1996,"id":686960,"datarank":0.3958585994422889,"base_score":2.639057329615259,"endowment":2.639057329615259,"self_citation_contribution":0.3958585994422889,"citation_network_contribution":0.0,"self_endowment_contribution":0.3958585994422889,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":13,"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":1794678,"name":"S. McBryant","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Assessment of major and minor groove DNA interactions by the zinc fingers of Xenopus transcription factor IIIA","abstract":"Zinc finger proteins of the Cys2His2 class are DNA sequence-specific transcription factors. Previous structural studies of zinc finger protein-DNA complexes have shown that amino acids in the finger tip and alpha-helix regions within individual finger domains make base-specific contacts with the major groove of DNA. The nine finger protein transcription factor IIIA (TFIIIA) from Xenopus oocytes binds a 43 base pair region of the 5S RNA gene through major groove interactions with two sets of three fingers (fingers 1-3 and 7-9) and with finger 5. Previous studies have suggested that zinc fingers 4 and 6 each bind in or across the minor groove to bridge these major groove-binding zinc fingers. Here it is shown that a polypeptide containing zinc fingers 1-5 (zf1-5) binds oligonucleotides with modifications in the major groove of the finger 4 binding site with wild-type affinity. Mutagenesis and binding site selection studies were performed to determine whether high affinity DNA binding by zf1-5 requires a particular sequence in the binding site for finger 4. Several mutations in this region of the 5S gene reduced the DNA-binding affinity of zf1-5; however, selection and amplification binding assays did not recover the wild-type finger 4 binding site sequence from a pool of mixed sequence oligonucleotides. Rather, a purine-rich sequence on the top strand was highly selected within the finger 4 binding site. We suggest that high affinity DNA binding by zinc finger 4 may be dictated by a sequence-specific DNA structure rather than by a unique DNA sequence. Deletion of finger 4 from zf1-5 results in a protein with poor binding affinity, demonstrating the importance of finger 4 in proper alignment of neighboring fingers with the DNA, and/or the importance of correct protein-protein interactions between fingers.","is_dataset_classified":null,"base_score":2.639057329615259,"endowment":2.639057329615259,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"8692697","pmcid":"PMC145982","openalex_id":"https://openalex.org/W2032460583","authors":[],"funders":[{"funder_name":"NIGMS NIH HHS","grant_id":"GM36643","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"GM47330","title":null},{"funder_name":"NIGMS NIH HHS","grant_id":"GM26453","title":null}],"total_grants":3,"fwci":0.9277,"citation_percentile":0.73806163,"influential_citations":0,"citation_trend":[{"year":2015,"count":1},{"year":2016,"count":1},{"year":2023,"count":1}],"oa_status":"green","license":null,"oa_locations":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/145982","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/145982","host_type":"repository"},{"url":"http://academic.oup.com/nar/article-pdf/24/13/2567/6963187/24-13-2567.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/24.13.2567","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/8692697","host_type":"repository"},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.99.4415","host_type":""}],"fields_of_study":["Genomics and Chromatin Dynamics","RNA Research and Splicing","RNA and protein synthesis mechanisms","Amino Acid Sequence","Animals","Base Sequence","Binding Sites","DNA","DNA-Binding Proteins","Molecular Sequence Data","Nucleic Acid Conformation","Oligodeoxyribonucleotides","Oocytes","Peptide Fragments","Protein Binding","Recombinant Proteins","Titrimetry","Transcription Factor TFIIIA","Transcription Factors","Xenopus","Zinc Fingers"],"mesh_terms":["Amino Acid Sequence","Animals","Base Sequence","Binding Sites","DNA","DNA-Binding Proteins","Molecular Sequence Data","Nucleic Acid Conformation","Oligodeoxyribonucleotides","Oocytes","Peptide Fragments","Protein Binding","Recombinant Proteins","Transcription Factors","Xenopus","Zinc Fingers","Titrimetry","Transcription Factor TFIIIA"],"keywords":["Zinc finger","Zinc finger nuclease","Biology","DNA","Binding site","Transcription factor","DNA binding site","Sp1 transcription factor","Oligonucleotide","DNA-binding protein","LIM domain","RING finger domain","Zinc finger transcription factor","Base pair","Protein–DNA interaction","HMG-box","Gene","Biochemistry","Promoter","Gene expression"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-18T20:58:31.097130Z","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":[]}