{"doi":"10.1101/2024.05.08.593220","title":"Domain consolidation in Bacterial 50S assembly revealed by Anti-Sense Oligonucleotide Probing","abstract":"Abstract Investigating the intricate and rapid folding kinetics of large RNA-protein complexes (RNPs), like the bacterial ribosome, remains a formidable challenge in structural biology. Previous genetic approaches to probe assembly have focused on modulating the expression of either r-proteins or assembly factors. Here, anti-sense oligonucleotides (ASOs) were used to disrupt native RNA/RNA and RNA/protein interactions, in order to generate novel folding intermediates. In an in vitro co-transcriptional assembly assay, 8 assembly inhibitor ASOs were identified. Using cryo-electron microscopy, 38 new intermediate structures were determined resulting from the specific inhibitions. In particular a novel intermediate class provided compelling evidence of independent rRNA domain folding before proper interdomain docking. Three PNAs targeting domain-I of 23S- rRNA further subdivided the previously identified assembly core into smaller blocks representing the earliest steps in assembly. The resulting assembly graph reveals template-directed RNA foldon docking and domain consolidation, which provides a hierarchical view of the RNP assembly process.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":490894,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9589,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":993705,"name":"Xiyu Dong","orcid":"0000-0002-1766-3324","position":1,"is_corresponding":false},{"id":471159,"name":"Sriram Aiyer","orcid":"0000-0001-6436-0521","position":2,"is_corresponding":false},{"id":1336367,"name":"Joan Lee","orcid":"0009-0002-3573-2167","position":3,"is_corresponding":false},{"id":1336670,"name":"Selena Djordjevic Marquardt","orcid":null,"position":4,"is_corresponding":false},{"id":275245,"name":"Dmitry Lyumkis","orcid":"0000-0002-8124-7472","position":5,"is_corresponding":false},{"id":461148,"name":"James R. Williamson","orcid":"0000-0002-8772-468X","position":6,"is_corresponding":false},{"id":884334,"name":"Kai Sheng","orcid":"0000-0001-9394-2256","position":0,"is_corresponding":true}],"reference_count":37,"raw_metadata":null,"created_at":"2026-07-19T02:08:41.211111Z","pmid":"38765969","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":[]}