{"doi":"10.1101/2024.09.09.612093","title":"Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering","abstract":"ABSTRACT The structures of RNA:RNA complexes regulate many biological processes. Despite their importance, protein-free RNA:RNA complexes represent a tiny fraction of experimentally-determined structures. Here, we describe a joint small-angle X-ray and neutron scattering (SAXS/SANS) approach to structurally interrogate conformational changes in a model RNA:RNA complex. Using SAXS, we measured the solution structures of the individual RNAs in their free state and of the overall RNA:RNA complex. With SANS, we demonstrate, as a proof-of-principle, that isotope labeling and contrast matching (CM) can be combined to probe the bound state structure of an RNA within a selectively deuterated RNA:RNA complex. Furthermore, we show that experimental scattering data can validate and improve predicted AlphaFold 3 RNA:RNA complex structures to reflect its solution structure. Our work demonstrates that in silico modeling, SAXS, and CM-SANS can be used in concert to directly analyze conformational changes within RNAs when in complex, enhancing our understanding of RNA structure in functional assemblies.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":503135,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9495,"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":654757,"name":"Wellington Leite","orcid":"0000-0002-5674-3968","position":1,"is_corresponding":false},{"id":430273,"name":"Jesse B. Hopkins","orcid":"0000-0001-8554-8072","position":2,"is_corresponding":false},{"id":910343,"name":"Ian Hall","orcid":"0000-0002-2536-4025","position":3,"is_corresponding":false},{"id":226920,"name":"Hugh O’Neill","orcid":"0000-0003-2966-5527","position":4,"is_corresponding":false},{"id":569662,"name":"Sarah C. Keane","orcid":"0000-0003-3206-9048","position":5,"is_corresponding":false},{"id":910342,"name":"Aldrex Munsayac","orcid":"0000-0001-7268-020X","position":0,"is_corresponding":true}],"reference_count":104,"raw_metadata":null,"created_at":"2026-07-19T02:10:27.781502Z","pmid":"39314299","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":[]}