{"doi":"10.1016/j.xpro.2024.103249","title":"Protocol for analyzing DNA dynamics in the presence of crowders and confined within cell-sized droplets","abstract":"Here, we present a protocol for encapsulating DNA molecules under crowded conditions within cell-sized lipid-coated droplets. We describe steps for preparing a lipid-oil mixture and adding an aqueous solution containing DNA, which, when mixed, forms water-in-oil droplets of radii between ∼5 and 100 μm. We then detail procedures for quantifying the dynamics of DNA molecules in these droplets by analyzing fluorescence microscopy time series using differential dynamic microscopy. This protocol can be utilized to investigate DNA transport within a range of biomimetic and crowded environments. For complete details on the use and execution of this protocol, please refer to Aporvari et al. 1 • Protocol for encapsulating DNA inside cell-sized droplets with molecular crowders • Steps for preparing cell-sized lipid-coated droplets • Guidance on characterizing DNA dynamics using differential dynamic microscopy (DDM) Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Here, we present a protocol for encapsulating DNA molecules under crowded conditions within cell-sized lipid-coated droplets. We describe steps for preparing a lipid-oil mixture and adding an aqueous solution containing DNA, which, when mixed, forms water-in-oil droplets of radii between ∼5 and 100 μm. We then detail procedures for quantifying the dynamics of DNA molecules in these droplets by analyzing fluorescence microscopy time series using differential dynamic microscopy. This protocol can be utilized to investigate DNA transport within a range of biomimetic and crowded environments.","journal":"STAR Protocols","year":2024,"id":480990,"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":0.9536,"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":582683,"name":"Ryan McGorty","orcid":"0000-0002-6577-060X","position":1,"is_corresponding":false},{"id":514742,"name":"Rae M. Robertson‐Anderson","orcid":"0000-0003-4475-4667","position":2,"is_corresponding":false},{"id":920447,"name":"Mehdi Shafiei Aporvari","orcid":"0000-0003-0993-5737","position":0,"is_corresponding":true}],"reference_count":21,"raw_metadata":null,"created_at":"2026-07-19T02:07:06.225103Z","pmid":"39120975","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":[]}