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Here, we introduce a DNA framework vesicle (DFV) nanoreactor that confines membrane interactions within nanoscale reaction windows, transforming membrane fusion into a geometry-defined and quantitatively resolvable process. By embedding lipid membranes and SNARE proteins within defined DNA apertures, DFVs convert stochastic vesicle encounters to interface-defined fusion reactions. Cryo-electron microscopy resolves a complete sequence of six fusion intermediates, while fluorescence kinetics and nanoflow cytometry provide event-resolved quantification of fusion dynamics. Fusion efficiency and multiplicity are governed by intermembrane distance, reaction interface geometry, and vesicle stoichiometry, establishing a quantitative relationship between nanoscale spatial constraints and fusion pathways. Extending this strategy to living cells, DFVs mediate SNARE-dependent surface fusion with VAMP2-expressing membranes and enable the direct cytosolic delivery of functional siRNA through fusion-driven transfer. Together, these results establish DNA framework nanoreactors as a general strategy for stabilizing, quantifying, and engineering membrane fusion, providing a chemical framework for interrogating complex membrane-associated interfacial processes.<\/jats:p>","DOI":"10.1021\/jacs.6c09262","type":"journal-article","created":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T07:02:24Z","timestamp":1786345344000},"page":"43029-43040","source":"Crossref","is-referenced-by-count":0,"title":["Geometry-Defined\nMembrane Fusion in a DNA Framework\nNanoreactor"],"prefix":"10.1021","volume":"148","author":[{"given":"Qian","family":"Shi","sequence":"first","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, China, 200127"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiulan","family":"Yang","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, China, 200127"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Li","sequence":"additional","affiliation":[{"name":"Chinese Academy of Sciences , , Pudong , ,","place":["Shanghai, China, 201203"]},{"name":"Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery , , ,","place":["Yantai, Shandong, China, 264117"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Bao","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, China, 200127"]},{"name":"Chinese Academy of Sciences , , , ,","place":["Hangzhou, Zhejiang, China, 310022"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengwen","family":"Wang","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, China, 200127"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kui","family":"Huang","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, China, 200127"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayi","family":"Liu","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, China, 200127"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sa","family":"Wang","sequence":"additional","affiliation":[{"name":"Chinese Academy of Sciences , , Pudong , ,","place":["Shanghai, China, 201203"]},{"name":"Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery , , ,","place":["Yantai, Shandong, China, 264117"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunyun","family":"Wang","sequence":"additional","affiliation":[{"name":"Nankai University , , ,","place":["Tianjin, China, 300071"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4404-5302","authenticated-orcid":true,"given":"Yuanfang","family":"Chen","sequence":"additional","affiliation":[{"name":"and University of Chinese Academy of Sciences , , ,","place":["Beijing, China, 100190"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2321-4653","authenticated-orcid":true,"given":"Yuhe Renee","family":"Yang","sequence":"additional","affiliation":[{"name":"and University of Chinese Academy of Sciences , , ,","place":["Beijing, China, 100190"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Bian","sequence":"additional","affiliation":[{"name":"Nankai University , , ,","place":["Tianjin, China, 300071"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-1107-7437","authenticated-orcid":true,"given":"Zhenyong","family":"Wu","sequence":"additional","affiliation":[{"name":"Chinese Academy of Sciences , , Pudong , ,","place":["Shanghai, China, 201203"]},{"name":"Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery , , ,","place":["Yantai, Shandong, China, 264117"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2630-6062","authenticated-orcid":true,"given":"Yang","family":"Yang","sequence":"additional","affiliation":[{"name":"Shanghai Jiao Tong University , , ,","place":["Shanghai, China, 200127"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,10]]},"reference":[{"issue":"5","key":"2026101414091600100_cit1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2024029118","article-title":"Symmetrical\narrangement of proteins under release-ready vesicles in presynaptic\nterminals","volume":"118","author":"Radhakrishnan","year":"2021","journal-title":"Proc. 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