ArticleNature chemical biology2025
Spatial barcoding reveals reaction radii and contact-dependent mechanism of proximity labeling.
Article in Nature chemical biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Mapping subcellular microenvironments using oligonucleotide-directed proximity labeling.Current opinion in chemical biology · 2026Review
- Mapping the architecture of protein complexes inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Dual-Organelle Secretome Conjugation and Organ-Uptake Tracking (DuO-SCOUT) Enables Deep and Sensitive Mapping of the Secreted Proteins.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Controlling distance, time and reactivity: Chemical principles of proximity labeling.Current opinion in chemical biology · 2026Review
- Recent Advances in Photocatalyst-Driven Protein Labeling and Proximity Mapping.Chemical record (New York, N.Y.) · 2026Review
- AbioRxiv : the preprint server for biology · 2026Article
- Radical diffusion, not lifetime, determines the range of peroxidase-based proximity labelling.Journal of cell science · 2026Article
- Directed Evolution Improves the Catalytic Efficiency of APEX2-Mediated Proximity-Dependent RNA Labeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- NanorulerQA: quantitative quality analysis of dual-color DNA nanorulers via single-molecule photobleaching step counting and spatio-temporal colocalization.Biomedical optics express · 2026Article
- Intrinsically disordered domains expand the CAR T cell toolbox.Nature chemical biology · 2026Article
- Multi-omics profiling reveals mitochondrial dysfunction and epigenetic dysregulation in postoperative cognitive dysfunction: identification of novel biomarkers in an aged mouse model.Biogerontology · 2025Article
- Toward Mapping Spatiotemporally Resolved Transcriptomes and RNA-Protein Interactions.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Proximity labeling techniques such as TurboID and APEX2 have become pivotal tools for studying protein interactions. However, the spatial patterns of labeling methods within the submicrometer range remain poorly understood. Here we used DNA nanostructure platforms to precisely measure the labeling radii of TurboID and APEX2 through in vitro assays. Our DNA nanoruler design enables the deployment of oligonucleotide-barcoded labeling targets with nanometer precision near the enzymes. By quantifying labeling yields using qPCR and mapping them against target distances, we uncovered surprising insights into the labeling mechanisms. Contrary to the prevailing diffusive labeling model, our results demonstrate that TurboID primarily operates through contact-dependent labeling. Similarly, APEX2 shows high labeling efficiency within its direct contact range. In parallel, it exhibits low-level diffusive labeling toward more distant phenols. These findings reframe our understanding in the mechanism of proximity labeling enzymes while highlighting the potential of DNA nanotechnology in spatially profiling reactive species.
Identifiers
41444830What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.