Tetrahedral DNA dendritic nanostructure-enhanced FISH for high-speed, sensitive spatial transcriptomics

Abstract

Understanding where genes are active within tissues is essential to explain how cells build and maintain organs, yet many spatial RNA assays are slow and weak, limiting short-transcript detection and masking cellular diversity. Here we show that TDDN-FISH (Tetrahedral DNA Dendritic Nanostructure–Enhanced Fluorescence In Situ Hybridization), a rapid, enzyme-free method using self-assembling DNA nanostructures, accelerates and amplifies RNA detection. Per round, TDDN-FISH is ~eightfold faster than HCR-FISH and generates stronger signals than smFISH, enabling short-RNA detection and low-magnification tissue imaging with single-cell and subcellular resolution. Iterative, multiplexed hybridization produces color-coded readouts for many targets in the same specimen, supporting high-throughput spatial transcriptomics. We apply TDDN-FISH to cultured cells and tissue sections to map RNA distributions with high specificity and reveal complex expression patterns. This platform streamlines workflows and broadens access to spatial RNA profiling for studies of cellular heterogeneity, tissue organization, and disease mechanisms.