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

## TL;DR

TDDN-FISH is a fast and sensitive method for detecting RNA in tissues, enabling detailed spatial transcriptomics with high resolution.

## Contribution

TDDN-FISH introduces a novel, enzyme-free DNA nanostructure-based FISH method that is significantly faster and more sensitive than existing techniques.

## Key findings

- TDDN-FISH is approximately eightfold faster than HCR-FISH and provides stronger signals than smFISH.
- The method enables detection of short RNAs and supports high-throughput spatial transcriptomics with single-cell resolution.

## 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.

Many spatial RNA monitoring assays can be hindered by barriers that limit short-transcript detection and mask cellular diversity. Here, the authors show TDDN-FISH – Tetrahedral DNA Dendritic Nanostructure–enhanced Fluorescence In Situ Hybridization. This is a rapid, enzyme-free method that uses self-assembling DNA nanostructures, thus accelerating RNA detection.