Research Background
In biomedical research and clinical diagnostics, multiplex nucleic acid detection is crucial for molecular diagnostics and spatial genomics. However, traditional fluorescence detection methods are often constrained by issues such as spectral overlap, non-specific signals, and insufficient coding capacity. These limitations constrain the application of fluorescence methods in multiplex detection, particularly in scenarios demanding high throughput and sensitivity.
Research Content
Our team led by Professor Su Xin proposes a Spatial Fluorescence Barcode (SFB) platform based on transient luminescent DNA microspheres (TLDBs), enabling monochromatic, high-multiplex readouts. This approach encodes targets through the spatial arrangement of DNA-functionalized microspheres, eliminating the need for multicolor labeling or spectral demultiplexing. Target recognition is achieved via toehold-mediated strand displacement reactions, while built-in nucleases enable autonomous enzymatic reset, allowing probe reuse. The system employs monochromatic spatial encoding, decoupling coding capacity from spectral channels while featuring simplified probe design and decoding workflows. Self-resetting probes not only streamline encoding but also enhance practicality by supporting repeated testing without requiring costly probe reconstitution. Researchers validated the platform's clinical applicability by reliably detecting pathogen-derived nucleic acids in infected blood and identifying cancer-associated microRNAs in tissue samples. Compared to existing barcoding technologies, Spatial Fluorescence Barcodes (SFBs) integrate monochromatic spatial encoding, simplified design, and autonomous reusability, offering a practical, scalable, and cost-effective solution for high-throughput nucleic acid analysis. This work, titled “Spatial fluorescence barcode by transiently luminescent DNA beads,” was published in the journal Nature Communications.
Summary and Outlook
The author's developed Spatial Fluorescence Barcoding (SFB) platform based on transient luminescent DNA beads (TLDB) successfully integrates monochromatic fluorescence imaging, spatial encoding, and enzyme-mediated probe reset technology. This innovative solution offers high specificity, reproducibility, and operational simplicity for multiplex nucleic acid detection. This technology effectively circumvents spectral crosstalk and coding capacity limitations inherent in traditional multicolor fluorescence approaches. It has demonstrated reliable performance in clinical detection of pathogen genes and cancer-associated miRNAs, validating its practical potential in molecular diagnostics and spatial genomics. Looking ahead, the SFB platform remains amenable to further optimization and expansion across multiple dimensions. First, enhancing system throughput and encoding capacity is a key direction, achievable by increasing bead packing density, integrating multi-field-of-view imaging, or introducing a small number of orthogonal color channels. Second, improving long-term cycling stability is crucial. Future efforts may explore using thermally more stable enzyme variants, photobleaching-resistant dyes, or quantum dots, combined with bead surface coating and enzyme immobilization strategies to maintain signal consistency. Additionally, rational probe design and kinetic normalization in image analysis can reduce signal fluctuations caused by chain displacement reaction variations, improving quantitative reproducibility. Finally, advancing the system toward automation and portable devices, while exploring its applications in broader scenarios such as single-cell analysis, spatial multi-omics, and point-of-care testing (POCT), will accelerate its translation into clinical and basic research, providing a powerful tool for precision medicine.
Original Information
Tian, D., Yang, J., Zhang, L. et al. Spatial fluorescence barcode by transiently luminescent DNA beads. Nat. Commun., (2025). https://doi.org/10.1038/s41467-025-67410-3