Chunhai Fan’s research while affiliated with Shanghai Jiao Tong University and other places

Cellular structure maintenance and function regulation critically depend on the composition and spatial distribution of numerous membrane proteins. However, current methods face limitations in spatial coverage and data scalability, hindering the comprehensive analysis of protein interactions in complex cellular nanoenvironment. Herein, we introduce p roximity- a ctivated D NA s canning e ncoded sequencing (PADSE-seq), an innovative technique that utilizes flexible DNA probes with adjustable lengths. These dynamic probes are anchored at a single end, enabling free swings within a nanoscale range to perform global scanning, recording, and accumulating of information on diverse proximal proteins in random directions along unrestricted paths. PADSE-seq leverages the autonomous cyclic cleavage of single-stranded DNA to sequentially activate encoded probes distributed throughout the local area. This process triggers strand displacement amplification and bidirectional extension reactions, linking proteins barcodes with molecular barcodes in tandem and further generating millions to billions of amplicons embedded with the combinatorial identifiers for next-generation sequencing analysis. As a proof of concept, we validated PADSE-seq for mapping the distribution of over a dozen kinds of proteins, including HER1, EpCAM, and PDL1, in proximity to HER2 in breast cancer cell lines, demonstrating its ability to decode multiplexed protein proximities at the nanoscale. Notably, we observed that the spatial distribution of proximal proteins around low-abundance target proteins exhibited greater diversity across regions with variable proximity ranges. This method offers a massive access for high-resolution and comprehensive mapping of cellular molecular interactions, paving the way for deeper insights into complex biological processes and advancing the field of precision medicine.

DNA molecules, with highly variable sequences and inherent programmability, emerge as a promising material for next‐generation information storage and data encryption. However, due to the singular encryption method or limited randomness of the secret key, current encryptions remain vulnerable to brute‐force attacks and the need for enhanced information security persists. This study introduces a programmable encryption strategy based on long‐chain DNA synthesis and sequential encoding. The proposed hairpin‐mediated primer exchange reaction (HAMER) system enables the generation of DNA keys and the recording of encoded information. Ultimately, encrypted text and image data can be decoded and retrieved through sequencing with customized access based on user permissions. This approach positions DNA as a high‐performance information material and establishes a programmable encryption framework, offering strong potential to meet the confidentiality, integrity, and availability demands of future information security systems.

Tracking RNA expression dynamics in living plants is critical for understanding gene regulation, yet real-time visualization remains a significant challenge. We have addressed this issue by de novo engineering an RNA-triggered fluorescence (RTF) reporter system precisely controlled by programmable RNA switches and achieved dynamic imaging of RNA expression at the cellular level and the whole-plant scale. The RNA switch-RTF system enabled the dynamic real-time tracking of developmentally regulated, tissue-specific, circadian, and stress-responsive mRNAs, as well as the movement of a mobile mRNA and an aphid-secreted cross-kingdom long non-coding RNA. By providing a powerful platform for real-time RNA imaging in vivo, our approach opens new avenues for studying gene regulation, signaling, and mobility in plants, with potential applications in synthetic biology and crop improvement.

The recognition and binding via receptor‐ligand interactions on cell membranes often weaken in complex environments, such as whole blood samples from cancer patients, making disease diagnosis and treatment evaluation unfavorable. Constructing multivalent ligands with sufficient fluid stability in complex environments remains a challenge. Herein, we develop a tetrahedral DNA framework (TDF) ensembled multivalent aptamers (TEA n , n = 1–3) with programmable ligands size, enabling efficient capture of circulating tumor cells (CTCs) and accurate monitoring of clinical treatment progress. The precisely structured TEA n ensures the size‐matching and cooperative hybridization with epithelial cell adhesion molecule (EpCAM) on cell membrane. Compared to traditional aptamer approach, the dissociation constants (K d ) of TEA 3 exhibits ∼20‐fold growth in serum due to its precise size and rigid DNA framework. This high‐affinity interaction significantly enhances capture efficiency by improving fluid stability of TEA n and magnetic beads complex in complex environment. In addition, this CTC detection strategy is applied for clinical tumor treatment evaluation and progress monitoring in liver cancer patient samples, achieving an accuracy of ∼83.3% in classifying patients as complete or partial responses (CR/PR). Overall, this strategy will strongly promote potential clinical application of DNA framework for cancer diagnosis and disease progression monitoring.

The recognition and binding via receptor‐ligand interactions on cell membranes often weaken in complex environments, such as whole blood samples from cancer patients, making disease diagnosis and treatment evaluation unfavorable. Constructing multivalent ligands with sufficient fluid stability in complex environments remains a challenge. Herein, we develop a tetrahedral DNA framework (TDF) ensembled multivalent aptamers (TEAn, n = 1–3) with programmable ligands size, enabling efficient capture of circulating tumor cells (CTCs) and accurate monitoring of clinical treatment progress. The precisely structured TEAn ensures the size‐matching and cooperative hybridization with epithelial cell adhesion molecule (EpCAM) on cell membrane. Compared to traditional aptamer approach, the dissociation constants (Kd) of TEA3 exhibits ∼20‐fold growth in serum due to its precise size and rigid DNA framework. This high‐affinity interaction significantly enhances capture efficiency by improving fluid stability of TEAn and magnetic beads complex in complex environment. In addition, this CTC detection strategy is applied for clinical tumor treatment evaluation and progress monitoring in liver cancer patient samples, achieving an accuracy of ∼83.3% in classifying patients as complete or partial responses (CR/PR). Overall, this strategy will strongly promote potential clinical application of DNA framework for cancer diagnosis and disease progression monitoring.

One of the drawbacks of nanozyme catalytic functions rests in their moderate catalytic activities due to the lack of effective binding sites concentrating the reaction substrate at the nanozyme catalytic interface. Methods to concentrate the substrates at the catalytic interface are essential to improving nanozyme functions. The present study addresses this goal by designing uric acid (UA) molecular-imprinted polyaniline (PAn)-coated Cu-zeolitic imidazolate framework (Cu-ZIF) nanoparticles as superior nanozymes, “polynanozymes”, catalyzing the H2O2 oxidation of UA to allantoin (peroxidase activity) or the aerobic, uricase mimicking, oxidation of UA to allantoin (oxidase activity). While bare Cu-ZIF nanoparticles reveal only peroxidase activity and the nonimprinted PAn-coated Cu-ZIF nanoparticles reveal inhibited peroxidase activity, the molecular-imprinted PAn-coated Cu-ZIF nanoparticles reveal a 6.1-fold enhanced peroxidase activity, attributed to the concentration of the UA substrate at the catalytic nanoparticle interface. Moreover, the catalytic aerobic oxidation of UA to allantoin by the imprinted PAn-coated Cu-ZIF nanoparticles is lacking in the bare particles, demonstrating the evolved catalytic functions in the molecularly imprinted polynanozymes. Mechanistic characterization of the system reveals that within the UA molecular imprinting process of the PAn coating, Cu⁺ reactive units are generated within the Cu-ZIF nanoparticles, and these provide reactive sites for generating O2–• as an intermediate agent guiding the oxidase activities of the nanoparticles. The study highlights the practical utility of molecular-imprinted polynanozymes in catalytic pathways lacking in the bare nanozymes, thus broadening the scope of nanozyme systems.