Preparation of long single-strand DNA concatemers for high-level fluorescence in situ hybridization

Dual amplification-based ultrasensitive and highly selective colorimetric detection of miRNA

In this study, we combined a Pradeep Kumar (PK)-probe with a ligation-transcription-ramified RCA (LTR) dual-amplification system for the isothermal colorimetric detection of miRNA 25-3P, where the PK-probe transformed from its pink color to colorless in the presence of the amplification byproduct pyrophosphate (PPi), thereby allowing the simple naked-eye qualitative detection of the miRNA. Through this double-amplification strategy, the limit of detection reached as low as 91.4 aM-quite extraordinary sensitivity for a colorimetric miRNA detection system based on absorbance readings. Our detection system also operated with high specificity, the result of using two different target-selective ligation steps (linear DNA ligation and circular DNA ligation) mediated by SplintR ligase, and so could discriminate single-mismatched from perfectly matched target sequences. We suspect that this ultrasensitive and selective PK-probe/LTR dual-amplification system should be a great colorimetric diagnostic for the detection of any miRNA with high efficiency.

Designing a Hybrid Chain Reaction Probe for Multiplex Transcripts Assay with High-Level Imaging

The hybrid chain reaction (HCR), an isothermal and enzyme-free amplification strategy, has found extensive use in fluorescent in situ hybridization (FISH) assays. However, the existing HCRs are limited, being time-consuming processes and low-efficiency imaging due to weak signal, significantly restricting their application in transcriptomic assays. To address the limitations, we developed nine orthogonal HCR hairpin-pair (hp) probes in this study to enable efficient signal amplification for multiplex assays. To enhance the efficiency and imaging quality of multiplex assays using these HCR probes, we employed two strategies. First, we coupled fluorescent molecules to HCR hairpins via disulfide bonds, facilitating easy removal through chemical cleavage. As a result, the workflow was greatly simplified. Second, we combined HCR with in situ rolling circle amplification (ISRCA), creating ISRCA-HCR, which achieved a 17-fold signal amplification. ISRCA-HCR demonstrated a high-level imaging capability for spatial cell type assays. This study shows the application for cell typing based on the developed HCR probes, enabling accurate and high-level signal amplification for multiplex FISH imaging. This provides an effective research tool for transcriptome and spatial cell type analysis.

Highly efficient and robust π-FISH rainbow for multiplexed in situ detection of diverse biomolecules

In the unprecedented single-cell sequencing and spatial multiomics era of biology, fluorescence in situ hybridization (FISH) technologies with higher sensitivity and robustness, especially for detecting short RNAs and other biomolecules, are greatly desired. Here, we develop the robust multiplex π-FISH rainbow method to detect diverse biomolecules (DNA, RNA, proteins, and neurotransmitters) individually or simultaneously with high efficiency. This versatile method is successfully applied to detect gene expression in different species, from microorganisms to plants and animals. Furthermore, we delineate the landscape of diverse neuron subclusters by decoding the spatial distribution of 21 marker genes via only two rounds of hybridization. Significantly, we combine π-FISH rainbow with hybridization chain reaction to develop π-FISH+ technology for short nucleic acid fragments, such as microRNA and prostate cancer anti-androgen therapy-resistant marker ARV7 splicing variant in circulating tumour cells from patients. Our study provides a robust biomolecule in situ detection technology for spatial multiomics investigation and clinical diagnosis.