Hcr Hairpin Probes
Hcr Hairpin Probes - Related Videos
06:00
HCR-DNA FISH: A Fluorescence In Situ Hybridization Technique to Detect Viral DNA in Infected Cells
0 Views •
2023
In this video, the cells infected with MCPyV virions were subjected to in situ hybridization chain reaction to detect MCPyV specific genomes. Further, the DNA-HCR technique was combined with FISH to visualize the MCPyV DNA in infected human skin cells.
02:59
Using Immuno-RNA Fluorescence In Situ Hybridization to Visualize SARS-CoV-2
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2025
This video demonstrates the application of Hybridization Chain Reaction (HCR)-Fluorescence In Situ Hybridization (FISH) for visualizing the spatial distribution of SARS-CoV-2 subgenomic RNA. Combining HCR with immunofluorescence techniques has the potential to provide insights into host-virus interactions at the single-cell level.
05:58
Using DNA-Based Tension Probes to Assess Receptor Forces Applied by Immune Cells
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2025
The video demonstrates a method for assessing receptor forces applied by immune cells using polyethylene glycol-anchored gold nanoparticles and DNA hairpin tension probes. CD8-positive T cell interactions trigger probe unfolding, emitting fluorescence while locking strands sustain the signal for quantifying the forces applied by immune cells.
03:47
Short Hairpin RNA-Mediated Gene Knockdown in iHSPCs In Vitro: A Lentivirus-Based shRNA Expression System Delivery into iHSPCs for Knockdown of Specific Gene Expression
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2025
In this video, we demonstrate a method to perform transduction of shRNA lentiviral vectors to obtain stable knockdown cell lines in immortalized hematopoietic stem and progenitor cells (iHSPCs).
05:38
Custom-made Microdialysis Probe Design
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Cited by 9 •
2015
Microdialysis is a commonly used technique in neuroscience research. Therefore commercial probes are in great demand.In this work a probe assembly is explained in detail to build a reliable, concentric, custom-made microdialysis probe for less than $10.
FAQs
HCR begins when a target-binding probe recognizes its complementary RNA or DNA sequence. The bound probe exposes or presents an initiator sequence, which opens one metastable hairpin. That opened hairpin then recruits the second hairpin, and alternating hybridization propagates the assembly. Repeated incorporation of fluorescently labeled hairpins produces a long polymer at the target site, converting sequence recognition into a spatially localized signal.
HCR hairpin probes can amplify fluorescence without an enzymatic amplification step. The signal instead arises from designed interactions among the initiator and two metastable hairpins. This architecture is useful for imaging in cells and tissues because signal generation remains associated with target binding while avoiding dependence on an enzyme-driven amplification reaction. In infection and immunology studies, that supports visualization of selected transcripts or pathogen sequences.
The target-binding event determines where the probe-initiated assembly begins, so fluorescence marks the location of the recognized RNA or DNA sequence. The resulting signal can therefore be interpreted in relation to cells, tissue regions, or infection sites rather than only as a bulk measurement. This spatial resolution helps connect molecular detection with cellular organization and tissue-specific gene expression.
A basic workflow starts by selecting a probe that recognizes the RNA or DNA sequence of interest. After binding occurs, its initiator sequence triggers opening of the first metastable hairpin. The second hairpin joins the growing assembly through repeated hybridization, creating a fluorescent polymer. Imaging then reveals where the target-associated signal occurs within cells or tissues.
The approach can be directed toward immune-cell transcripts, pathogen genomes, or host-response sequences, depending on the selected target-binding probe. Detecting these different molecular classes allows investigators to examine both the infectious agent and the biological response in the same research context. This makes the method relevant to studies of infection dynamics, immune activity, and tissue-specific gene expression.
Multiplex imaging allows multiple molecular targets to be examined together, extending HCR hairpin probe analysis beyond a single sequence. In immunology and infection research, this can support comparisons among pathogen signals, immune-cell transcripts, and host responses within the same spatial setting. The combined information helps reveal cellular heterogeneity and relationships between infection-related molecules and tissue organization.