Related Experiment Video
Updated: May 26, 2026
06:51
Dual-modality Molecular Cartography: Integrating Multiplex mRNA Detection with Protein Imaging Mass Cytometry
Published on: November 14, 2025
Quantum Dot Encoding for In-Solution Single-Molecule Biomarker Counting in Metastatic Prostate Cancer
Chia-Wei Kuo1,2, Siva Nalla1,2, Suresh Sarkar1,3
1Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.
ACS Nano
|May 25, 2026
Summary
We developed novel surface-free assays for precise microRNA (miR) quantification in solution. These assays improve sensitivity and throughput for detecting cancer biomarkers, aiding precision medicine advancements.
Area of Science:
- Biomarker quantification
- Molecular diagnostics
- Cancer research
Background:
- Current digital assays for single-molecule biomarker quantification often rely on surface pull-down steps, limiting sensitivity and throughput.
- Accurate quantification of microRNAs (miRs) is crucial for diagnosing and monitoring diseases like metastatic castration-resistant prostate cancer (mCRPC).
Purpose of the Study:
- To develop novel surface-free, wash-free, in-solution assays for sequence-specific quantification of microRNAs (miRs).
- To achieve high analytical sensitivity and throughput for biomarker detection, particularly for mCRPC-relevant miRs.
- To enable reliable detection of trace biomarkers for cancer precision medicine.
Main Methods:
- Development of DNA nanoflowers (DNFs) densely encoded with quantum dots (QDs) for in situ stoichiometric assembly with target miRs.
- Detection of QD-DNFs as single events in solution using fluorescence microscopy or flow cytometry without washing steps.
- Machine learning-guided assay optimization to achieve high analytical sensitivity and agreement with absolute target counts.
- Utilizing ratiometric and multi-color (5-color) QD signatures for distinguishing multiple miR sequences.
Main Results:
- Achieved a limit of detection of approximately 10 aM with high agreement to absolute target counts (intraclass correlation coefficient = 0.95).
- Demonstrated the ability to distinguish multiple miR sequences using QD signatures with a single excitation source.
- Successfully applied the assays to detect exosomal miRs from small plasma volumes in mCRPC patients, showing strong agreement with RT-qPCR.
- Observed more reliable detection of the prognostic biomarker miR-375 compared to RT-qPCR, correlating higher levels with poor patient survival.
Conclusions:
- The developed in-solution, surface-free assays offer enhanced analytical sensitivity and throughput for miR quantification.
- These assays have the potential for calibration-free measurements and reliable detection of trace biomarkers.
- The technology shows promise for advancing cancer precision medicine through improved biomarker analysis in patient samples.
