Structural and Kinetic Profiling of Rolling Circle Amplification via Solid-State Nanopore Sensing Using miR-21 as a Model
Issued Date
2025-09-26
Resource Type
eISSN
23793694
Scopus ID
2-s2.0-105017112174
Journal Title
ACS Sensors
Volume
10
Issue
9
Start Page
7014
End Page
7024
Rights Holder(s)
SCOPUS
Bibliographic Citation
ACS Sensors Vol.10 No.9 (2025) , 7014-7024
Suggested Citation
Loha K., Boonkoom T., Pitakjakpipop H., Alam I., Treetong A., Boonbanjong P., Chatnuntawech I., Teerapittayanon S., Keyser U.F., Schulte A., Japrung D. Structural and Kinetic Profiling of Rolling Circle Amplification via Solid-State Nanopore Sensing Using miR-21 as a Model. ACS Sensors Vol.10 No.9 (2025) , 7014-7024. 7024. doi:10.1021/acssensors.5c02039 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/112407
Title
Structural and Kinetic Profiling of Rolling Circle Amplification via Solid-State Nanopore Sensing Using miR-21 as a Model
Corresponding Author(s)
Other Contributor(s)
Abstract
Rolling Circle Amplification (RCA) is a robust isothermal nucleic acid amplification technique widely used in molecular diagnostics. In this study, we combine RCA with solid-state nanopore sensing to monitor the amplification process at the single-molecule level using miR-21 as a model biomarker. This label-free platform enables detailed analysis of amplification kinetics and structural transitions over time. Changes in translocation dwell time and current blockage were evaluated across RCA incubation periods (30 min, 1 h, 2 h), revealing time-dependent increases consistent with the generation of longer and more complex DNA concatemers. These findings were validated by Urea-PAGE and atomic force microscopy (AFM), while Mfold-based secondary structure predictions further supported the evolution of more stable and folded configurations. Additionally, a custom-developed signal extraction application facilitated reproducible event classification and visualization. Overall, this integrated approach provides new insights into RCA behavior and highlights the potential of nanopore-based sensing for the development of sensitive, structure-resolved diagnostic tools.