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Updated: May 1, 2026
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Published on: October 31, 2013
3D structural integrity and interactions of single-stranded protein-binding DNA in a functionalized nanopore
Mohammed Arif I Mahmood1, Waqas Ali, Ashfaq Adnan
1Nano-Bio Lab, ‡Department of Electrical Engineering, §Nanotechnology Research Center, Shimadzu Institute for Research Technologies, ∥Department of Mechanical and Aerospace Engineering, ⊥Department of Bioengineering, #Joint Graduate Studies Committee of Bioengineering Program, University of Texas at Arlington and University of Texas Southwestern Medical Center at Dallas, University of Texas at Arlington , Arlington, Texas 76019, United States.
Aptamers, or DNA aptamers, are used to detect cancer cells by binding to biomarkers. Molecular dynamics simulations show how electric fields affect aptamer structure and improve cancer cell detection.
Area of Science:
- Biophysics
- Biochemistry
- Nanotechnology
Background:
- Aptamers are DNA sequences that bind to specific biomarkers, showing promise for cancer cell isolation and detection.
- Grafting aptamers within nanopores allows for selective capture and binding of target molecules.
- Understanding aptamer behavior under experimental conditions, like electric fields, is crucial for their application.
Purpose of the Study:
- To investigate the effects of external electric fields on the 3D conformation of DNA aptamers grafted in nanopores.
- To determine how these aptamer structures influence the translocation dynamics of target molecules.
- To explore a novel scenario of protein translocation with prebound DNA aptamers.
Main Methods:
- All-atom molecular dynamics simulations were employed.
- The study simulated the interaction of electric fields with DNA aptamer structures within nanopores.
- A thrombin-specific G-quartet and thrombin complex was used as a model system.
Main Results:
- External electric fields were shown to affect the 3D conformation of DNA aptamers.
- The presence of grafted aptamers altered target molecule translocation time, velocity, and detection frequency.
- Simulations provided insights into protein translocation dynamics when DNA aptamers are prebound.
Conclusions:
- DNA aptamers grafted in nanopores maintain functionality under electric fields, enabling selective biomarker detection.
- Molecular dynamics simulations are valuable for optimizing aptamer-based nanopore sensing systems.
- This research advances the development of sensitive and specific diagnostic tools for diseases like cancer.
