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Probing Conformational Polymorphism of DNA Assemblies with Nanopores
Yingying Sheng1, Ke Zhou1, Quansheng Liu2
1Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
Analytical Chemistry
|April 3, 2020
Summary
Researchers developed a new method to study DNA nanostructures using poly(dC) tails and nanopores. This technique accurately identifies different DNA assemblies and their conformational changes in solution.
Area of Science:
- Biophysics
- Nanotechnology
- Molecular Biology
Background:
- Single-stranded DNA (ssDNA) self-assembles into complex nanostructures via Watson-Crick base pairing.
- Existing methods for characterizing DNA assembly conformations are limited.
- Novel interactions can arise from unnatural nucleobases or small molecule binding.
Purpose of the Study:
- To develop a novel strategy for probing conformational polymorphism in DNA assemblies.
- To provide a method for observing DNA nanostructure formation and disassembly.
- To complement existing DNA structure analysis techniques.
Main Methods:
- Functionalizing ssDNA with poly(dC)30 tails.
- Utilizing α-hemolysin nanopores to detect DNA structures.
- Analyzing current blockade patterns generated by DNA assemblies within the nanopore.
- Monitoring DNA nanostructure disassembly in solution.
Main Results:
- Distinct current blockade patterns were observed for different DNA nanostructures (duplex, triplex, etc.).
- The method successfully monitored the dynamic disassembly of DNA nanostructures.
- The technique demonstrated high accuracy and broad applicability for conformational analysis.
Conclusions:
- The developed nanopore-based strategy offers a powerful new tool for studying DNA nanostructures.
- This method provides real-time insights into DNA assembly dynamics and conformational states.
- It complements traditional techniques like CD spectroscopy, fluorescence, and NMR, offering enhanced accuracy and versatility.
