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Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures
Abhinav Banerjee1, Micky Anand1, Simanta Kalita2
1Department of Biochemistry, Indian Institute of Science, Bangalore, India.
Nature Nanotechnology
|August 17, 2023
Summary
Understanding DNA dinucleotide base stacking is crucial. This study quantifies base-stacking energies using DNA nanotechnology and single-molecule imaging, revealing significant stabilization effects for DNA nanostructures.
Area of Science:
- Molecular Biology
- Nanotechnology
- Biophysics
Background:
- DNA structure relies on base-pairing and base-stacking interactions.
- Quantifying dinucleotide base-stacking energetics at the single-molecule level remains a challenge.
Purpose of the Study:
- To measure the free energy of dinucleotide base stacking using single-molecule techniques.
- To apply these energetics in designing DNA nanostructures and probes.
Main Methods:
- Utilized multiplexed DNA-based point accumulation in nanoscale topography (DNA-PAINT) imaging.
- Employed designer DNA nanostructures to isolate and measure stacking interactions.
- Analyzed binding kinetics of imager strands to quantify stabilization.
Main Results:
- A single dinucleotide base stack can stabilize DNA duplex nanostructures up to 250-fold.
- Measured dinucleotide base-stacking energies range from -0.95 ± 0.12 kcal/mol (C|T) to -3.22 ± 0.04 kcal/mol (A|C).
Conclusions:
- Provides quantitative single-molecule energetics for dinucleotide base stacking.
- Demonstrates applications in designing DNA-PAINT probes for super-resolution imaging.
- Aids in the design of functional DNA nanostructures, aptamers, and predicting local DNA structure.
