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Single-Molecule Nanomechanical Genotyping with DNA Origami-Based Shape IDs.
Qian Li1, Jie Chao2, Honglu Zhang3
1School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
Methods in Molecular Biology (Clifton, N.J.)
|May 11, 2023
Summary
This study introduces DNA origami shape IDs for precise labeling of genomic DNA, enabling atomic force microscopy to genotype single DNA molecules with high resolution.
Area of Science:
- Biophysics
- Nanotechnology
- Genomics
Background:
- Atomic force microscopy (AFM) offers high-resolution imaging of biomolecules.
- Genotyping single DNA molecules requires precise labeling techniques.
Purpose of the Study:
- To develop DNA origami-based shape IDs for site-specific labeling of genomic DNA.
- To demonstrate the capability of AFM for differentiating closely spaced labeling sites.
Main Methods:
- Utilized DNA origami structures (triangular and cross shapes) as site-specific labels.
- Labeled target genomic DNA sequences containing two single-nucleotide polymorphisms (SNPs).
- Employed AFM nanomechanical imaging for visualization and analysis.
Main Results:
- Successfully generated DNA origami shape IDs for labeling genomic DNA.
- Achieved site-specific labeling of DNA sequences with adjacent sites separated by ~10 nm.
- Demonstrated the differentiation of labeling sites using AFM imaging.
- Enabled direct genotyping of single human genomic DNA molecules.
Conclusions:
- DNA origami shape IDs are effective for high-resolution AFM-based genomic DNA analysis.
- This method allows for precise genotyping of single DNA molecules.
- The technique advances nanomechanical imaging applications in genomics.
