Atomic force microscopy (AFM) has emerged as a critical tool for characterizing the structural integrity and spatial organization of DNA origami lattices at nanoscale resolution. In this study, we present a high-resolution AFM analysis of polycrystalline DNA origami lattices assembled on mica surfaces, focusing on their topological order, defect distribution, and long-range homogeneity across macroscopic areas. The experiments were conducted using a 7.5 × 2.5 cm² mica substrate, with lattice formation achieved via surface-assisted hierarchical self-assembly under optimized ionic conditions (10 mM Mg²⁺, 75 mM Na⁺). After assembly, samples were stabilized with Ni²⁺ ions to prevent structural disintegration during post-processing steps.
High-resolution AFM images were acquired in ScanAsyst mode using Air cantilevers, with scan sizes ranging from 2.CKAP4 Antibody Protocol 5 × 2.5 µm² to 5 × 5 µm² and pixel resolutions of 1024 × 1024. Image preprocessing included mean plane subtraction and polynomial alignment to correct for drift and tilt.Factor XIIIa Antibody Formula Automated analysis was performed using a previously established method based on Delaunay triangulation of DNA origami triangle centers. This approach enabled quantitative assessment of lattice quality through two key topological parameters: the variance in nearest-neighbor distances (σ²) and the fraction of six-coordinated triangles (p6).
The results revealed a highly ordered polycrystalline structure composed of single-crystalline domains several hundred nanometers in size, separated by grain boundaries rich in defects.PMID:34774292 These defects—zero-, one-, and two-dimensional—arose primarily from the incorporation of partially folded monomers or during lattice annealing processes. Despite these features, the overall lattice exhibited consistent packing throughout the surface. The p6 values remained stable between 0.36 and 0.42 across all analyzed regions, confirming that the lattice maintains near-uniform coordination despite its polycrystalline nature.
Notably, the absence of systematic trends in the data—such as edge effects or central degradation—was confirmed through heat map visualization of p6 values mapped to imaging locations. This indicates that the assembly process is robust and reproducible over centimeter-scale dimensions. Furthermore, the Fourier transform analysis of individual crystalline grains showed clear hexagonal symmetry, although full-field FFTs were obscured by scanning artifacts and residual surface contamination, particularly from dried DNA fragments deposited during washing.
These findings highlight the capability of AFM to resolve both local microstructural details and global pattern uniformity in large-area DNA origami lattices. The technique enables precise evaluation of lattice perfection, defect density, and homogeneity—essential metrics for applications requiring predictable nanostructure placement. With further integration into automated imaging workflows, such high-resolution AFM characterization will play a pivotal role in advancing the scalability and reliability of DNA-based nanofabrication technologies.MedChemExpress (MCE) offers a wide range of high-quality research chemicals and biochemicals (novel life-science reagents, reference compounds and natural compounds) for scientific use. We have professionally experienced and friendly staff to meet your needs. We are a competent and trustworthy partner for your research and scientific projects.Related websites: https://www.medchemexpress.com