Size-exclusion chromatography (SEC) is a purification technique for achieving high purity of the DNA nanostructure1. SEC separates molecules by hydrodynamic radius. This allows it to purify MDa-scale DNA nanostructures from free DNA staples, from aggregates, and from dimers. Depending on the shape and flexibility of the nanostructure, it can also separate from free scaffold. Unlike PEG purification and ultrafiltration, SEC does not increase the concentration of your sample so it is less likely to induce aggregation.
Despite its powerful capabilities, SEC is not widely implemented for DNA nanostructure purification for several reasons. High-resolution SEC requires expensive equipment and reagents, SEC dilutes the sample, and SEC is a single-sample purification method, reducing speed of purification for batches of samples.
References
- Ebrahimimojarad, A. et al. A Robust and Efficient Method to Purify DNA-Scaffolded Nanostructures by Gravity-Driven Size Exclusion Chromatography. Langmuir 40, 8365–8372 (2024).