Magnetic-bead purification1 is used, but less commonly, for DNA nanostructure purification. Two main approaches exist:
- Streptavidin–biotin capture — your DNA nanostructure is designed to contain a biotin-functionalized strand.
- DNA-handle capture — your DNA nanostructure contains a staple extension complementary to an oligo on the magnetic bead.
For both methods, the DNA nanostructure is mixed with and captured by magnetic beads. Multiple rounds of washing then remove unbound contaminants like unincorporated excess staples and free scaffold. Finally, the nanostructures are released from the bead into solution and collected.
For DNA-handle capture, nanostructures are released using toehold-mediated strand displacement. For streptavidin–biotin capture, nanostructures can be released using excess free biotin in solution however this is inefficient. An alternative is using desthiobiotin oligos. Desthiobiotin has a lower affinity for streptavidin than biotin and is thus more efficiently displaced using free biotin2.
Magnetic-bead purification is highly scalable and automatable, however it has many limitations. The cost per sample is high, non-specific adsorption to beads can lead to incomplete purification, and methods for elution from beads often require optimization.
References
- Sequential Pull-Down Purification of DNA Origami Superstructures — Ye et al., 2021. Small. https://onlinelibrary.wiley.com/doi/full/10.1002/smll.202007218.
- Hirsch, J. D. et al. Easily reversible desthiobiotin binding to streptavidin, avidin, and other biotin-binding proteins: uses for protein labeling, detection, and isolation. Analytical Biochemistry 308, 343–357 (2002).