When synthesizing a scaffolded DNA nanostructure, DNA staples are typically added in a 5–10× molar excess. This excess helps drive the formation to completion and minimize the number of unoccupied scaffold sites. Even with a 10× excess of staples, incorporation of a given staple has been found to be between 48% and 95%1. Using an even higher excess of staples could increase the percentage. However, an increase in staple excess comes with a higher price of synthesis. To reduce the cost, recent work has explored reusing excess staple oligonucleotides2. Thus, when synthesizing a new nanostructure it is important to optimize the staple:scaffold ratio to ensure high staple incorporation efficiency without driving the cost of synthesis excessively high.
References
- Strauss, M. T., Schueder, F., Haas, D., Nickels, P. C. & Jungmann, R. Quantifying absolute addressability in DNA origami with molecular resolution. Nat Commun 9, 1600 (2018).
- Reusing excess staple oligonucleotides for economical production of DNA origami. Nucleic Acids Research, https://academic.oup.com/nar/article/53/11/gkaf527/8166789.