Anisotropic Shrinkage of DNA Origami After a Wet-to-Dry Transition On Mica Surface

DNA nanotechnology is a fast emerging area with many potential applications such as nanofabrication, targeted drug delivery and self-assembly. DNA origami, for example, can serve as a scaffold for the assembly of functional materials. While most studies on DNA origami are done in aqueous solution, their application as templates for functional structures will inevitably occur in the dry state. Therefore, it is important to study the wet-to-dry transition of DNA origami and how this transition is affected by intrinsic factors such as origami design and external variables such as interfacial forces, buffer and drying conditions. Here we present a comparative study of the wet-to-dry transition in two different types of rectangular DNA origami on mica surface. The first type of origami is the tall rectangle (TR) with 10.67 bp/turn designed by Rothemund (2006).¹ This structure is distorted from its designed flat structure because of the deviation from a relaxed double stranded DNA configuration (i.e. 10.5 bp/turn).² We also considered a flatter tall rectangle (TRF) with 10.44 bp/turn designed by Woo and Rothemund (2011) in which twist in the direction perpendicular to helix stacking was reduced by introducing an irregular crossover pattern and leaving out parts of the scaffold unused in origami design.² While both structures shrink about 8-15% in transition from wet to dry state, TRF shrinks more anisotropically as compared to TR. Anisotropic shrinkage in TRF may be attributed to a more relaxed design where the inter-helix gap can be reduced more freely. Further, the unused parts of the DNA scaffold provide a cushion that facilitates shrinkage between two helices.² These differences in the wet-dry transition may be due to the unidirectional curvature of TRF, which allows preferential shrinkage along the length. In contrast, twist in both the directions perhaps puts more constraints in TR and the shrinkage is nearly isotropic. In the presence of weaker helical interaction, origami may be more likely to reduce interhelical spacing during drying.

The results suggest that it is important to consider the shrinkage during drying of origami while designing and assembling precision circuits as a change of few nanometers may compromise the functionality of the device.

References

1.    Rothemund, P. W. K. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

2.    Woo, S. and Rothemund, P. W. K. Programmable molecular recognition based on the geometry of DNA nanostructures. Nat. Chem. 3, 620-627 (2011).