Competitive binding of gold nanospheres and nanorods on DNA origami substrates

DNA-directed assembly of gold nanoparticles into precise two- and three-dimensional patterns has enabled bold advances in probing their optical properties such as the local enhancement in their surface plasmon resonance. DNA nanostructures synthesized using the principles of DNA origami have been programmed to contain unique capture sites for positioning metal nanoparticles in diverse geometries for applications in biosensing, therapy, and miniature electronics. However, to enable scalability beyond simple 2-3 nanoparticle architectures, it is important to understand the requirement for orthogonal capture sequences for attaching more than a single gold nanoparticle on a DNA nanostructure. In this work, we sought to assemble an angular gold nanorod-nanosphere-nanorod pattern on a DNA origami triangle with multiple capture sites utilizing a common capture sequence. Results indicate that gold nanospheres preferentially bound to all the capture sites on the DNA origami triangle and prevented attachment of gold nanorods. This suggests that requirement for orthogonal capture sites is correlated with the physical properties of the individual nanoparticle such as shape and size.