Factors Affecting the Speed and Yield of Qdot Binding to DNA Origami

 

Seung Hyeon (Sarah) Ko, Gregg M. Gallatin, and J. Alexander Liddle

 

For the last two decades, DNA has been used to generate various nanostructures with molecular precision, and those nanostructures have been utilized as templates for the assembly of other nanoscale components to build more complex, functional devices.  DNA origami is a particularly attractive vehicle for this purpose, being readily configurable into different geometries and easily functionialized to provide a diverse set of binding sites. Organizing metallic nanoparticles in a controlled manner is of great interest in nanoelectronics and nanophotonics/plasmonics. In recent years, conjugates of nanoparticles and DNA origami have been used to build a variety of nanoarchitectures, but still with limited success. To achieve reliable yields of such nanostructures, however, it is important to understand the interplay of factors affecting the binding of nanoparticles to DNA origami.

Here we show that the speed and the yield of streptavidin-coated quantum dots binding to biotinylated DNA origami is controlled by valency at the binding location, biotin linker length, and the organization and spacing of the binding locations on DNA template. In addition, we have determined forward and backward reaction rate coefficients through analysis of time course data, and it provides us physical insight into these types of self-assembly processes.