IN Situ study of the kinetics of quantum dot binding to DNA origami in solution

 

Seung Hyeon (Sarah) Ko,* Kan Du,* Andrew Berglund, J. Alexander Liddle

                                    (*: equal contribution)

 

DNA is an ideal material as a building block of rationally designed nanostructures due to its ability to self-assemble into highly ordered structures based on simple Watson-Crick base pairings. DNA nanostructures also can be modified to contain functional materials with useful biological and electronic properties including metallic nanoparticles. 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. DNA origami carries about 100 addressable binding sites at ~6 nm resolution, which is much smaller than the features constructed using traditional electron beam lithography. With such molecular precision, DNA origami has been actively used as a template to organize a variety of molecules.  Understanding the kinetics of the binding process is important for designing assembly processes that produce the desired structures with high yields.

Here we show in situ study of the kinetics of quantum dot (Qdot) binding to DNA origami in solution using a three-dimensional, real-time tracking system that enables us to observe individual Qdots and DNA origami. We have studied the binding process of Qdots to DNA origami which is engineered with 1, 2 or 3 binding sites. By measuring the diffusion coefficient, photon autocorrelation function (g2), and fluorescent intensity of freely diffusing particles, we are able to distinguish free Qdots and origami with 1, 2 and 3 Qdots respectively.