(251s) On-Chip Separation of Triangular and Cylindrical DNA Origami Nanostructures Using Slanted Nanofilter Array

DNA origami (DO) has enabled design and fabrication of DNA nanostructures of a variety of shape and functions. Based on such features, many novel DO molecules have been devised as a molecular probe to detect important target molecules such as disease related protein or miRNA, which is designed to undergo certain configuration/shape change in the presence of the target molecules [1]. Such reconfiguration of DO has been typically detected with other instruments such as AFM and single molecular FRET. However, for practical applications such as point-of-care (POC) and detection of low concentration target molecule, more rapid and less costly methods with improved detection limit are demanded. At the same time, many on-chip micro/nanofluidic separation methods have been developed recently, enabling rapid and continuous separation of differently shape molecules with high resolution. By utilizing such on-chip separation devices, it is expected that DO of different shape/configuration is rapidly separated and reconfiguration efficiency is easily analyzed.

In this work, as a first step toward the establishment of such on-chip DO based molecular detection system, the difference in electrophoretic migration is characterized for two differently shaped DOs, triangular DO and cylindrical DO, inside a recently reported nanofluidic sieving device called Slanted Nanofilter Array. Specifically, the mean and STD of deflection angle for each DO were measured, varying device parameters such as electric field strength and nanochannel depth. In Slanted Nanofilter Array, the deflection angle of each molecule is uniquely determined by its size and shape based on Ogston sieving mechanism, and the separation resoultion and detection limit is greatly increased by the integrated preconcentration region in the device [2]. Subsequently, a rigid body Brownian dynamics simulation was performed to compare with the experimental result, and it was shown that the experimental result could be well reproduced in the simulation both quantitatively and qualitatively. Furthermore, in order to increase the accuracy of the simulation, electrohydrodynamic parameters such as electrophoretic mobility and diffusion coefficient were measured with conventional CZE for each DNA origami nanostructure. Accordingly, the experimental results gained in this work are expected to be vital information for the design of an on-chip DO based molecular detection system.