(365f) Insulator-Based Dielectrophoretic (iDEP) Manipulation of DNA Origami In a Microfluidic System

Dielectrophoresis is the movement of particles caused by polarization in a nonuniform electric field. This technique has been used for manipulating, separating and detecting particles using devices within micrometer to submicrometer range. It has potential in coupling with microfluidic systems to build lab-on-a-chip devices for sorting, separation and analysis. Although the method is well established for micrometer-sized particles and biological cells, the underlying mechanism for biomolecules is still little understood. Here, we focus on a fundamental study of DNA dielectrophoresis of structure-defined DNA nanoparticles in an iDEP microfluidic system. DNA was chosen as model biomolecule because it's structure has been well studied and molecular assemblies with defined shapes such as 2D and 3D origamis can be created based on the principal of complementary base pairing. In particular, we explore the polarizability dependent dielectrophoretic behavior of 6-helix bundle and triangle DNA origamis with large structural difference and demonstrate distinct iDEP behavior.

A microdevice to study the iDEP behavior is built of a PDMS channel integrating an array of insulating posts to create electric field gradients upon application of external potential. The channel is 100 μm wide, 1 cm in length, integrating elliptic posts with a feature size of 6 μm and 10 μm along their minor and major axis, respectively. The depth of the channel and the height of the posts are 5 μm. Numerical simulation with COMSOL is used to determine the electric field distribution in the post array. Within our experimental limits, we thus find the device could achieve 10⁵ V/m in electric field and 10¹⁶ V²/m³ in gradient of electric field square (▽E²). To study the DNA origami's trapping behavior, the DNA molecules are intercalated with a fluorescent dye and DEP manipulation is recorded via fluorescence video microscopy.

The 6-helix bundle origami is a tube of 380 nm length and 7 nm diameter, while the triangle origami is a flat structure with a length of 130 nm along it's symmetric axis and with 2 nm in height. It is expected that 6-helix bundle origami perform a different trapping behavior from triangle origami according to differences in their molecular structure. In our experiment, the sample of around 200 pM concentration is filled in the channel and an electric field of 100 V/cm is applied along the channel. For 6-helix bundles, trapping of the particles around the posts is monitored at different AC frequency. For triangle origami, no trapping is observed, however concentrated streamlines are detected along the posts parallel to the direction of the electric field. We attribute the latter finding to the smaller size and thus reduced polarizability of the DNA triangle origami, resulting in an overall reduced DEP trapping force. Concentration streamlines arise due to a small pressure driven flow component.

Furthermore, a frequency dependence of the trapping behavior is monitored for the 6-helix bundle origami. As the AC frequency increases, the trapping areas around the posts shrink, while the fluorescence intensity of the trapping area increases. The migration of the DNA particles within DEP traps between the maxima of trapping forces around the insulator posts is also observed. This is most likely caused by the electrophoretic migration within the DEP trap. As the frequency increases, migration due to the electrophoresis is restricted in the trapping region, causing the shrinkage of the trapping area.

In conclusion, we demonstrated the DEP manipulation for DNA origami with the size down to 130nm. The two investigated DNA origamis (6-helix bundle and triangle origami) showed distinct difference in trapping strength. For 6-helix bundle in particular, frequency dependence in the trapping behavior is also observed. Our aim is to exploit the DNA origami trapping behavior quantitatively in the future to reveal the mechanism involved in DNA polarizability and apply the gained knowledge for the optimization of analytical techniques based on DEP.