Polarizability of Six-Helix Bundle and Triangle DNA Origami and Their Escape Characteristics from a Dielectrophoretic Trap

Abstract

DNA nanoassemblies, such as DNA origamis, hold promise in biosensing, drug delivery, nanoelectronic circuits, and biological computing, which require suitable methods for migration and precision positioning. Insulator-based dielectrophoresis (iDEP) has been demonstrated as a powerful migration and trapping tool for μm- and nm-sized colloids as well as DNA origamis. However, little is known about the polarizability of origami species, which is responsible for their dielectrophoretic migration. Here, we report the experimentally determined polarizabilities of the six-helix bundle origami (6HxB) and triangle origami by measuring the migration times through a potential landscape exhibiting dielectrophoretic barriers. The resulting migration times correlate to the depth of the dielectrophoretic potential barrier and the escape characteristics of the origami according to an adapted Kramer's rate model, allowing their polarizabilities to be determined. We found that the 6HxB polarizability is larger than that of the triangle origami, which correlates with the variations in charge density of both origamis. Further, we discuss the orientation of both origami species in the dielectrophoretic trap and discuss the influence of diffusion during the escape process. Our study provides detailed insight into the factors contributing to the migration through dielectrophoretic potential landscapes, which can be exploited for applications with DNA and other nanoassemblies based on dielectrophoresis.

DNA dielectrophoresis: Theory and applications a review

“…Their results allow careful design and optimization of applications of DNA origami such as nanoassembly [126]. In 2015, Gan et al determined the polarizability of DNA origami structures, which strongly depended on the structure of the origami [125]. Hence, a controlled assembly of specific DNA origami out of a mixture of differently shaped origami should be possible.…”

“…The majority of the devices for trapping DNA with iDEP consist of posts or constrictions in microfluidic devices [25,60,92,[123][124][125][126]. Another way for generating an inhomogeneous electric field is by using a nanopipette.…”

On the Impact of Electrostatic Correlations on the Double-Layer Polarization of a Spherical Particle in an Alternating Current Field

“…37–40 For example, recent experiments on estimating the tension inside actin filaments induced by the DEP suggest that this tension force is higher than the one obtained by the PNP model in a condensed electrolyte. 6 In addition, in the existence of multivalent ions, the standard PNP model even cannot qualitatively predict the experimental results.…”

Insulator Based Dielectrophoresis: Micro, Nano, and Molecular Scale Biological Applications

“…Later in 2015, Gan et al [ 121 ] manipulated origami DNA in a microdevice using the iDEP technique and measured the polarizability of the origami species ( Figure 9 a). Polarizability of the origami DNA was found to be responsible for the DNA migration in the applied iDEP field [ 121 ]. Six-helix bundle origami (6HxB) polarizabilities were experimentally investigated, and triangle origami [ 121 ] were reported.…”

“…Polarizability of the origami DNA was found to be responsible for the DNA migration in the applied iDEP field [ 121 ]. Six-helix bundle origami (6HxB) polarizabilities were experimentally investigated, and triangle origami [ 121 ] were reported. The experiments further discuss origami species orientation influence with respect to diffusion escape process in the dielectrophoretic trap.…”