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Assembly and mechanics of DNA origami filaments

The mechanical properties of biopolymers are often characterized in terms of a persistence length. The persistence length of a biopolymer describes the length over which it can appreciably bend due to thermal energy. A more practical way to think of this is to consider a polymer or filament whose fully extended length (contour length) is much larger than the persistence length. Since the polymer contains many persistence length units where it can undergo significant bending, it will coil up into a so-called 'random coil.' On the other hand, a polymer or filament whose contour length is much smaller than the persistence length will remain essentially straight, or in other words not deform, when subject to thermal energy. Take the examples of fluctuations shown here for a dna double-helix (persistence length of ~50nm and contour length of 15 um, this movie was taken from Cohen et al.), a DNA origami bundled filament consisting of 6 dsDNA helices (we have measured persistence lengths of ~1um and this filament has a contour length of ~ 10um), and an amyloid fiber (persistence length of ~5um and this example has a contour length of ~7um).

Double-stranded DNA (Lp ~ 50nm, Lc ~ 15um). This movie was taken from Cohen et al., PNAS 2007. 104(31):12622-12627. DNA origami 6-helix bundle filament (Lp ~ 1um, Lc ~ 10um) Amyloid fiber (Lp ~ 5um, Lc ~ 7um)

 

Double-stranded DNA has a persistence length of ~50nm. DNA origami nanostructures generally incorporate many dsDNA helices and hence are much stiffer. 6 helix-bundles have been measured to exhibit persistence length of ~1-2 μm (Liedl et al., Kauert et al.), which agrees with our measurements. In general, most DNA origami nanostructures incorporate many (>6) helices. The mechanical properties of these stiffer nanostructures have not been characterized. Furthermore, it is currently not understood how to predict the mechanical behavior of DNA nanostructures based on cross-sectional geometry (i.e. number and arrangement of dsDNA helices). We are characterizing the mechanical properties of several DNA origami nanostrucures with varying cross-sections to understand how the mechanical properties scale with geometry. Typical dimensions of DNA origami nanostructures are generally 10-100nm. Even relatively flexible 6-helix bundle DNA origami nanostructures would appear to be nearly rigid at this lengthscale. Therefore to measure thermal deformations, we are fabricating DNA origami filaments through hierarchical self-assembly that are long enough to experience measureable thermal deformations. An example of a filament containing 18 bundles helices is shown in the TEM image below.

By measuring the conformation of many filaments using TEM imaging, we can creat conformational distributions that can be analyzed to determine the filament bending stiffness. The videos below show simulated conformational distributions for several different persistence length (Lp) filaments. All simulated filaments are 1μm long. 

For more info see:

Castro, C.E., Su, H., Marras, A.E., Zhou, L., Johnson, J., Mechanical Design of DNA Nanostructures. Nanoscale, 2015. 

 

Support - Ohio State University Institute for Materials Research (IMR)