Design, characterization and functionalization of DNA materials [thesis]

Daniel Schiffels
In recent years it has been demonstrated, that the sequences of a set of DNA molecules can be specifically programmed to drive their self-assembly into a predesigned nanoscale shape with nanometer precision. The two main techniques, "tiled" assembly and "DNA origami" have been used for the construction of DNA crystals, DNA nanotubes as well as single- and multi-layer DNA objects including cuboids, curved and twisted bundles and even complex 3D geometries such as hollow containers. Because of
more » ... ners. Because of this unique spatial control, today, DNA nanotechnology is actively used in a wide range of research areas such as structural biology, nanomedicine, single-molecule detection and plasmonics. We systematically measure the bending stiffness (persistence length) of DNA nanotubes (HX-tubes) as function of their circumference by analyzing micron-scale thermal fluctu- ations using fluorescence video microscopy (A, B). We further characterize intrinsic and thermal HX-tube twist by direct visualization of gold nano particles (AuNP), bound to specific positions of the tubes by electron microscopy (TEM) (C). We find that persistence length scales with the tube's second moment of inertia, intrinsic twist tends not to be present except when forced by sequence design and thermal twist occurs on lengths much shorter than the persistence length. We show that these results can be understood in terms of a quantitative DNA nanotube elasticity model, which takes the deformations of the DNA duplexes, as well as the strand cross-overs between them into account. To gain a better understanding of the interplay between the molecular architecture of DNA nanotubes and their micrometer-scale persistence length we study the thermal bending fluctuations of several six-helix-tubes with variations in the density and placement of strand cross-over and backbone nicks. We find that staggering cross-overs in one cross- sectional plane as well as decreasing the overall density of cross-overs significantly decreases persistence length and discuss these results in [...]
doi:10.5282/edoc.16375 fatcat:whiwnyjdrzhizgcdsm7cfi4oqm