Design, Assembly, and Function of DNA Origami Mechanisms.

This chapter provides an overview of the common procedures used in making functional DNA origami devices. These procedures include the design, assembly, purification, and characterization of the DNA origami structures, with a focus on dynamic devices.

A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules.

Single molecule force spectroscopy is a powerful approach to probe the structure, conformational changes, and kinetic properties of biological and synthetic macromolecules. However, common approaches to apply forces to biomolecules require expensive and cumbersome equipment and relatively large probes such as beads or cantilevers, which limits their use for many environments and makes integrating with other methods challenging. Furthermore, existing methods have key limitations such as an inability to apply compressive forces on single molecules.

Quantitative Modeling of Nucleosome Unwrapping from Both Ends.

In eukaryotic cells, DNA is packaged into chromatin where nucleosomes are the basic packaging unit. Important cellular processes including gene expression, DNA replication, and DNA repair require nucleosomal DNA to be unwrapped so that functional proteins can access their target sites, which otherwise are sterically occluded. A key question in this process is what the unwrapped conformations individual nucleosomes adopt within chromatin are.

Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis.

Significant advances have been made towards the design, fabrication, and actuation of dynamic DNA nanorobots including the development of DNA origami mechanisms. These DNA origami mechanisms integrate relatively stiff links made of bundles of double-stranded DNA and relatively flexible joints made of single-stranded DNA to mimic the design of macroscopic machines and robots. Despite reproducing the complex configurations of macroscopic machines, these DNA origami mechanisms exhibit significant deviations from their intended motion behavior since nanoscale mechanisms are subject to significant thermal fluctuations that lead to variations in the geometry of the underlying DNA origami components.

Probing Nucleosome Stability with a DNA Origami Nanocaliper.

The organization of eukaryotic DNA into nucleosomes and chromatin undergoes dynamic structural changes to regulate genome processing, including transcription and DNA repair. Critical chromatin rearrangements occur over a wide range of distances, including the mesoscopic length scale of tens of nanometers. However, there is a lack of methodologies that probe changes over this mesoscopic length scale within chromatin.