A DNA origami-based device for investigating DNA bending proteins by transmission electron microscopy.

The DNA origami technique offers precise positioning of nanoscale objects with high accuracy. This has facilitated the development of DNA origami-based functional nanomechanical devices that enable the investigation of DNA-protein interactions at the single particle level. Herein, we used the DNA origami technique to fabricate a nanoscale device for studying DNA bending proteins. For a proof of concept, we used TATA-box binding protein (TBP) to evaluate our approach. Upon binding to the TATA box, TBP causes a bend to DNA of ∼90°. Our device translates this bending into an angular change that is readily observable with a conventional transmission electron microscope (TEM). Furthermore, we investigated the roles of transcription factor II A (TF(II)A) and transcription factor II B (TF(II)B). Our results indicate that TF(II)A introduces additional bending, whereas TF(II)B does not significantly alter the TBP-DNA structure. Our approach can be readily adopted to a wide range of DNA-bending proteins and will aid the development of DNA-origami-based devices tailored for the investigation of DNA-protein interactions.

Measuring the Affinities of RNA and DNA Aptamers with DNA Origami-Based Chiral Plasmonic Probes.

Reliable characterization of binding affinities is crucial for selected aptamers. However, the limited repertoire of universal approaches to obtain the dissociation constant (KD) values often hinders the further development of aptamer-based applications. Herein, we present a competitive hybridization-based strategy to characterize aptamers using DNA origami-based chiral plasmonic assemblies as optical reporters. We incorporated aptamers and partial complementary strands blocking different regions of the aptamers into the reporters and measured the kinetic behaviors of the target binding to gain insights on aptamers' functional domains. We introduced a reference analyte and developed a thermodynamic model to obtain a relative dissociation constant of an aptamer-target pair. With this approach, we characterized RNA and DNA aptamers binding to small molecules with low and high affinities.

Light-Responsive Dynamic DNA-Origami-Based Plasmonic Assemblies.

DNA nanotechnology offers a versatile toolbox for precise spatial and temporal manipulation of matter on the nanoscale. However, rendering DNA-based systems responsive to light has remained challenging. Herein, we describe the remote manipulation of native (non-photoresponsive) chiral plasmonic molecules (CPMs) using light. Our strategy is based on the use of a photoresponsive medium comprising a merocyanine-based photoacid. Upon exposure to visible light, the medium decreases its pH, inducing the formation of DNA triplex links, leading to a spatial reconfiguration of the CPMs. The process can be reversed simply by turning the light off and it can be repeated for multiple cycles. The degree of the overall chirality change in an ensemble of CPMs depends on the CPM fraction undergoing reconfiguration, which, remarkably, depends on and can be tuned by the intensity of incident light. Such a dynamic, remotely controlled system could aid in further advancing DNA-based devices and nanomaterials.

Chemical and physical processes in the retention of functional groups in plasma polymers studied by plasma phase mass spectroscopy.

Surface engineering of functionalised polymer films is a rapidly expanding field of research with cross disciplinary implications and numerous applications. One method of generating functionalised polymer films is radio frequency induced plasma polymerisation which provides a substrate independent coating. However, there is currently limited understanding surrounding chemical interactions in the plasma phase and physical interactions at the plasma-surface interface, and their effect on functional group retention in the thin film. Here we investigate functionalised plasma polymer films generated from four precursors containing primary amines. Using XPS and fluorine tagging with 4-(trifluoromethyl)benzaldehyde, the primary amine content of plasma polymer films was measured as a function of applied power at constant precursor pressure. The results were then correlated with analysis of the plasma phase by mass spectrometry which showed loss of amine functionality for both neutral and ionic species. Surface interactions are also shown to decrease primary amine retention due to abstraction of hydrogen by high energy ion impacts. The stability of the plasma polymers in aqueous solution was also assessed and is shown to be precursor dependent. Increased understanding of the chemical and physical processes in the plasma phase and at the surface are therefore critical in designing improved plasma polymerisation processes.