Purification of DNA Nanoparticles Using Photocleavable Biotin Tethers.

The number of applications of self-assembled deoxyribonucleic acid (DNA) origami nanoparticles (DNA NPs) has increased drastically, following the development of a variety of single-stranded template DNA (ssDNA) that can serve as the scaffold strand. In addition to viral genomes, such as M13 bacteriophage and lambda DNAs, enzymatically produced ssDNA from various template sources is rapidly gaining traction and being applied as the scaffold for DNA NP preparation. However, separating fully formed DNA NPs that have custom scaffolds from crude assembly mixes is often a multistep process of first separating the ssDNA scaffold from its enzymatic amplification process and then isolating the assembled DNA NPs from excess precursor strands. Only then is the DNA NP sample ready for downstream characterization and application. In this work, we highlight a single-step purification of custom sequence- or M13-derived scaffold-based DNA NPs using photocleavable biotin tethers. The process only requires an inexpensive ultraviolet (UV) lamp, and DNA NPs with up to 90% yield and high purity are obtained. We show the versatility of the process in separating two multihelix bundle structures and a wireframe polyhedral architecture.

Bending Unwinds DNA.

In biology, DNA is often tightly bent to small radii. Solely based on the groove asymmetry, a 30-year-old theoretical paper predicted that such bending should unwind DNA, but this effect has not been directly experimentally quantified so far. We developed a ligation-based assay with nicked DNA circles of variable length, thereby decoupling the twist-dependent ligation efficiency from the large bending strain which dominates conventional circularization assays. We demonstrate that tightly bent DNA indeed unwinds to over 11 base pairs/turn, exactly as predicted. Our discovery requires reassessing the molecular mechanisms and energetics of all processes where DNA is tightly bent or relaxed again, including DNA packaging, gene regulation and expression.

Block Copolymer Micellization of DNA Origami Promotes Solubility in Organic Solvents.

The DNA origami technique allows the precise synthesis of complex, biocompatible nanomaterials containing small molecules, biomolecules, and inorganic nanoparticles. The negatively charged phosphates in the backbone make DNA highly water-soluble and require salts to shield its electrostatic repulsion. DNA origamis are therefore not soluble in most organic solvents. While this is not problematic for applications in biochemistry, biophysics, or nanomedicine, other potential applications, processes, and substrates are incompatible with saline solutions, which include the synthesis of many nanomaterials, and reactions in templated synthesis, the operation of nanoelectronic devices, or semiconductor fabrication. To overcome this limitation, we coated DNA origami with amphiphilic poly(ethylene glycol) polylysine block copolymers and transferred them into various organic solvents including chloroform, dichloromethane, acetone, or 1-propanol. Our approach maintains the shape of the nanostructures and protects functional elements bound to the structure, such as fluorophores, gold nanoparticles, or proteins. The DNA origami polyplex micellization (DOPM) strategy hence enables solubilization or a phase transfer of complex structures into various organic solvents, which significantly expands the use of DNA origami for a range of potential applications and technical processes.

Reversible encapsulations and stimuli-responsive biological delivery from a dynamically assembled cucurbit[7]uril host and nanoparticle guest scaffold.

The positive outcome of any therapeutic molecule requires control over its delivery rate. When delivered without control, administration of large doses is required to stimulate a therapeutic effect, frequently leading to increased toxicity or undesirable side effects. Recent advances introduced "smart" materials that actively release drugs in response to environmental stimuli. Although a variety of endogenous and exogenous triggers are reported, they are either difficult to control or lack tissue penetration depth. We report here a dynamic drug delivery scaffold based on a cucurbit[7]uril (CB[7]) host and benzylammonium functionalized gold nanoparticle (AuNP) guest that utilizes a bioorthogonal small molecule to achieve therapeutic control. In addition to their ability to reach deep tissue, small molecule activation is benefitted by their external controllability. Through cell culture studies we demonstrate that the host-guest supramolecular scaffold provides a nontoxic platform that effectively encapsulates a variety of therapeutic molecules and controls the payload release upon exposure to a high-affinity competitive guest molecule. This study presents a new strategy for controlling drug release rate through the use of competitive interactions of orthogonally presented guest molecules with immediate advantages in dosage control.