Programming Structured DNA Assemblies to Probe Biophysical Processes

Abstract

Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1–100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.

Photocontrolled Dopamine Polymerization on DNA Origami with Nanometer Resolution

“…Inspired by Nature, bottom‐up strategies often exploit the self‐assembly capacity of various building blocks to produce ordered structures such as liposomes, polymeric nanoparticles, and viral protein mimics . Although these structures exhibit a relatively high level of uniformity in terms of size, shape, and functionality, they often lack diverse shapes and the potential for asymmetric and orthogonal molecular modifications . DNA origami technology, however, provides the opportunity to simultaneously incorporate chemically diverse functional components with controlled stoichiometry to design nanoobjects with ultimate molecular control…”

“…[1] Although these structures exhibit a relatively high level of uniformity in terms of size, shape, and functionality, they often lack diverse shapes and the potential for asymmetric and orthogonal molecular modifications. [2] DNA origami technology, however, provides the opportunity to simultaneously incorporate chemically diverse functional components with controlled stoichiometry to design nanoobjects with ultimate molecular control. [3] Rationally designed DNA origami objects originate from the sequence-specific binding properties of DNA: a long, single-stranded DNA scaffold is folded into a distinct archi-tecture guided by a set of short staple strands, which hybridize at programmed positions along this scaffold.…”

Lichtgesteuerte Polymerisation von Dopamin auf DNA‐Origami im Nanometer‐Regime

“…Gemäß dem Vorbild der Natur wird bei der sogenannten Bottom‐up‐Methode die Fähigkeit diverser Grundbausteine zur Selbstorganisation genutzt, um hochgradig geordnete Strukturen herzustellen, wie etwa Liposome, polymerbasierte Nanopartikel oder virusähnliche Proteinanaloga . Obwohl diese Strukturen ein relativ hohes Maß an Einheitlichkeit in Größe, Form und Funktionalität aufweisen, ist die Verwirklichung asymmetrischer und orthogonaler molekularer Modifikationen häufig nicht zu erreichen . Im Gegensatz dazu bietet die DNA‐Origami‐Technik die einzigartige Möglichkeit, Nanoobjekte mit unübertroffener Strukturpräzision herzustellen.…”

“…[1] Obwohl diese Strukturen ein relativ hohes Maß an Einheitlichkeit in Grçße, Form und Funktionalität aufweisen, ist die Verwirklichung asymmetrischer und orthogonaler molekularer Modifikationen häufig nicht zu erreichen. [2] Im Gegensatz dazu bietet die DNA-Origami-Technik die einzigartige Mçglichkeit, Nanoobjekte mit unübertroffener Strukturpräzision herzustellen. Der Vorteil liegt dabei in der Fähigkeit, funktionelle Komponenten unterschiedlicher chemischer Natur gleichzeitig anzubringen.…”

Controlling wireframe DNA origami nuclease degradation with minor groove binders

“…The two major classes of DNA origami developed over the past decade are denselypacked, brick-like assemblies 4 and wireframe assemblies 5 . The development of top-down sequence design algorithms has enabled facile prototyping of the latter class of objects [6][7][8][9] , and scalable enzymatic and bacterial production of single-stranded DNA scaffolds with custom sequence and length have paved the way for pre-clinical and clinical studies [10][11][12][13] . DNA nanostructures have further been deployed in a variety of preliminary studies as therapeutic delivery platforms.…”