DNA-Nanostructure-Guided Assembly of Proteins into Programmable Shapes

The development of methods to synthesize artificial protein complexes with precisely controlled configurations will enable diverse biological and medical applications. Using DNA to link proteins provides programmability that can be difficult to achieve with other methods. Here, we use DNA origami as an "assembler" to guide the linking of protein-DNA conjugates using a series of oligonucleotide hybridization and displacement operations. We constructed several isomeric protein nanostructures, including a dimer, two types of trimer structures, and three types of tetramer assemblies, on a DNA origami platform by using a C3-symmetric building block composed of a protein trimer modified with DNA handles. Our approach expands the scope for the precise assembly of protein-based nanostructures and will enable the formulation of functional protein complexes with stoichiometric and geometric control.

Thermodynamic Size Control in Curvature-Frustrated Tubules: Self-Limitation with Open Boundaries

We use computational modeling to investigate the assembly thermodynamics of a particle-based model for geometrically frustrated assembly, in which the local packing geometry of subunits is incompatible with uniform, strain-free large-scale assembly. The model considers discrete triangular subunits that drive assembly toward a closed, hexagonal-ordered tubule, but have geometries that locally favor negative Gaussian curvature. We use dynamical Monte Carlo simulations and enhanced sampling methods to compute the free energy landscape and corresponding self-assembly behavior as a function of experimentally accessible parameters that control assembly driving forces and the magnitude of frustration. The results determine the parameter range where finite-temperature self-limiting assembly occurs, in which the equilibrium assembly size distribution is sharply peaked around a well-defined finite size. The simulations also identify two mechanisms by which the system can escape frustration and assemble to unlimited size, and determine the particle-scale properties of subunits that suppress unbounded growth.

Controlled Organization of Inorganic Materials Using Biological Molecules for Activating Therapeutic Functionalities

Precise control over the assembly of biocompatible three-dimensional (3D) nanostructures would allow for programmed interactions within the cellular environment. Nucleic acids can be used as programmable crosslinkers to direct the assembly of quantum dots (QDs) and tuned to demonstrate different interparticle binding strategies. Morphologies of self-assembled QDs are evaluated via gel electrophoresis, transmission electron microscopy, small-angle X-ray scattering, and dissipative particle dynamics simulations, with all results being in good agreement. The controlled assembly of 3D QD organizations is demonstrated in cells via the colocalized emission of multiple assembled QDs, and their immunorecognition is assessed via enzyme-linked immunosorbent assays. RNA interference inducers are also embedded into the interparticle binding strategy to be released in human cells only upon QD assembly, which is demonstrated by specific gene silencing. The programmability and intracellular activity of QD assemblies offer a strategy for nucleic acids to imbue the structure and therapeutic function into the formation of complex networks of nanostructures, while the photoluminescent properties of the material allow for optical tracking in cells in vitro.

Coordination-mediated programmable assembly of unmodified oligonucleotides on plasmonic silver nanoparticles

DNA-decorated metal nanoparticles have found numerous applications, most of which rely on thiolated DNA (SH-DNA)-modified gold nanoparticles (AuNPs). Whereas silver nanoparticles (AgNPs) are known to have stronger plasmonic properties than AuNPs, modification of AgNPs with SH-DNA is technically challenging, partially due to the instability of Ag-S bonding. Here we demonstrate a facile approach to self-assemble unmodified DNA on AgNPs by exploiting intrinsic silver-cytosine (Ag-C) coordination. The strong Ag-C coordination allows for the ready formation of DNA-AgNP conjugates, which show favorable stability under conditions of high ionic strength and high temperature. These nanoconjugates possess much higher efficient molecular recognition capability and faster hybridization kinetics than thiolated DNA-modified AgNPs. More importantly, we could programmably tune the DNA density on AgNPs with the regulation of silver-cytosine coordination numbers, which in turn modulated their hybridizability. We further demonstrated that these DNA-AgNP conjugates could serve as excellent building blocks for assembling silver and hybrid silver-gold nanostructures with superior plasmonic properties.