High-speed, high-purity separation of gold nanoparticle–DNA origami constructs using centrifugation

Abstract

DNA origami is a powerful platform for assembling gold nanoparticle constructs, an important class of nanostructure with numerous applications. Such constructs are assembled by the association of complementary DNA oligomers. These association reactions have yields of <100%, requiring the development of methods to purify the desired product. We study the performance of centrifugation as a separation approach by combining optical and hydrodynamic measurements and computations. We demonstrate that bench-top microcentrifugation is a simple and efficient method of separating the reaction products, readily achieving purities of >90%. The gold nanoparticles play a number of critical roles in our system, functioning not only as integral components of the purified products, but also as hydrodynamic separators and optical indicators of the reaction products during the purification process. We find that separation resolution is ultimately limited by the polydispersity in the mass of the gold nanoparticles and by structural distortions of DNA origami induced by the gold nanoparticles. Our study establishes a methodology for determining the design rules for nanomanufacturing DNA origami-nanoparticle constructs.

Interplay of particle shape and suspension properties: a study of cube-like particles

“…We also determined the second osmotic virial coefficient for hard cube-like particles using analytic expressions coupled with numerical integration and found that our results were in excellent agreement with a Monte Carlo method. In the future, we expect the techniques discussed will be applicable to studying other property-shape relationships 59 as well as quantifying shape or individual particle properties. 60 One potential example is the properties of dimers, trimers, and finite linear arrays of superballs.…”

Intrinsic conductivity of carbon nanotubes and graphene sheets having a realistic geometry

“…Briefly, the potentials allow us to create representative configurations of CNTs and GSs. The same models that we use for CNTs and GSs have been successfully applied before to model duplex DNA [62] and DNA origami [52], where the parameters of the interaction potentials are chosen to take into account the effects of hydration, polarizability, and charge condensation that are difficult to treat by atomistic modeling.…”

“…The smaller exponent value corresponds to “crumpled” sheets, where mass scaling exponent for the radius of gyration is near 1/3. In addition, we previously investigated a model equivalent to our coarse–grained GS model to study DNA origami, another two–dimensional polymer structure [52, 81]. Exfoliated clay [6, 9], polymerized layers [82] and many other biological structures such the erythrocyte membrane [83] can also be modeled as a two–dimensional polymers.…”

“…While our illustrative particle types have significant research interest, our computational methods apply to almost any type of particle that one might encounter, even nanoparticles with grafted polymer layers [52] or nanoparticles with protein or other complex adsorbed structures such as DNA–wrapped CNTs [53]. …”

Volume determination of irregularly-shaped quasi-spherical nanoparticles

“…Nanomaterials in the form of nanoparticles (NPs) represent an important part of nanotechnology. NP usage is increasing at a rapid pace with the development of new types of nanomaterials, as indicated by the existence of over 1,300 diverse listed consumer goods (3) (e.g., sunscreen, cosmetics, clothes, food, drugs, paints, varnishes, and a self-cleaning coating for floors, walls and windows) in addition to medical (4) and high technology (5) applications. Reports indicate that nanotechnology and the use of NPs has the potential to radically change the way cancer is treated (6).…”