Internal Structure of Nanoparticle Dimers Linked by DNA

Abstract

T he use of DNA to link nanoparticles (NPs) into complex self-assembled structures is an increasingly popular approach to the bottom-up design of nanoclusters and materials. 1À5 The selectivity and reversibility of DNA base-pair recognition, coupled with the relative stiffness of double-stranded DNA (dsDNA) 6À8 and a tunable assembly kinetics, 9 make DNA an ideal choice to create programmable interactions between NPs. This is accomplished by tethering multiple strands of DNA to a core NP (gold, silver, or CdSe core). 10À12 The outermost part of tethered strands is singlestranded DNA (ssDNA) with a specific sequence that will either link directly to another NP or connect to another NP via an additional linking strand. 13,14 The hybridization of ssDNA in linking regions directs the self-assembly of nanoparticles into largerscale structures. Their organization is controlled by the DNA sequences and linker architecture, 15À19 as well as by the NP geometry. 20 Using this approach, the precise fabrication of small nanoclusters and the formation of two-and three-dimensional superlattices has been achieved. 20À27While the approach of single-step, direct assembly is promising, many biological materials ; such as bone, hair, skin, and spider silk 28 ; take advantage of a more complex hierarchical scheme. In such a scenario, assembly at each scale results in units or structures that enable assembly at a larger scale. These processes have been evolved over aeons, so the development of synthetic multiscale self-assembly will prove challenging. In the context of DNA-tethered NPs, the most basic unit in such a hierarchical approach is a dimer of two NPs. As a first step toward a synthetic multiscale assembly, here we examine in detail the structure of dimer units. The structure of these dimers is complicated by the fact that the surface curvature of the NP is on a scale comparable to the length of the connecting DNA. In such a regime, the behavior of polymer chains (such as DNA) attached to the surface is known to deviate significantly from the free-chain behavior. 29,30 In this paper, we examine the structure of DNA-linked NP dimers by a combination of in situ dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS), complemented by molecular simulations and theory. The DLS method probes a hydrodynamic measure of an angular-averaged dimer size. The in situ SAXS experiments reveal more detailed information on the interparticle distances within the dimer. The numerical modeling provides a detailed molecular picture that helps to interpret the experimental findings and develop a theoretical description.When the NPs are linked by dsDNA with a separation less than the persistence length, the interparticle distance is a linear function of the DNA length, due to the rigidity of dsDNA. For longer ssDNA linkers, the * Address correspondence to ogang@bnl.gov, fstarr@wesleyan.edu.Received for review April 6, 2012 and accepted July 13, 2012. Published online 10.1021/nn301528hABSTRACT We construct nanoparticle dimers lin...

Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames

“…Such structure factor can be reasonably well described (Figure 7C, blue curve) by dumbbell model 50,51 with functional form S( q )~sin(d q )/d q , where d is a distance between the NP centers, thus, indicating scattering signature of the NP pairs. The flexibility of 1D array at the points of octahedron attachment to NPs and the large angle over which the attachment can occur, contribute to the non-collinearity of 1D array.…”

Diamond family of nanoparticle superlattices

“…To further validate this conclusion, we performed numerical simulations of ground state structures of the DNA-origami linked nanoparticle structures using a coarse-grained representation, previously validated experimentally (30). We examined configurations of basis particles linked by tetrahedra in either FCC or HCP arrangements.…”

Size Evolution of Protein-Protected Gold Clusters in Solution: A Combined SAXS–MS Investigation

“…For example, Gang et al have described DNA-mediated self-assembly of nanoparticles in heterogeneous systems where they programmed nanoparticlecoated DNA molecules to self-assemble into three-dimensional superlattices, and corresponding structural information was obtained from SAXS. 54 In another report from the same group, nanoparticle dimers linked via DNA were prepared, and the size and other information were collected via DLS and SAXS studies. One dimensional linear meso-structure of nanorod-DNA assembly has also been looked at by in situ SAXS.…”