Highlights

Precise positioning of gold nanoparticles with DNA origami nanostructures

DNA is becoming a key player in self-assembly approaches towards advances in nanotechnology. The DNA origami method allows the design and assembly of nano objects which can serve as scaffolds for the arrangement of guest molecules. To fully exploit the placement precision of DNA origami templates we investigated gold nanoparticle (AuNP) positioning on DNA origami structures with SAXS. By these measurements we quantified the effect of attachment site and DNA linker type on the distance of two AuNPs on DNA origami in native solution conditions.

Nadrian Seeman pioneered the use of DNA as nanoscale construction material that is based on Watson-Crick base pairing and that has proven to enable the assembly of DNA objects of tailored shape and functionality (e.g. N.C. Seeman, “DNA in a material world”, Nature, 2003). The DNA origami technique – developed by Paul Rothemund (Nature, 2006) - relies on folding a ~ 8 kilo bases long single-stranded DNA scaffold into a desired shape by short, synthetic “staple” oligonucleotides. The addressability of the resulting DNA-object allows also for positioning of guest particles such as fluorophores or metal nanoparticles. To verify for correct assembly and to quantify the positioning accuracy of such DNA constructs in solution, we used small angle x-ray scattering (SAXS).

We measured the SAXS pattern of dimers and a trimer of nanoparticles connected to different attachment sites A, B, C on a DNA origami block using different linker types and of a helical arrangement of AuNPs on a DNA origami cylinder (Fig. 1a). The pair density distribution functions (PDDF) were obtained from the scattering data. The PDDFs of the dimers AB, AC and BC show different positions of the second maximum corresponding to different center-to-center distances of the AuNPs. (Fig. 1b) The PDDF of the trimer ABC is composed of the distances of the dimers that constitute the trimer. The AuNP distances obtained from fitting of the SAXS data and from the PDDF are in good agreement with the values estimated from the design of the assemblies.
 

Figure 1.  (a) Trimer ABC with gold nanoparticles attachment sites A, B, and C of a DNA origami block. (b) PDDF obtained from the scattering of the dimers AB, AC, and BC and trimer ABC (blue solid line, dashed line, dash-dot line, and black solid line, respectively). The TEM images of all three dimers and the trimer are shown. Adapted with permission from C. Hartl et al., Nano Lett. 18 (4), 2609-2615 (2018); DOI: 10.1021/acs.nanolett.8b00412. Copyright 2018 American Chemical Society.

The attachment sites consist of three DNA single strands with a specific sequence, protruding from the origami. For the attachment the surface of the AuNPs is covered with single stranded DNA of the complementary sequence. We probed three different linker types: (i) 15 bases protrusion (blue), (ii) 9 bases protrusion (orange), and (iii) 15 bases protrusion combined with AuNPs modified with DNA in an orientation that is expected to form a zipper configuration (green) (Fig. 2a). SAXS measurements of AuNPs sitting at opposite sides of the block (Fig. 2b) show that configuration (i) gives the largest and configuration (ii) the smallest center-to-center distance of the AuNPs. Sterical hindrance of long DNA single strands on the AuNPs or spacer oligonucleotides in configuration (iii) can prevent the AuNPs to be zipped tightly to the surface. In the configuration of dimers of nanoparticles sitting next to each other on the DNA origami block (Fig. 2c) center-to-center distances differ only slightly from each other with again configuration (i) giving the largest and (ii) the smallest AuNP distance. Possible influences could be repulsion due to long single stranded DNA covering the nanoparticles and effects of the flexibility of the different linker types. Due to the competing forces SAXS is crucial in order to establish the precise binding length of nanoparticles to DNA constructs.

The measurements further reveal that the PDDF of a helical arrangement of AuNPs provides information about the distances of neighboring AuNPs. From the neighbor distances conclusions about the geometry of the helix such as the radius can be drawn.

Altogether, we find, that SAXS measurements can give valuable information about AuNP distances of DNA origami mediated gold nanoparticle assemblies in solution conditions. This information can be used to tailor the assemblies to obtain the desired properties in changing environmental conditions.

Figure 2.  (a) Scheme of the three tested connector types: (i) A15 to T19 (blue), (ii) A9 to T8 (orange), and (iii) A15 to 3′ T19, zipper configuration (green). (b, c) PDDF for each of the three different connector types for dimers AC (b) and AB (c) are shown together with corresponding TEM images. Adapted with permission from C. Hartl et al., Nano Lett. 18 (4), 2609-2615 (2018); DOI: 10.1021/acs.nanolett.8b00412. Copyright 2018 American Chemical Society.

Retrieve article

Position Accuracy of Gold Nanoparticles on DNA Origami Structures Studied with Small-Angle X-ray Scattering ;
C. Hartl, K. Frank, H. Amenitsch, S. Fischer, T. Liedl and B. Nickel;
Nano Letters 18 (4), pp 2609–2615 (2018). doi: 10.1021/acs.nanolett.8b00412

Contact persons: nickel@lmu.de, tim.liedl@lmu.de