Modulating the Bond Strength of DNA-Nanoparticle Superlattices

Abstract

A method is introduced for modulating the bond strength in DNA-programmable nanoparticle (NP) superlattice crystals. This method utilizes noncovalent interactions between a family of [Ru(dipyrido[2,3-a:3',2'-c]phenazine)(N-N)2](2+)-based small molecule intercalators and DNA duplexes to postsynthetically modify DNA-NP superlattices. This dramatically increases the strength of the DNA bonds that hold the nanoparticles together, thereby making the superlattices more resistant to thermal degradation. In this work, we systematically investigate the relationship between the structure of the intercalator and its binding affinity for DNA duplexes and determine how this translates to the increased thermal stability of the intercalated superlattices. We find that intercalator charge and steric profile serve as handles that give us a wide range of tunability and control over DNA-NP bond strength, with the resulting crystal lattices retaining their structure at temperatures more than 50 °C above what nonintercalated structures can withstand. This allows us to subject DNA-NP superlattice crystals to conditions under which they would normally melt, enabling the construction of a core-shell (gold NP-quantum dot NP) superlattice crystal.

Keywords: DNA; DNA intercalator; crystallization; nanoparticle; self-assembly.

Figure 1.

Ru^II complexes with extended ancillary ligands varying in steric profile and charge.

Figure 2.

DNA–NP superlattice melting temperatures increase after intercalation and correlate to binding affinity of different intercalators. (a) Superlattice samples (50 nM NP total) incubated in 12.1 μM of different Ru^II complexes exhibit unique shifts in melting transition. (b) Superlattice melting temperatures after intercalation with complexes 1, 3, and 6 as a function of degree of association. (c) The binding affinity of Ru^II complexes for one dsDNA bp plotted as a function of ΔT_m of DNA–programmable superlattices.

Figure 3.

Structural effects of intercalation emerge from SAXS and SEM. (a) Scattering patterns of the superlattice in increasing concentrations from 0 to 37.3 μM of complex 1. (b) Isotropic strain resulting from uniform lattice expansion and (c) RMS microstrain induced in superlattice upon intercalation. (d) DNA–NP superlattice single crystals retain structure upon intercalation. Before and after intercalation with complex 1. Scale bars are 2 μm.

Figure 4.

Core Au–Shell QdNP crystals. TEM images of micron sized core–shell structures synthesized in a stepwise manner. A difference in electron densities between AuNPs (denser) and QdNPs (lighter) results in contrast between the core and shell portions. Scale bars are 1 μm.

Scheme 1.. Ru^II Intercalation into DNA–Nanoparticle Superlattice

^{a a}DNA–functionalized gold nanoparticles are assembled with linkers and annealed into a crystalline structure. Ru^II complex is added and the mixture

Scheme 2.. Modulation of Superlattice Bond Strength with Ru^II Intercalation Enables Stepwise Synthesis of Core–Shell Crystals

^{a a}DNA–AuNP superlattice single crystals are intercalated with complex 1 overnight before being combined with complementary DNA–QdNPs. Slow cooling allows the DNA–QdNPs to assemble into a shell around core crystals. The presence of the intercalator increases the melting temperature of the AuNP core crystal, allowing it to stay intact during the annealing process that leads to shell formation.