Determination of counterion distribution around DNA coated nanoparticles (DNA-AuNP) by small angle X-ray scattering (SAXS)

The interactions between DNA-Au nanoparticles (AuNP) and the surrounding cationic counterion layer critically determine the melting behavior of DNA duplexes on isolated DNA-AuNP and in crystalline assemblies of DNA-AuNPs. Also, the counterion layer is speculated to cause the enhanced stability of DNA-AuNPs against nuclease degradation, as compared to isolated DNAs. This makes DNA-AuNPs attractive for bio-diagnostic and therapeutic applications. To probe the ion cloud around DNA-AuNPs, we apply the isomorphous heavy ion replacement SAXS approach. Specifically, the SAXS measurements are carried out on DNA-AuNPS dispersed in a series of solutions that contain different monovalent ions (Na$^{\mathrm{+}}$, K$^{\mathrm{+}}$, Rb$^{\mathrm{+}}$ or Cs$^{\mathrm{+}})$. The combined analysis of all four intensity profiles makes it possible to extract, in a model-independent manner, the cation profile contribution $I_{cat}$ ($q)$ from the SAXS intensity that is averaged over the polydispersity of AuNPs. The $I_{cat}$ ($q)$ is found to be consistent with the cation dependent SAXS intensities that are derived on the basis of classical DFT calculations for the counterion distribution around DNA-AuNPs.