Cooperative effects in DNA-functionalized polymeric nanoparticles

DNA-functionalized nanoparticles (NPs), called spherical nucleic acids (SNAs), have attracted considerable attention due to their unique properties and numerous applications. In particular, DNA-functionalized dye-loaded polymeric NPs (DNA-NPs), owing to their exceptional fluorescence brightness, have emerged as powerful nanomaterials for the ultrasensitive detection and imaging of nucleic acids. Herein, we addressed a fundamental question unexplored for polymeric DNA-NPs: how does the dense packing of oligonucleotides on the particle surface impact their capacity to specifically hybridize with complementary sequences? Using Förster resonance energy transfer (FRET) between DNA-NPs and labelled complementary strands, we found that the DNA on the surface of the NPs exhibits dramatic enhancement in duplex stability compared to free DNA duplexes (>20 °C). This effect increases at higher densities of coding DNA on the NP surface, which suggests that DNA cooperativity is responsible for the enhancement in duplex stability. For example, 8 nt DNA duplexes were perfectly stable at RT on the surface of DNA-NPs. Furthermore, these DNA-NPs preserve the capacity to distinguish mutations, even at the single-nucleotide level within a 21 nt sequence, when an appropriate hybridization temperature is used. The hybridization between DNA-NPs and the complementary sequences proceeds on the min time scale at probe and target concentrations of ≥10 and ≥100 pM, respectively. Below these, this diffusion-controlled process becomes too slow, indicating the fundamental limitation in DNA/RNA sensing assays that require sufficiently high nanoprobe concentration. The present study sheds light on the capacity of DNA-NPs to specifically hybridize with the target sequences and provides insights into the development of nucleic acid sensing assays.