Cooperative effects in DNA-functionalized polymeric nanoparticles

DNA-functionalized nanoparticles (NPs), called as spherical nucleic acids (SNA), attract strong 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 emerge as powerful nanomaterials for ultrasensitive detection and imaging of nucleic acids. Here, we addressed a fundamental question unexplored for polymeric DNA-NPs: how dense packing of oligonucleotides at the particle surface impacts their capacity to specifically hybridize with complementary sequences. Using Forster Resonance Energy Transfer (FRET) between DNA-NPs and labelled complementary strands, we found that the DNA at the NPs surface exhibit dramatic enhancement in the duplex stability compared to free DNA duplexes (>20 °C). This effect increases at higher densities of DNA on NPs surface, which suggests that DNA cooperativity is responsible for the duplex stability enhancement. For example, 8 nt DNA duplexes were perfectly stable at RT on the surface of DNA-NPs. Furthermore, these DNA-NPs preserve capacity to distinguish mutations, even at the single nucleotide level within 21 nt sequence, when 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 ≥ 10 and ≥100 pM, respectively. Below that, this diffusion-controlled processes becomes too slow, which points on the fundamental limitation in the 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 in the development of nucleic acid sensing assays.