A simple yet novel one-pot approach is developed to prepare carbon nanoparticles with diameters of ∼2 nm and modified by oligonucleotides. We use single-stranded deoxyribonucleic acid (ssDNA), which serves as a unique 'bio-solvent' for carbon nanoparticle (CNP) preparation and as a target molecule for functionalisation. Proposed interactions relevant to the stabilisation of the final oligonucleotide-CNP complex include π-π stacking and π-HN bonding with sp2 carbon atoms on the CNP surface. Furthermore, oligonucleotide-enriched CNPs can be readily extracted within seconds from a crude mixture of single-walled carbon nanotubes (SWCNTs) without any need for post-synthesis chemical modification. The established CNPs are biocompatible, possess intrinsic fluorescence, and do not result in the undesirable photobleaching effect, rendering them potential candidates for in vivo biological applications.