The assembly and isolation of DNA oligonucleotide-functionalized gold nanoparticles (AuNPs) has become a well-developed technology that is based on the strong bonding interactions between gold and thiolated DNA. However, achieving DNA-functionalized semiconductor quantum dots (QDs) that are robust enough to withstand precipitation at high temperature and ionic strength through simple attachment of modified DNA to the QD surface remains a challenge. We report the synthesis of stable core/shell (1–20 monolayers) QD–DNA conjugates in which the end of the phosphorothiolated oligonucleotide (5–10 nucleotides) is “embedded” within the shell of the QD. These reliable QD–DNA conjugates exhibit excellent chemical and photonic stability, colloidal stability over a wide pH range (4–12) and at high salt concentrations (>100 mM Na⁺ or Mg²⁺), bright fluorescence emission with quantum yields of up to 70%, and broad spectral tunability with emission ranging from the UV to the NIR (360–800 nm).