We study the formation and fluorescent properties of silver nanoclusters encapsulated in condensed DNA nanoparticles. Fluorescent globular DNA nanoparticles are formed using a dsDNA–cluster complex and polyallylamine as condensing agents. The fluorescence emission spectrum of single DNA nanoparticles is obtained using tip-enhanced fluorescence microscopy. Fluorescent clusters in condensed DNA nanoparticles appear to be more protected against destructive damage in solution compared to clusters synthesized on a linear polymer chain. The fluorescent clusters on both dsDNA and ssDNA exhibit the same emission bands (at 590 and 680 nm) and the same formation efficiency, which suggests the same binding sites. By using density functional theory, we show that the clusters may bind to the Watson–Crick guanine–cytosine base pairs and to single DNA bases with about the same affinity.