The study investigates the formation of memory assemblies in hippocampal neurons through the DNA-sensing pathway of TLR9. After learning, discrete clusters of excitatory CA1 neurons exhibit persistent double-stranded DNA (dsDNA) breaks, nuclear envelope ruptures, and perinuclear release of histone and dsDNA fragments. These neurons acquire an inflammatory phenotype, characterized by TLR9 signaling activation and accumulation of centrosomal DNA damage repair complexes. Neuron-specific knockdown of *Tlr9* impairs memory formation and gene expression changes in specific excitatory CA1 neuron clusters. TLR9 plays a crucial role in centrosome function, including DNA damage repair, ciliogenesis, and perineuronal net formation. The findings suggest that a novel cascade of learning-induced molecular events, involving dsDNA damage and TLR9-mediated repair, leads to the recruitment of neurons to memory circuits. Compromised TLR9 function can lead to genomic instability and cognitive impairments, highlighting the importance of maintaining TLR9 inflammatory signaling for neurocognitive health.The study investigates the formation of memory assemblies in hippocampal neurons through the DNA-sensing pathway of TLR9. After learning, discrete clusters of excitatory CA1 neurons exhibit persistent double-stranded DNA (dsDNA) breaks, nuclear envelope ruptures, and perinuclear release of histone and dsDNA fragments. These neurons acquire an inflammatory phenotype, characterized by TLR9 signaling activation and accumulation of centrosomal DNA damage repair complexes. Neuron-specific knockdown of *Tlr9* impairs memory formation and gene expression changes in specific excitatory CA1 neuron clusters. TLR9 plays a crucial role in centrosome function, including DNA damage repair, ciliogenesis, and perineuronal net formation. The findings suggest that a novel cascade of learning-induced molecular events, involving dsDNA damage and TLR9-mediated repair, leads to the recruitment of neurons to memory circuits. Compromised TLR9 function can lead to genomic instability and cognitive impairments, highlighting the importance of maintaining TLR9 inflammatory signaling for neurocognitive health.