This contribution presents a sol–gel based cluster encapsulation methodology to produce bifunctional patchy particles. The particles possess azide moieties on the surfaces of the patch and carboxylic acids on the shell. Two types of DNA with distinct terminal sequences are site-specifically conjugated to the particle patches or the shell employing two orthogonal coupling strategies: strain-promoted alkyne–azide cycloaddition and carbodiimide-mediated amidation. We can activate and deactivate assembly on the patches and/or the shell through thermal control, demonstrating reversible and stepwise self-assembly.