Polymer beads (such as Dynabeads) are commonly used to capture and isolate DNA and proteins, relevant for many applications in biochemistry and nanobiology. Current approaches to link DNA with beads involve non-covalent attachments such as biotin-streptavidin which pose a risk of spontaneous dissociation, potentially influencing data interpretation. We present a protocol to circumvent this risk by exploiting SNAP-tag technology to establish stable covalent anchoring (bioconjugate) between DNA and Dynabeads. We describe steps for generating benzylguanylated (BG) closed covalent circular DNA (BG-cccDNA), conjugating DNA with SNAP-tag and with beads, and enzymatic treatment and elution of conjugated DNA. We have successfully employed this technique to study the effect of Dynabeads as micrometer-scale DNA roadblocks on the motor activity of bacterial SMC Wadjet complex.