The multi-step base excision repair (BER) pathway is initiated by a set of enzymes, known as DNA glycosylases, able to scan DNA and detect modified bases among a vast number of normal bases. While DNA glycosylases in the BER pathway generally bend the DNA and flip damaged bases into lesion specific pockets, the HEAT-like repeat DNA glycosylase AlkD detects and excises bases without sequestering the base from the DNA helix. We show by single-molecule tracking experiments that AlkD scans DNA without forming a stable interrogation complex. This contrasts with previously studied repair enzymes that need to flip bases into lesion-recognition pockets and form stable interrogation complexes. Moreover, we show by design of a loss-of-function mutant that the bimodality in scanning observed for the structural homologue AlkF is due to a key structural differentiator between AlkD and AlkF; a positively charged β-hairpin able to protrude into the major groove of DNA.

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Springer Nature
Commun. Biol

Ahmadi, A., Till, K., Backe, P., Blicher, P., Diekmann, R., Schüttpelz, M., … Dalhus, B. (2021). Non-flipping DNA glycosylase AlkD scans DNA without formation of a stable interrogation complex. Commun. Biol, 4(1), 875: 1–8. doi:10.1038/s42003-021-02400-x