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Published January 2010 | Supplemental Material + Published
Journal Article Open

Dna2 is a structure-specific nuclease, with affinity for 5'-flap intermediates


Dna2 is a nuclease/helicase with proposed roles in DNA replication, double-strand break repair and telomere maintenance. For each role Dna2 is proposed to process DNA substrates with a 5'-flap. To date, however, Dna2 has not revealed a preference for binding or cleavage of flaps over single-stranded DNA. Using DNA binding competition assays we found that Dna2 has substrate structure specificity. The nuclease displayed a strong preference for binding substrates with a 5'-flap or some variations of flap structure. Further analysis revealed that Dna2 recognized and bound both the single-stranded flap and portions of the duplex region immediately downstream of the flap. A model is proposed in which Dna2 first binds to a flap base, and then the flap threads through the protein with periodic cleavage, to a terminal flap length of ~5 nt. This resembles the mechanism of flap endonuclease 1, consistent with cooperation of these two proteins in flap processing.

Additional Information

© 2010 Oxford University Press. Received August 17, 2009. Revised October 27, 2009. Accepted October 28, 2009. We would like to thank the Bambara and Campbell research groups for helpful discussion and critical reading of the manuscript. National Institutes of Health (grant no. GM024441 to R.A.B., with additional support from GM087666 to J.L.C.). Funding for open access charge: National Institutes of Health (grant no. GM024441). J.A.S. was supported by an Elon Huntington Hooker graduate fellowship. Conflict of interest statement. None declared.

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