Stimulation of Homologous Recombination through Targeted Cleavage by Chimeric Nucleases

Abstract

Chimeric nucleases that are hybrids between a nonspecific DNA cleavage domain and a zinc finger DNA recognition domain were tested for their ability to find and cleave their target sites in living cells. Both engineered DNA substrates and the nucleases were injected into Xenopus laevis oocyte nuclei, in which DNA cleavage and subsequent homologous recombination were observed. Specific cleavage required two inverted copies of the zinc finger recognition site in close proximity, reflecting the need for dimerization of the cleavage domain. Cleaved DNA molecules were activated for homologous recombination; in optimum conditions, essentially 100% of the substrate recombined, even though the DNA was assembled into chromatin. The original nuclease has an 18-amino-acid linker between the zinc finger and cleavage domains, and this enzyme cleaved in oocytes at paired sites separated by spacers in the range of 6 to 18 bp, with a rather sharp optimum at 8 bp. By shortening the linker, we found that the range of effective site separations could be narrowed significantly. With no intentional linker between the binding and cleavage domains, only binding sites exactly 6 bp apart supported efficient cleavage in oocytes. We also showed that two chimeric enzymes with different binding specificities could collaborate to stimulate recombination when their individual sites were appropriately placed. Because the recognition specificity of zinc fingers can be altered experimentally, this approach holds great promise for inducing targeted recombination in a variety of organisms.

ACKNOWLEDGMENTS

This project is an equal collaboration between the Carroll and Chandrasegaran labs.

We thank Frank Whitby for providing Fig. 4. We are grateful to Jeremy Berg for advice on zinc finger recognition, to H. O. Smith for continuing interest in this project, and to Tim Formosa, Wes Sundquist, and Mario Capecchi for comments on various versions of the manuscript.

This work was supported in part by grants from the National Institutes of Health (GM50739 and GM58504) and the University of Utah to D.C. and by grants from the National Institutes of Health (GM53923) and the National Science Foundation (MCB 9415861) to S.C. Assistance was also provided by the Markey Center for Protein Biophysics, the Huntsman Cancer Institute at the University of Utah, and the Environmental Health Sciences Core Facility at Johns Hopkins University. S.C. is a member of the Scientific Advisory Board of Sangamo Biosciences, Inc.