Nucleic Acids Research, 2003, Vol. 31, No. 21 6180-6190
© 2003 Oxford University Press
DNA mismatches and GC-rich motifs target transposition by the RAG1/RAG2 transposase
Department of Molecular Biophysics and Biochemistry, 1 Section of Immunobiology, 2 Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
*To whom correspondence should be addressed. Tel: +1 203 737 2255; Fax: +1 203 785 3855; Email: david.schatz{at}yale.edu
Present address:
Chia-Lun Tsai, Department of Molecular Biology, Wellman 9, Massachusetts General Hospital, Boston, MA 02114, USA
In addition to their essential role in V(D)J recombination, the RAG proteins function as a transposase capable of inserting the V(D)J recombination intermediate, the signal end DNA fragment, into target DNA. RAG-mediated transposition has been suggested to contribute to genome instability and the development of lymphoid malignancies. Previous studies suggested that the RAG transposase exhibits a target site preference for GC rich sequences and hairpin structures. Here we demonstrate that a transposition hot spot (5'-GCCGCCGGGCC-3'), smaller portions of this hot spot and other GC rich motifs are able to target RAG-mediated transposition. Tracks of GC base pairs have been shown to have an unusually high rate of base pair breathing. Intriguingly, we find that DNA mismatches can efficiently target RAG-mediated transposition and suppress the use of other target sites. Hairpins, however, are not generally preferred targets. Our results indicate that target DNA melting may be a crucial step during RAG-mediated transposition, and that target site selection by the RAG transposase may be intimately linked to mutagenic and metabolic processes that transiently present favorable DNA structures to the transposition machinery.
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