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Immunity. 1998 Jul;9(1):115-25.

V(D)J recombination signal recognition: distinct, overlapping DNA-protein contacts in complexes containing RAG1 with and without RAG2.

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Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.


Protein interactions with V(D)J recombination signal sequences (RSSs) were mapped in complexes containing RAG1 with (M1/2) or without (M1) RAG2. In both complexes, RAG interactions with the DNA backbone are biased toward one side of the helix; nonamer contacts resemble those of Hin with hixL. In the M1 complex, DNA contacts are centered on the nonamer. In the M1/2 complex, protein-RSS interactions extend through the spacer and into the nonamer-proximal portion of the heptamer. Chemical modifications near the heptamer-coding junction are overrepresented in the M1/2 complex, providing evidence for perturbation of DNA structure in this region. Thus, while RAG1 alone can bind the nonamer, RAG2 is required for heptamer occupancy.

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