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Mol Cell Biol, April 1998, p. 2029-2037, Vol. 18, No. 4
0270-7306/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.

Structure of Nonhairpin Coding-End DNA Breaks in Cells Undergoing V(D)J Recombination

Mark S. Schlissel*

Department of Medicine, Department of Molecular Biology and Genetics, and Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205

Received 10 October 1997/Returned for modification 10 November 1997/Accepted 24 November 1997

The V(D)J recombinase recognizes a pair of immunoglobulin or T-cell receptor gene segments flanked by recombination signal sequences and introduces double-strand breaks, generating two signal ends and two coding ends. Broken coding ends were initially identified as covalently closed hairpin DNA molecules. Before recombination, however, the hairpins must be opened and the ends must be modified by nuclease digestion and N-region addition. We have now analyzed nonhairpin coding ends associated with various immunoglobulin gene segments in cells undergoing V(D)J recombination. We found that these broken DNA ends have different nonrandom 5'-strand deletions which were characteristic for each locus examined. These deletions correlate well with the sequence characteristics of coding joints involving these gene segments. In addition, unlike broken signal ends, these nonhairpin coding-end V(D)J recombination reaction intermediates have 3' overhanging ends. We discuss the implications of these results for models of how sequence modifications occur during coding-joint formation.

* Mailing address: Department of Medicine, The Johns Hopkins University School of Medicine, Room 1068, Ross Building, 720 Rutland Ave., Baltimore, MD 21205. Phone: (410) 502-6453. Fax: 410-955-0964. E-mail: mss{at}welchlink.welch.jhu.edu.




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