• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of embojLink to Publisher's site
EMBO J. Jun 17, 1996; 15(12): 3197–3206.
PMCID: PMC450263

Distinct DNA sequence and structure requirements for the two steps of V(D)J recombination signal cleavage.


Cleavage of V(D)J recombination signals by purified RAG1 and RAG2 proteins permits the dissection of DNA structure and sequence requirements. The two recognition elements of a signal (nonamer and heptamer) are used differently, and their cooperation depends on correct helical phasing. The nonamer is most important for initial binding, while efficient nicking and hairpin formation require the heptamer sequence. Both nicking and hairpin formation are remarkably tolerant of variations in DNA structure. Certain flanking sequences inhibit hairpin formation, but this can be bypassed by base unpairing, and even a completely single-stranded signal sequence is well utilized. We suggest that DNA unpairing around the signal-coding border is essential for the initiation of V(D)J combination.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (2.1M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Boubnov NV, Wills ZP, Weaver DT. Coding sequence composition flanking either signal element alters V(D)J recombination efficiency. Nucleic Acids Res. 1995 Mar 25;23(6):1060–1067. [PMC free article] [PubMed]
  • Burlingame RP, Obukowicz MG, Lynn DL, Howe MM. Isolation of point mutations in bacteriophage Mu attachment regions cloned in a lambda::mini-Mu phage. Proc Natl Acad Sci U S A. 1986 Aug;83(16):6012–6016. [PMC free article] [PubMed]
  • Cheung S, Arndt K, Lu P. Correlation of lac operator DNA imino proton exchange kinetics with its function. Proc Natl Acad Sci U S A. 1984 Jun;81(12):3665–3669. [PMC free article] [PubMed]
  • Cuomo CA, Oettinger MA. Analysis of regions of RAG-2 important for V(D)J recombination. Nucleic Acids Res. 1994 May 25;22(10):1810–1814. [PMC free article] [PubMed]
  • Ezekiel UR, Engler P, Stern D, Storb U. Asymmetric processing of coding ends and the effect of coding end nucleotide composition on V(D)J recombination. Immunity. 1995 Apr;2(4):381–389. [PubMed]
  • Gellert M. Molecular analysis of V(D)J recombination. Annu Rev Genet. 1992;26:425–446. [PubMed]
  • Gerstein RM, Lieber MR. Coding end sequence can markedly affect the initiation of V(D)J recombination. Genes Dev. 1993 Jul;7(7B):1459–1469. [PubMed]
  • Hesse JE, Lieber MR, Mizuuchi K, Gellert M. V(D)J recombination: a functional definition of the joining signals. Genes Dev. 1989 Jul;3(7):1053–1061. [PubMed]
  • Kleinfield R, Hardy RR, Tarlinton D, Dangl J, Herzenberg LA, Weigert M. Recombination between an expressed immunoglobulin heavy-chain gene and a germline variable gene segment in a Ly 1+ B-cell lymphoma. Nature. 322(6082):843–846. [PubMed]
  • LaFemina RL, Callahan PL, Cordingley MG. Substrate specificity of recombinant human immunodeficiency virus integrase protein. J Virol. 1991 Oct;65(10):5624–5630. [PMC free article] [PubMed]
  • Lavoie BD, Chan BS, Allison RG, Chaconas G. Structural aspects of a higher order nucleoprotein complex: induction of an altered DNA structure at the Mu-host junction of the Mu type 1 transpososome. EMBO J. 1991 Oct;10(10):3051–3059. [PMC free article] [PubMed]
  • Lewis SM. The mechanism of V(D)J joining: lessons from molecular, immunological, and comparative analyses. Adv Immunol. 1994;56:27–150. [PubMed]
  • McBlane JF, van Gent DC, Ramsden DA, Romeo C, Cuomo CA, Gellert M, Oettinger MA. Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps. Cell. 1995 Nov 3;83(3):387–395. [PubMed]
  • Ramsden DA, Gellert M. Formation and resolution of double-strand break intermediates in V(D)J rearrangement. Genes Dev. 1995 Oct 1;9(19):2409–2420. [PubMed]
  • Ramsden DA, Baetz K, Wu GE. Conservation of sequence in recombination signal sequence spacers. Nucleic Acids Res. 1994 May 25;22(10):1785–1796. [PMC free article] [PubMed]
  • Reth M, Gehrmann P, Petrac E, Wiese P. A novel VH to VHDJH joining mechanism in heavy-chain-negative (null) pre-B cells results in heavy-chain production. Nature. 322(6082):840–842. [PubMed]
  • Roth DB, Nakajima PB, Menetski JP, Bosma MJ, Gellert M. V(D)J recombination in mouse thymocytes: double-strand breaks near T cell receptor delta rearrangement signals. Cell. 1992 Apr 3;69(1):41–53. [PubMed]
  • Roth DB, Menetski JP, Nakajima PB, Bosma MJ, Gellert M. V(D)J recombination: broken DNA molecules with covalently sealed (hairpin) coding ends in scid mouse thymocytes. Cell. 1992 Sep 18;70(6):983–991. [PubMed]
  • Roth DB, Zhu C, Gellert M. Characterization of broken DNA molecules associated with V(D)J recombination. Proc Natl Acad Sci U S A. 1993 Nov 15;90(22):10788–10792. [PMC free article] [PubMed]
  • Sadofsky MJ, Hesse JE, McBlane JF, Gellert M. Expression and V(D)J recombination activity of mutated RAG-1 proteins. Nucleic Acids Res. 1993 Dec 11;21(24):5644–5650. [PMC free article] [PubMed]
  • Sadofsky MJ, Hesse JE, Gellert M. Definition of a core region of RAG-2 that is functional in V(D)J recombination. Nucleic Acids Res. 1994 May 25;22(10):1805–1809. [PMC free article] [PubMed]
  • Sadofsky MJ, Hesse JE, van Gent DC, Gellert M. RAG-1 mutations that affect the target specificity of V(D)j recombination: a possible direct role of RAG-1 in site recognition. Genes Dev. 1995 Sep 1;9(17):2193–2199. [PubMed]
  • Sakano H, Hüppi K, Heinrich G, Tonegawa S. Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature. 1979 Jul 26;280(5720):288–294. [PubMed]
  • Savilahti H, Rice PA, Mizuuchi K. The phage Mu transpososome core: DNA requirements for assembly and function. EMBO J. 1995 Oct 2;14(19):4893–4903. [PMC free article] [PubMed]
  • Schlissel M, Constantinescu A, Morrow T, Baxter M, Peng A. Double-strand signal sequence breaks in V(D)J recombination are blunt, 5'-phosphorylated, RAG-dependent, and cell cycle regulated. Genes Dev. 1993 Dec;7(12B):2520–2532. [PubMed]
  • Surette MG, Harkness T, Chaconas G. Stimulation of the Mu A protein-mediated strand cleavage reaction by the Mu B protein, and the requirement of DNA nicking for stable type 1 transpososome formation. In vitro transposition characteristics of mini-Mu plasmids carrying terminal base pair mutations. J Biol Chem. 1991 Feb 15;266(5):3118–3124. [PubMed]
  • Timsit Y, Vilbois E, Moras D. Base-pairing shift in the major groove of (CA)n tracts by B-DNA crystal structures. Nature. 1991 Nov 14;354(6349):167–170. [PubMed]
  • van den Ent FM, Vink C, Plasterk RH. DNA substrate requirements for different activities of the human immunodeficiency virus type 1 integrase protein. J Virol. 1994 Dec;68(12):7825–7832. [PMC free article] [PubMed]
  • van Gent DC, McBlane JF, Ramsden DA, Sadofsky MJ, Hesse JE, Gellert M. Initiation of V(D)J recombination in a cell-free system. Cell. 1995 Jun 16;81(6):925–934. [PubMed]
  • van Gent DC, Mizuuchi K, Gellert M. Similarities between initiation of V(D)J recombination and retroviral integration. Science. 1996 Mar 15;271(5255):1592–1594. [PubMed]

Articles from The EMBO Journal are provided here courtesy of The European Molecular Biology Organization


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Compound
    PubChem Compound links
  • PubMed
    PubMed citations for these articles
  • Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...