Differential reaction kinetics, cleavage complex formation, and nonamer binding domain dependence dictate the structure-specific and sequence-specific nuclease activity of RAGs

J Mol Biol. 2012 Jan 20;415(3):475-88. doi: 10.1016/j.jmb.2011.11.002. Epub 2011 Nov 12.


During V(D)J recombination, RAG (recombination-activating gene) complex cleaves DNA based on sequence specificity. Besides its physiological function, RAG has been shown to act as a structure-specific nuclease. Recently, we showed that the presence of cytosine within the single-stranded region of heteroduplex DNA is important when RAGs cleave on DNA structures. In the present study, we report that heteroduplex DNA containing a bubble region can be cleaved efficiently when present along with a recombination signal sequence (RSS) in cis or trans configuration. The sequence of the bubble region influences RAG cleavage at RSS when present in cis. We also find that the kinetics of RAG cleavage differs between RSS and bubble, wherein RSS cleavage reaches maximum efficiency faster than bubble cleavage. In addition, unlike RSS, RAG cleavage at bubbles does not lead to cleavage complex formation. Finally, we show that the "nonamer binding region," which regulates RAG cleavage on RSS, is not important during RAG activity in non-B DNA structures. Therefore, in the current study, we identify the possible mechanism by which RAG cleavage is regulated when it acts as a structure-specific nuclease.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / genetics*
  • DNA / metabolism*
  • DNA-Binding Proteins / metabolism*
  • Homeodomain Proteins / metabolism*
  • Kinetics
  • Substrate Specificity
  • V(D)J Recombination*


  • DNA-Binding Proteins
  • Homeodomain Proteins
  • Rag2 protein, mouse
  • RAG-1 protein
  • DNA