Biopolym. Cell. 2008; 24(2):112-122.
http://dx.doi.org/10.7124/bc.000798
Structure and Function of Biopolymers
Structural analysis of possible target-sites of RAG1/2 protein, discovered in mouse genome in silico, and their identification in repeating elements
1Gubsky A. Yu., 2Zinkovsky V. G.
  1. Odessa I. I. Mechnikov National University
    Dvoryanskaya Str., 2, Odessa, Ukraine, 65082
  2. Opole University
    pl. Kopernika 11a, Opole, Poland, 45-040

Abstract

We have established that the quantity of possible target-sites of RAG1/2 (cRSS) is 5.4 times higher than theoretically expected one using mathematical methods and specially developed algorithms. 71% of cases revealed cRSS in the structure of 390 types of repeats. The structure of 5% motives includes nucleotides, typical for the majority of signal sequences of recombination of functional V, D, J segments of Ig, Tcr mouse genes (fRSS). The existence of 25 % of such motives in mouse DNA may be considered as the consequence of random nucleotide combinations. In the majority of cases the structures of spacers 12cRSS and 23cRSS are 58–67 % and 30–47 % homologous to spacers 12fRSS and 23fRSS respectively.
Keywords: cRSS, V(D)J-recombination, RAG1, RAG2
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