Biopolymers and cell. 2008; 24 (2): 112 - 122

Structural analysis of possible target-sites of RAG1/2 protein, discovered in mouse genome in silico, and their identification in repeating elements

A. Yu. Gubsky, V. G. Zinkovsky

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.