[113] It was also observed that structure specificity of RAGs could be attributed to the sequence at the single-stranded region. Cytosines were the most preferred, followed by thymines while purines were not cleaved at all. A consensus sequence of ‘C(d)C(s)C(s)’

(d, double-stranded; s, single-stranded) was also proposed for the generation of breaks at single-strand/double-strand transitions.[114] The nonamer binding region of RAG1 was not selleck kinase inhibitor important for RAG cleavage at non-B DNA structures, in contrast to that at RSS.[115] The study showed low cleavage kinetics and a lack of cleavage complex formation at heteroduplex DNA, as the two mechanisms that ensured the control of the pathological activity of RAGs.[115] In an ideal scenario, RAGs target RSS within the immunoglobulin/TCR loci. However, a large number of RSS-like sequences (cryptic RSS) exist throughout the genome and this would lead to the non-specific targeting of RAGs leading to DNA double-strand breaks outside the immunoglobulin/TCR loci, resulting in genomic rearrangements. If the rearrangement Target Selective Inhibitor Library in vivo juxtaposes the immunoglobulin/TCR

regulatory sequences like promoters or enhancers to proto-oncogenes, it could lead to over-expression of the oncogenes culminating in lymphoid malignancies. RAGs are known to generate breaks at sequences resembling heptamer or nonamer because of misrecognition in several leukaemias and lymphomas, which include translocations like MTS1, LMO2, TTG-1, SIL and SCL.[116-119] The discovery that RAGs can detect and cleave non B-DNA structures further increased the spectrum of non-specific cleavage by RAGs.[110] In case of t(14;18) translocation at follicular lymphoma wherein nearly 75% of the breakpoints are dispersed over a 150-bp region called major breakpoint region of BCL2,[120] it has been shown that a non-B structure Gemcitabine cell line can form, which is specifically targeted and cleaved by RAGs.[110,

111] Later, the nature of this structure was identified as a G-quadruplex.[112, 121] It has also been shown that RAGs can cleave at an eight-nucleotide motif ‘CCACCTCT’ in the minor breakpoint cluster of the BCL2 in a nonamer-independent manner.[122] To generate a functional antibody or TCR, several of the genomic segments propagating in the embryo have to select each other, merge in various combinations and further modify themselves. Though the main players in the process have been identified, the mechanism by which each of the individual proteins acts and broadly how the chronological order is regulated are not known. The structure of RAG proteins still remains elusive. Several questions regarding the structure specificity of RAGs are unclear. Biochemical and biophysical studies on the domains within the core and non-core regions of these proteins, studies on the full length proteins in vivo, and detection of their interacting partners are being pursued.