Third complementarity-determining region of mutated V-H immunoglobulin genes contains shorter V, D, J, P, and N components than non-mutated genes

The third complementarity-determining region (CDR3) of immunoglobulin varia ble genes for the heavy chain (V-H) has been shown to be shorter in length in hypermutated antibodies than in non-hypermutated antibodies. To determin e which components of CDR3 contribute to the shorter length, and if there i s an effect of age on the length, we analysed 235 cDNA clones from human pe ripheral blood of V(H)6 genes rearranged to immunoglobulin M (IgM) constant genes. There was similar use of diversity (D) and joining (J(H)) gene segm ents between clones from young and old donors, and there was similar use of D segments among the mutated and non-mutated heavy chains. However, in the mutated heavy chains, there was increased use of shorter J(H)4 segments an d decreased use of longer J(H)6 segments compared to the non-mutated protei ns. The overall length of CDR3 did not change with age within the mutated a nd non-mutated categories, but was significantly shorter by three amino aci ds in the mutated clones compared to the non-mutated clones. Analyses of th e individual components that comprise CDR3 indicated that they were all sho rter in the mutated clones. Thus, there were more nucleotides deleted from the ends of V-H, D, and JH gene segments, and fewer P and N nucleotides add ed. The results suggest that B cells bearing immunoglobulin receptors with shorter CDR3s have been selected for binding to antigen. A smaller CDR3 may allow room in the antibody binding pocket for antigen to interact with CDR s 1 and 2 as well, so that as the VDJ gene undergoes hypermutation, substit utions in all three CDRs can further contribute to the binding energy.