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Anti-DNA antibodies play important roles in the pathogenesis of autoimmune diseases and they also serve as unique models for the study of protein-DNA recognition. DNA-1 and 11F8 are anti-ss DNA antibodies derived from autoimmune lupus-prone mice. They are very similar to each other in terms of CDR sequence and preference for binding T-rich ssDNA. Here, we present the 1.95 Å resolution structure of DNA-1 complexed with a stem-loop DNA ligand, denoted G5-14. G5-14 is a synthetic oligonucleotide with the ten-nucleotide sequence identical to the stem-loop portion above the bulge of G1-17, which is an oligonucleotide identified by in vitro selection experiments and binds with high affinity and specificity to Fab 11F8. 11F8 localizes to kidney tissue by binding to DNA adherent to the GBM and eventually leads to renal damage in a mouse model. The DNA-1/G5-14 structure shows that the two DNA strands dimerize to form a double-stranded DNA dumbbell and have a large conformational change including the breaking and reformation of hydrogen bonds. The most striking feature of the Fab/DNA interactions is the use of extensive π-π stacking of the DNA bases and the protein side chains to form base-base and basearomatic stacking interactions. DNA-1 seems to bind to the stem loop ligand in a way different from 11F8. These results provide insights into the specific recognition model of anti-DNA Abs and the potential challenges in structure based drug design to treat autoimmune diseases.

Structure of an antigen-binding fragment bound to stem-loop DNA and crystallization of recombinant haemophilus influenzae e(P4) acid phosphatase