Anti-DNA antibodies exhibit different binding motif preferences for single stranded or double stranded DNA

A common feature for most anti-DNA antibodies (Abs) is their induction in an antigen (Ag)-driven specific clonal expansion pattern though crossreactivity. However, the fine sequences in DNA Ags that interact directly with immune system and the ability of DNA to induce immune responses is poorly understood. In order to define the characteristics of possible antigenic determinants in DNA Ags, we immunized mice with the pBR322 plasmid and used antisera as source of anti-DNA Abs. A systemic evolution of ligands by exponential enrichment (SELEX) procedure was performed on an oligodeoxynucleotide library either in single stranded (ss-) or double stranded (ds-) form. The SELEXed fragments were cloned and sequenced. The resulting sequences were analyzed using the Multiple Alignment Construction and Analysis Workbench program. We show that the fragments of ss- or ds- form bound by a same stock of antibodies were different in their conserved sequences. ss-DNA fragments recognized by anti-DNA Abs were rich in cacc, caccc, accc or cccc blocks, while the same stock of Abs exhibited significant preference for the (5'gcg3'/3'cgc5') motif located in ds-DNA. At the same time sera from unimmunized control mice showed no sequence preference in either ss-DNA or ds-DNA. Future improvement of this work and the potential use of SELEX for studies of DNA Ags are also discussed.