Using SELEX (systematic evolution of ligands by exponential enrichment), we serendipitously discovered a ssDNA aptamer that binds selectively to the anti-FLAG M2 antibody. The aptamer consisted of two motifs (CCTTA and TGTCTWCC) separated by 2-3 bases, and the elimination of one or the other motif abrogated binding. The DNA aptamer and FLAG peptide competed for binding to the antigen-binding pocket of the M2 antibody. In addition, the aptamer eluted FLAG-tagged proteins from the antibody, suggesting a commercial application in protein purification. These findings demonstrate the feasibility of using SELEX to develop ssDNA aptamers that block the function of a specific antibody, a capability that could lead to the development of novel therapeutic modalities for patients with systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases. 1. Introduction Antinuclear antibodies are diagnostic markers of systemic lupus erythematosus, rheumatoid arthritis, and other autoimmune diseases [1]. In these B lymphocyte disorders, a large variety of autoantibodies are made against nuclear self-antigens, including ribonucleoproteins, nucleosomes, chromatin, and polynucleotides (RNA, ssDNA, and dsDNA). Among these, anti-DNA antibodies have been the most extensively studied [2]. Anti-DNA antibodies bind with high-affinity to either single- or double-stranded DNA and many tend to favor association with pyrimidine bases [3, 4]. Several reports have also described antinuclear antibodies cross-reacting with peptide self-antigens and depositing in the brain, kidneys, and skin [5–9]. As proposed by several investigators, this deposition may be a cause of inflammation-mediated tissue damage, especially in the kidneys where nephritis is a major source of morbidity [1, 2]. In mouse models of systemic lupus erythematosus, attempts were made to block the function of these cross-reacting antibodies using peptide aptamers, derived either from their cognate peptide self-antigens or from phage display libraries [10, 11]. In some cases, the peptide aptamer competitively associated with the antinuclear autoantibodies, thereby preventing antibody-mediated tissue damage [10, 11]. Thus, direct antibody inhibition might be an effective therapy in patients with autoimmune diseases driven by the presence of antinuclear antibodies. Another viable approach to block antinuclear antibodies might be to use DNA aptamers, given the high-affinity of these antibodies for DNA and evidence of nucleotide base specificity. But this approach has clearly been underexplored, perhaps due
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