Combinatorial Selection and Edited Combinatorial Selection of Phosphorothioate Aptamers Targeting Human Nuclear Factor-κB RelA/p50 and RelA/RelA

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Abstract
Nuclear factor-κB (NF-κB) transcription factors are important in regulating the immune response and play critical roles in the pathogenesis of chronic inflammatory diseases and a variety of human cancers. Agents that target specific NF-κB dimers may serve as therapeutic agents for the prevention of pathogenic immune responses. We have selected monothiophosphate-modified aptamers, or “thioaptamers”, to the NF-κB p50/RelA heterodimer using combinatorial selection techniques. We also utilized a “double sieve” or editing approach for the generation of thioaptamers with enhanced selectivity to the RelA/RelA homodimer. The thioaptamers from these selections and our previous selections on the p50/p50 and RelA/RelA homodimers all had unique sequences and bound tightly to the recombinant NF-κB dimers against which they were selected. The selected thioaptamers also appear to maintain their selectivity and specificity among other cellular proteins, because they have the ability to bind NF-κB proteins within nuclear extracts from lipopolysaccharide (LPS)-induced macrophages and B cells.