An RNA aptamer that selectively recognizes symmetric dimethylation of arginine 8 in the histone H3 N-terminal peptide.

Epigenetic modifications of N-terminal histone tails, especially histone H3, are important for the regulation of the target genes in chromatin. Specific methods for detection of these modifications in histone H3 N-terminal peptides are valuable tools for diagnostic and therapeutic purposes. As an alternative to antibodies, RNA aptamers display compatible binding affinities and selectivites against various biologically relevant targets. Systematic evolution of ligands by exponential enrichment (SELEX) was performed against histone H3R8Me2sym. A 14-amino acid peptide that mimics this modified histone tail was prepared in a biotinylated form and 10 selection cycles of SELEX were carried out. This produced 4 aptamers, one of which (clone 1) was observed to have low nanomolar binding affinity (K(d)=12 nM) against the cognate peptide. The affinity of this aptamer is comparable to 2 commercially available antibodies against differently modified histone H3 peptides and it displays a greater selectivity than the antibodies.