Abasic site-based DNA aptamers for analytical applications

Abstract

We here describe a class of duplex DNA aptamers that possess an abasic site as an active cavity for binding events. A structurally optimised 23-meric duplex (5′-TCT GCG TCC AGX GCA ACG CAC AC-3′/3′-AGA CGC AGG TCT CGT TGC GTG TG-5′, X = abasic site; a propyl linker, T = receptor base) binds to riboflavin with a dissociation constant of 1.9 μM (at 20°C, pH 7.0, I = 0.11 M), and it exhibits a high selectivity for riboflavin over flavin mononucleotide and flavin adenine dinucleotide. A fluorescent signalling aptamer is also developed by the incorporation of fluorescent 2-aminopurine (2-AP) into the duplex to flank the abasic site. This 2-AP-modified abasic site-containing duplex DNA (5′-TCTGC GTCCT PXT TAACG CACAC-3′/3′-AGACG CAGGA TCA ATTGC GTGTG-5′, P = 2-AP, X = abasic site; a propyl linker, C = receptor base) is capable of selectively binding to the bronchodilator theophylline with a dissociation constant of 10 μM (at 5°C, pH 7.0, I = 0.11 M), and it is applicable to monitoring serum theophylline concentrations. In addition, we describe a design strategy for label-free aptamer-based fluorescence-signalling systems based on an abasic site-binding fluorescent ligand. A DNA aptamer against adenosine is examined as a model system, and an abasic site is designed to be incorporated into the aptamer system, so that the adenosine binding causes either a release or binding of abasic site-binding ligands with a clear fluorescent signalling. The designed system is highly selective and sensitive with a detection limit of 1–2 μM for adenosine. These results are discussed as a potential basis for the further development of an aptamer-based analytical assay.