| Sumario: | Binding target strands with single base selectivity at a terminal position is difficult with natural DNA or RNA hybridization probes. Nature uses a degenerate genetic code that is based on RNA:RNA codon:anticodon duplexes tolerating wobble base pairs at the terminus. The importance of short RNA strands in regulatory processes in the cell make it desirable to develop receptor-like approaches for high fidelity binding, even at the very 3′-terminus of a probe. Here, we report the three-dimensional structure of a DNA duplex with a 3′-terminal 2′-anthraquinoylamido-2′-deoxyuridine (Uaq) residue that was solved by NMR and restrained molecular dynamics. The Uaq residue binds the 5′-terminus of the target strand through a combination of π-stacking, hydrogen bonding, and interactions in the minor groove. The acylated aminonucleoside is the best molecular cap for 3′-termini reported to date. The Uaq motif assists binding of DNA strands, but is particularly effective in enhancing the affinity for RNA target strands, with a ΔT in the UV melting point of up to +18.2°C per residue. Increased base pairing selectivity is induced for all sequence motifs tested, even in cases where unmodified duplexes show no preference for the canonical base pair at all. A single mismatched nucleobase facing the 3′-terminus gives ΔΔT values as large as -23.9 °C (RNA) or -29.5 °C (DNA). The 5′-phosphoramidite of the Uaq cap reported here allows for routine incorporation during automated syntheses.
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