High Fidelity Base Pairing at the 3′-Terminus

• Published in: Journal of the American Chemical Society Vol. 131; no. 35; pp. 12671 - 12681
• Main Authors: Patra, Amritraj, Richert, Clemens
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 09.09.2009; Amer Chemical Soc
• Subjects: Base Pairing; Base Sequence; Chemistry; Chemistry, Multidisciplinary; Deoxyuridine - chemistry; DNA - chemistry; DNA - genetics; Models, Molecular; Nucleic Acid Denaturation; Physical Sciences; RNA - chemistry; RNA - genetics; Science & Technology; Transition Temperature; GENETIC-CODE; MOLECULAR-DYNAMICS; AROMATIC STACKING; OLIGONUCLEOTIDE DUPLEXES; METABOLITE-RESPONSIVE RIBOZYME; HYDROPHOBIC BASE; CHARGE-TRANSPORT; WOBBLE HYPOTHESIS; THERMODYNAMIC PARAMETERS; DUPLEX DNA
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja9033654

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 m 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 m 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.