High fidelity base pairing at the 3'-terminus.
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 pi-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 DeltaT(m) in the UV melting point of up to +18.2 degrees 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 DeltaDeltaT(m) values as large as -23.9 degrees C (RNA) or -29.5 degrees C (DNA). The 5'-phosphoramidite of the Uaq cap reported here allows for routine incorporation during automated syntheses.
Patra
Amritraj
A
Institute for Organic Chemistry, University of Karlsruhe (TH), 76131 Karlsruhe, Germany.
Richert
Clemens
C
D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D003857:Deoxyuridine / Q000737:chemistry; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D044366:Transition Temperature
D012313:RNA; D004247:DNA; D003857:Deoxyuridine