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Synthesis of a 5′-6-Locked, 1,10-Phenanthroline-Containing Nucleoside and Its Incorporation into DNA

A rigid nucleoside containing a phenanthroline ligand for metal-ion chelation was synthesized through condensation of 1,10-phenanthroline-5,6-dione with 5-amino-2'-deoxy-cytidine. During the condensation, a 5'-6 ether linkage was formed between the sugar and the base. The phosphoramidite of the nucleoside was used to synthesize oligodeoxynucleotides by means of automated oligonucleotide synthesis, placing the phenanthroline nucleoside on the 5'-end of the oligomers. The free nucleoside is fluorescent; however, the fluorescence of the nucleoside was effectively quenched in both single- and double-stranded DNA. Thermal denaturation experiments on DNA duplexes containing the modified nucleoside showed similar base-pairing properties as T and stronger stacking interactions with a flanking A·T base pair than with a G·C pair. CD spectra of helixes containing the modified nucleoside were characteristic of B-DNA. A model structure of a B-DNA helix, where the nucleoside was paired with A, showed only minor deviations from B-DNA parameters, except for a noticeable buckle of the modified base pair due to the constraints of the 5'-6 linkage. Due to the relative ease of the synthesis and minimal distortions of the helix structure, the phenanthroline nucleoside reported here shows promise for facile 5'-labeling of nucleic acids with metal complexes. This strategy can likely be extended to fusing other aromatic or aliphatic rings to a nucleotide base for incorporating the 5'-end of nucleic acid duplexes.