Synthesis of DNA with phenanthridinium as an artificial DNA base.
A phenanthridinium-containing DNA building block was synthesized as an ethidium nucleoside analogue starting from 3,8-diamino-6-phenyl-phenanthridine. Using this building block, oligonucleotides bearing the phenanthridinium moiety as an artificial DNA base were prepared via automated solid-phase phosphoramidite chemistry. The modified phenanthridinium-containing DNA duplexes were characterized by UV/vis absorption spectroscopy (including the melting behavior), CD spectroscopy, and steady-state fluorescence spectroscopy. These experiments reveal the expected similarity of the synthetic phenanthridinium moiety with noncovalently bound ethidium. More importantly, the results show clearly that the artificial phenanthridinium base is intercalated within the DNA base stack. The counterbase as part of the complementary strand seems to have only a minor influence on the intercalation properties of the phenanthridinium moiety.
Huber
Robert
R
Institute for Organic Chemistry and Biochemistry, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.
Amann
Nicole
N
Wagenknecht
Hans-Achim
HA
D000478:Alkylation; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000138:chemical synthesis* / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000138:chemical synthesis; D010617:Phenanthridines / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet; D013696:Temperature
D009841:Oligonucleotides; D010617:Phenanthridines; C014740:phenanthridinium; D004247:DNA