Self-complementary oligodeoxyribonucleotides containing 2'-O-(anthraquinone-2-methyl)adenosine

Incorporation of an intercalating agent into an oligodeoxynucleotide (ODN) has the potential to enhance binding affinity upon duplex formation, to increase ODN hydrophobicity, and to enhance resistance to nuclease hydrolysis. Site-specific intercalation has been achieved through the synthesis of 2'-O-(anthraquinone-2-methyl)adenosine(rA*) and its incorporation into the palindromic dodecanucleotide d(CGCrA*CATGTGCG). Melting temperature, CD spectra, 1D and 2D (DQF-COSY and NOESY) NMR spectra, and molecular models were obtained and compared with the unmodified dodecamer. The data clearly establish that intercalation of the anthraquinone ring into a predominantly B-type helix occurs between the A4-T9 and C5-G8 base pairs, significantly stabilizing the duplex and enhancing the hydrophobicity of the ODN.