Synthesis and Properties of an Oligonucleotide Modified with an Acridine Derivative at the Artificial Abasic Site

The synthesis of an oligodeoxynucleotide (ODN) modified with 2-methoxy-6-chloro-9-aminoacridine (Acr) at an abasic site is described. A stereochemically defined aminodiol, l-threoninol, was used to serve as artificial abasic nucleoside. The molecule was modified so as to be suitable for the standard phosphoramidite method and was incorporated into the interior of an ODN. In addition, N-hydroxysuccinimidyl N-[9-(6-chloro-2-methoxy)acridinyl]-6-aminocaproate has been synthesized for postsynthetic modification of the amino substrate of the l-threoninol moiety in the ODN. By using absorption spectroscopy, it is shown that oligo(dA) conjugated with acridine binds with complementary strand in a 1:1 ratio. The melting temperature showed that the nonmodified (abasic) duplex is destabilized as a result of lacking in base at the abasic site, but the covalently linked acridine ring compensates for the destabilization effect. The fluorescence quantum yield of the acridine ring was enhanced by connection to oligo(dA) and, further, by formation of a double-strand with the complementary ODN. The quantum yield is larger than that of intermolecular intercalation. The excitation spectra of Acr−ODN in the duplex is quite similar to the absorption spectra. The results indicate that the covalently linked acridine ring is selectively intercalated into the adjacent abasic site.