Synthesis and interactive properties of an oligonucleotide with anthraquinone at the sugar fragment

The synthesis of a self-complementary oligonucleotide possessing an anthraquinonylmethyl substituent at the designated sugar fragment, 5'-CCU(2'AQ)AGCTAGG (1), is described. The anthraquinonylmethyl group was introduced to 2'-hydroxyl moiety of uridine, which was then converted to the protected phosphorobisdiethylamidite derivative. This reagent was used for the solid-phase synthesis of the modified oligonucleotide 1. The UV and CD melting behaviors indicate that the modified oligonucleotide 1 can form a duplex in aqueous buffer solution similar to the unmodified strand 5'-CCTAGCTAGG (7). The observed melting temperatures for the duplexes 1 and 7 were 57.4 and 40.0 degrees C, respectively. The temperature-dependent change in the intensity of the induced CD at around 335 nm reflected directly to the melting behaviors of duplex 1, indicating that the anthraquinone groups intercalate into the base pairs in the duplex. The intercalation-induced stability of the duplex translates into a free energy cost of 5.2 kcal/mol. The present work provides a novel method for enhancing the affinity of oligonucleotides for their complementary sequences.