Reversible circularization of an anthracene-modified DNA conjugate through bimolecular triplex formation and its analytical application

Abstract

We prepared an oligodeoxyribonucleotide conjugate (5-3ant₂18) carrying two anthracenes, each of which was tethered to both ends of the conjugate through hexamethylene linker chains. The conjugate has a mirror repeat of two heptamer sequences, such that it forms a bimolecular triplex with the single stranded target, forming a two-fold U-shaped conformation. The conformation of the conjugate in its triplex structure could be frozen instantaneously by circularization through photodimerization of the anthracenes. Compared with the duplex formation of linear probes with relevant sequences, bimolecular triplex formation of 5-3ant₂18 shows a unique feature in its target recognition; it binds the target tightly, yet still retains high sequence selectivity. Circularization of 5-3ant₂18 by UV photoirradiation was verified as the probe reaction for a DNA assay. The probe reaction could be performed in a few seconds over a wide range of temperatures, at least between 0 and 25 °C. In addition, the reaction could be regarded as a reversible method for the preparation of circular DNA that shows higher affinity for the target.