Two DNA conjugates modified with ferrocene and β-cyclodextrin were prepared as a pair of probes that work cooperatively for DNA sensing, in which the electrochemical signal of ferrocene on one probe was significantly "quenched" by the formation of an inclusion complex with β-cyclodextrin of the other probe on the DNA templates.

We prepared an oligodeoxyribonucleotide conjugate (5-3ant(2)18) 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 5-3ant(2)18 shows a unique feature in its target recognition; it binds the target tightly, yet still retains high sequence selectivity. Circularization of 5-3ant(2)18 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.

The techniques of chemical ligation have attracted great attention as an alternative to enzymatic joining of DNA ends. Here we introduce the photoligation of anthracene-modified ODN conjugates through anthracene cyclodimer formation. The effect of the positions and the kinds of single base mismatch on the template was evaluated using eight templates with one-base displacements. We found out that the yield of the ligation was affected by mispairing in a positiondependent manner. Such results would be attributed to the disruption of the local structure at the ligation site.

We tethered an anthracene group to one end of oligonucleotide to make anthracene -ODN conjugates (5 0 AntODN15 and 3 0 AntODN25). The sequences of the conjugates were designed to hybridise to adjacent sites of the template with their anthracene units stacked each other. The conjugates dimerised only in the presence of the template by light irradiation. The dimerisation efficiency was affected by one-base mismatch in the tandem duplexes. Furthermore, we studied the signal amplification experiments under thermal cycling in the presence of the targets with full match and mismatch sequences.

We attached anthracene molecules covalently to one end of oligodeoxyribonucleotides to form three pairs of anthracene-ODN conjugates. The sequences of each pair of the conjugates were designed to bind adjacent sequences of the template with the anthracene units directed such that they stacked each other. The conjugates dimerized only in the presence of the template by light irradiation. We found that the ligation yields largely depended on the substituted position of anthracene groups. Sequence selectivity in the dimerization yield was preserved even in the system with highest reactivity. SNP bases could be discriminated rapidly by combining the techniques of MS spectroscopy.