Development of a new strand-invader with artificial nucleotides

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In this project, we aimed at developing a new strand-invader by combining unmodified peptide nucleic acid (PNA) and modified DNA (TN -DNA) involving new base-surrogate=Threoninol-Nucleotide (TN) that tethers a functional molecule such as intercalator on D-threoninol. As a possible strand-invader, the duplex stability should be in the following order; DNA/PNA, TN-DNA/DNA > DNA/DNA > TN-DNA/PNA. First, we searched a functional molecule and optimum way of introducing TN into DNA that satisfies above requisites. We found that planar molecule (intercalator) with electron-withdrawing group could significantly stabilize the DNA duplex. Furthermore, introduction of TN at every two nucleotides into DNA remarkably facilitated the duplex formation with DNA and retarded hybridization with PNA. On the basis of these results, we combined unmodified PNA and TN-DNA involving anthraquinone as a strand-invader, which was successfully invaded into the target DNA duplex.