Expansion of the genetic alphabet by creating an artificial extra base pair, unnatural base pair, could provide a powerful tool for the site-specific incorporation of new components into nucleic acids and proteins through the genetic information flow in the central dogma. Recently, we have developed a hydrophobic unnatural base pair between 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) and its variants that exhibit high efficiency and fidelity in PCR as the third base pair. After 40 cycles of exponential amplification PCR (10 cycles PCR repeated 4 times), more than 97% of the Ds-Px pair can be retained in 10-billion-fold amplified DNA fragments. In addition, we found that certain modifications of the unnatural base pair increase the fidelity in PCR without decrease in amplification efficiency. By using the unnatural base pair system, we generated new diagnostic systems for detecting target DNA sequences and new artificial DNA molecules for targeting proteins.

Unnatural base pair systems for DNA-based biotechnology toward diagnostic and therapeutic applications

243rd National Meeting (2012)

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