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For the site-specific labeling and modification of RNA by genetic alphabet expansion, we developed a PCR and transcription system using two hydrophobic unnatural base pairs: 7-(2-thienyl)-imidazo[4,5- b ]pyridine ( Ds ) and 2-nitro-4-propynylpyrrole ( Px ) as a third pair for PCR amplification and  Ds  and pyrrole-2-carbaldehyde ( Pa ) for the incorporation of functional components as modified  Pa  bases into RNA by T7 transcription. To prepare  Ds -containing DNA templates with long chains, the  Ds - Px  pair was utilized in a fusion PCR method, by which we demonstrated the synthesis of 282-bp DNA templates containing  Ds  at specific positions. Using these  Ds -containing DNA templates and a biotin-linked  Pa  substrate (Biotin- Pa TP) as a modified  Pa  base, 260-mer RNA transcripts containing Biotin- Pa  at a specific position were generated by T7 RNA polymerase. This two-unnatural-base-pair system, combining the  Ds - Px  and  Ds - Pa  pairs with modified  Pa  substrates, provides a powerful tool for the site-specific labeling and modification of desired positions in large RNA molecules.

PCR Amplification and Transcription for Site-Specific Labeling of Large RNA Molecules by a Two-Unnatural-Base-Pair System