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Updated: Jun 10, 2026

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation
Published on: December 29, 2021
Site-specific incorporation of extra components into RNA by transcription using unnatural base pair systems
1Systems and Structural Biology Center, RIKEN, and TagCyx Biotechnologies, Yokohama, Kanagawa, Japan.
Abstract:
The expansion of the genetic alphabet, by an unnatural base pair system, provides a powerful tool for the site-specific incorporation of extra, functional components into nucleic acids by replication and transcription. We developed several unnatural base pairs that function in PCR and in vitro transcription. Among them, a hydrophobic, unnatural base pair between 7-(2-thienyl)-imidazo[4,5-b]pyridine (denoted by Ds) and pyrrole-2-carbaldehyde (denoted by Pa) exhibits high fidelity in PCR and T7 transcription. Modified Pa bases linked with functional groups of interest can also be site-specifically incorporated into RNA opposite Ds in DNA templates, by T7 RNA polymerase. Here, we describe the methods for the site-specific biotinylation of RNA molecules by transcription using the Ds-Pa pair with biotinylated PaTP (Biotin-PaTP).
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Transcription
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
Transcription
Transcription Can Produce Different Kinds of RNA Molecules
In eukaryotes,...
Transfer RNA Synthesis
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Transfer RNA Synthesis
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Nucleic Acid Structure
DNA Structure
DNA has a double-helix structure. The...
Ribosomal RNA Synthesis
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...