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Molecules 2012, 17(3), 2855-2876; doi:10.3390/molecules17032855

Site-Specific Incorporation of Functional Components into RNA by an Unnatural Base Pair Transcription System

TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
RIKEN Systems and Structural Biology Center (SSBC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Author to whom correspondence should be addressed.
Received: 16 December 2011 / Revised: 22 February 2012 / Accepted: 24 February 2012 / Published: 7 March 2012
(This article belongs to the Special Issue DNA-Templated Synthesis)
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Toward the expansion of the genetic alphabet, an unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) functions as a third base pair in replication and transcription, and provides a useful tool for the site-specific, enzymatic incorporation of functional components into nucleic acids. We have synthesized several modified-Pa substrates, such as alkylamino-, biotin-, TAMRA-, FAM-, and digoxigenin-linked PaTPs, and examined their transcription by T7 RNA polymerase using Ds-containing DNA templates with various sequences. The Pa substrates modified with relatively small functional groups, such as alkylamino and biotin, were efficiently incorporated into RNA transcripts at the internal positions, except for those less than 10 bases from the 3′-terminus. We found that the efficient incorporation into a position close to the 3′-terminus of a transcript depended on the natural base contexts neighboring the unnatural base, and that pyrimidine-Ds-pyrimidine sequences in templates were generally favorable, relative to purine-Ds-purine sequences. The unnatural base pair transcription system provides a method for the site-specific functionalization of large RNA molecules.
Keywords: unnatural base pair; transcription; T7 RNA polymerase unnatural base pair; transcription; T7 RNA polymerase

This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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Morohashi, N.; Kimoto, M.; Sato, A.; Kawai, R.; Hirao, I. Site-Specific Incorporation of Functional Components into RNA by an Unnatural Base Pair Transcription System. Molecules 2012, 17, 2855-2876.

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