ArticleNature protocols2010
Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis.
Article in Nature protocols, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- High-Affinity Six-Letter DNA XenoAptamer Generation by Genetic Alphabet Expansion.Journal of the American Chemical Society · 2026Article
- Article
- Detecting Hachimoji DNA: An Eight-Building-Block Genetic System with MoSACS applied materials & interfaces · 2024Article
- Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores.Journal of the American Chemical Society · 2023Article
- Incorporation of isotopic, fluorescent, and heavy-atom-modified nucleotides into RNAs by position-selective labeling of RNA.Nature protocols · 2018Article
- Site-specific labeling of RNA by combining genetic alphabet expansion transcription and copper-free click chemistry.Nucleic acids research · 2015Article
- Enzymatic incorporation of an azide-modified UTP analog into oligoribonucleotides for post-transcriptional chemical functionalization.Nature protocols · 2012Article
- Site-specific incorporation of functional components into RNA by an unnatural base pair transcription system.Molecules (Basel, Switzerland) · 2012Article
- Highly specific unnatural base pair systems as a third base pair for PCR amplification.Nucleic acids research · 2012Article
- Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2012Review
- FRET-based identification of mRNAs undergoing translation.PloS one · 2012Article
- PCR amplification and transcription for site-specific labeling of large RNA molecules by a two-unnatural-base-pair system.Journal of nucleic acids · 2012Article
- Amplification, mutation, and sequencing of a six-letter synthetic genetic system.Journal of the American Chemical Society · 2011Article
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Authors and funding
4 authors.
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Abstract
Methods for fluorescent probing at a defined position of RNA provide powerful tools for analyzing the local structural conformation of functional RNA molecules by tracking fluorescence changes. In this article, we describe the site-specific fluorescent probing of RNA by transcription with an expanded genetic alphabet, using an extra, unnatural base pair between 2-amino-6-(2-thienyl)purine (s) and pyrrole-2-carbaldehyde (Pa). The protocol comprises template DNA preparation containing Pa, transcription involving fluorescent s incorporation and structural analysis of transcripts. The s base is strongly fluorescent, and its nucleoside 5'-triphosphate is site-specifically incorporated into RNA transcripts, opposite Pa in DNA templates, by conventional T7 transcription. The fluorescent intensity of s changes depending on its environment around the probe site, providing clues about the local structural features of RNA molecules. This is the first protocol for RNA transcript preparation with fluorescent labeling at a desired position. The procedure for s-containing RNA preparation takes about 2-3 d.
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