ArticleNucleic acids research2015
Systematic reconstruction of binding and stability landscapes of the fluorogenic aptamer spinach.
Article in Nucleic acids research, 2015. 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.
- Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine.Nature communications · 2021Article
- Photophysics of DFHBI bound to RNA aptamer Baby Spinach.Scientific reports · 2021Article
- Accelerating Post-SELEX Aptamer Engineering Using Exonuclease Digestion.Journal of the American Chemical Society · 2021Article
- Computational design of three-dimensional RNA structure and function.Nature nanotechnology · 2019Article
- Programmable RNA detection with a fluorescent RNA aptamer using optimized three-way junction formation.RNA (New York, N.Y.) · 2019Article
- Intracellular Imaging with Genetically Encoded RNA-based Molecular Sensors.Nanomaterials (Basel, Switzerland) · 2019Review
- RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers.Angewandte Chemie (International ed. in English) · 2019Review
- Light-Up RNA Aptamers and Their Cognate Fluorogens: From Their Development to Their Applications.International journal of molecular sciences · 2017Review
- Crystal structure and fluorescence properties of the iSpinach aptamer in complex with DFHBI.RNA (New York, N.Y.) · 2017Article
- A Fluorescent Split Aptamer for Visualizing RNA-RNA Assembly In Vivo.ACS synthetic biology · 2017Article
- A genetically encoded fluorescent tRNA is active in live-cell protein synthesis.Nucleic acids research · 2017Article
- Engineering and characterization of fluorogenic glycine riboswitches.Nucleic acids research · 2016Article
- iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications.Nucleic acids research · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fluorogenic RNAs that are based on the complex formed by 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) derivatives and the RNA aptamer named Spinach were used to engineer a new generation of in vitro and in vivo sensors for bioanalytics. With the resolved crystal structure of the RNA/small molecule complex, the engineering map becomes available, but comprehensive information regarding the thermodynamic profile of the molecule is missing. Here, we reconstructed the full thermodynamic binding and stability landscapes between DFHBI and a truncated sequence of first-generation Spinach. For this purpose, we established a systematic screening procedure for single- and double-point mutations on a microfluidic large-scale integrated chip platform for 87-nt long RNAs. The thermodynamic profile with single base resolution was used to engineer an improved fluorogenic spinach generation via a directed rather than evolutional approach.
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