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Structure-fluorescence activation relationships of a large Stokes shift fluorogenic RNA aptamer

Please always quote using this URN: urn:nbn:de:bvb:20-opus-192340
  • The Chili RNA aptamer is a 52 nt long fluorogen-activating RNA aptamer (FLAP) that confers fluorescence to structurally diverse derivatives of fluorescent protein chromophores. A key feature of Chili is the formation of highly stable complexes with different ligands, which exhibit bright, highly Stokes-shifted fluorescence emission. In this work, we have analyzed the interactions between the Chili RNA and a family of conditionally fluorescent ligands using a variety of spectroscopic, calorimetric and biochemical techniques to reveal keyThe Chili RNA aptamer is a 52 nt long fluorogen-activating RNA aptamer (FLAP) that confers fluorescence to structurally diverse derivatives of fluorescent protein chromophores. A key feature of Chili is the formation of highly stable complexes with different ligands, which exhibit bright, highly Stokes-shifted fluorescence emission. In this work, we have analyzed the interactions between the Chili RNA and a family of conditionally fluorescent ligands using a variety of spectroscopic, calorimetric and biochemical techniques to reveal key structure - fluorescence activation relationships (SFARs). The ligands under investigation form two categories with emission maxima of ~540 nm or ~590 nm, respectively, and bind with affinities in the nanomolar to low-micromolar range. Isothermal titration calorimetry was used to elucidate the enthalpic and entropic contributions to binding affinity for a cationic ligand that is unique to the Chili aptamer. In addition to fluorescence activation, ligand binding was also observed by NMR spectroscopy, revealing characteristic signals for the formation of a G-quadruplex only upon ligand binding. These data shed light on the molecular features required and responsible for the large Stokes shift and the strong fluorescence enhancement of red and green emitting RNA-chromophore complexes.show moreshow less

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Author: Christian Steinmetzger, Irene Bessi, Ann-Kathrin Lenz, Claudia HöbartnerORCiD
URN:urn:nbn:de:bvb:20-opus-192340
Document Type:Journal article
Faculties:Fakultät für Chemie und Pharmazie / Institut für Organische Chemie
Language:English
Parent Title (English):Nucleic Acids Research
Year of Completion:2019
Pagenumber:gkz1084
Source:Nucleic Acids Research, , gkz1084, https://doi.org/10.1093/nar/gkz1084
DOI:https://doi.org/10.1093/nar/gkz1084/5628921
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 54 Chemie / 547 Organische Chemie
Tag:Chili RNA Aptamer; Stokes-shifted fluorescence emission; fluorogen-activating RNA aptamer (FLAP); key structure - fluorescence activation relationships (SFARs); ligand binding
Release Date:2019/12/03
EU-Project number / Contract (GA) number:682586
OpenAIRE:OpenAIRE
Licence (German):License LogoCC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International