RNA Ligation for Mono and Dually Labeled RNAs |
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Authors: | Dr. Anaïs Depaix Agnieszka Mlynarska-Cieslak Dr. Marcin Warminski Dr. Pawel J. Sikorski Prof. Dr. Jacek Jemielity Dr. Joanna Kowalska |
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Affiliation: | 1. Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland;2. Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland |
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Abstract: | Labeled RNAs are invaluable probes for investigation of RNA function and localization. However, mRNA labeling remains challenging. Here, we developed an improved method for 3′-end labeling of in vitro transcribed RNAs. We synthesized novel adenosine 3′,5′-bisphosphate analogues modified at the N6 or C2 position of adenosine with an azide-containing linker, fluorescent label, or biotin and assessed these constructs as substrates for RNA labeling directly by T4 ligase or via postenzymatic strain-promoted alkyne-azide cycloaddition (SPAAC). All analogues were substrates for T4 RNA ligase. Analogues containing bulky fluorescent labels or biotin showed better overall labeling yields than postenzymatic SPAAC. We successfully labeled uncapped RNAs, NAD-capped RNAs, and 5′-fluorescently labeled m7Gp3Am-capped mRNAs. The obtained highly homogenous dually labeled mRNA was translationally active and enabled fluorescence-based monitoring of decapping. This method will facilitate the use of various functionalized mRNA-based probes. |
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Keywords: | biochemistry mRNA RNA labeling T4 ligase probe |
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