Quadruplex-Flanking Stem Structures Modulate the Stability and Metal Ion Preferences of RNA Mimics of GFP
| Autor: | Christopher L. Barkau, Keith T. Gagnon, Eman A Ageely, Zachary J. Kartje, Kushal J. Rohilla |
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| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Aptamer Cell Mutant Green Fluorescent Proteins Brassica Biology 010402 general chemistry G-quadruplex 01 natural sciences Biochemistry Green fluorescent protein 03 medical and health sciences Spinacia oleracea medicine Nucleic acid structure Molecular Mimicry food and beverages RNA General Medicine biology.organism_classification 0104 chemical sciences G-Quadruplexes 030104 developmental biology medicine.anatomical_structure Spectrometry Fluorescence Metals RNA Plant Mutation Molecular Medicine Spinach Nucleic Acid Conformation |
| Zdroj: | ACS chemical biology. 11(9) |
| ISSN: | 1554-8937 |
| Popis: | The spinach family of RNA aptamers are RNA mimics of green fluorescent protein (GFP) that have previously been designed to address the challenges of imaging RNA inside living cells. However, relatively low levels of free intracellular magnesium limited the practical use of these aptamers. Recent cell-based selections identified the broccoli RNA aptamer, which requires less magnesium for fluorescence, but the basis for magnesium preference remained unclear. Here, we find that the broccoli RNA structure is very similar to that of baby spinach, a truncated version of the spinach aptamer. Differences in stability and metal ion preferences between these two aptamers, and among broccoli mutants, are primarily associated with the sequence and structure of predicted quadruplex-flanking stem structures. Mutation of purine-purine pairs in broccoli at the terminal stem-quadruplex transition caused reversion of broccoli to a higher magnesium dependence. Unique duplex-to-quadruplex transitions in GFP-mimic RNAs likely explain their sensitivity to magnesium for stability and fluorescence. Thus, optimizations designed to improve aptamers should take into consideration the role of metal ions in stabilizing the transitions and interactions between independently folding RNA structural motifs. |
| Databáze: | OpenAIRE |
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