Live-Cell Imaging of Long Noncoding RNAs Using Molecular Beacons

2019 ◽  
pp. 21-33
Author(s):  
Yachen Ying ◽  
Shiqi Mao ◽  
Christopher J. Krueger ◽  
Antony K. Chen
Keyword(s):  
Live Cell Imaging ◽  
Cell Imaging ◽  
Noncoding Rnas ◽  
Live Cell ◽  
Long Noncoding Rnas ◽  
Molecular Beacons

scholarly journals PinMol: Python application for designing molecular beacons for live cell imaging of endogenous mRNAs

2018 ◽  
Author(s):  
Livia V. Bayer ◽  
Omar S. Omar ◽  
Diana P. Bratu ◽  
Irina E. Catrina
Keyword(s):  
Live Cell Imaging ◽  
Cell Imaging ◽  
Molecular Beacon ◽  
Structural Information ◽  
Live Cell ◽  
Molecular Beacons ◽  
Intramolecular Interactions ◽  
Live Cells ◽  
Target Rna

ABSTRACTMolecular beacons are nucleic acid oligomers labeled with a fluorophore and a quencher that fold in a hairpin-shaped structure, which fluoresce only when bound to their target RNA. They are used for the visualization of endogenous mRNAs in live cells. Here, we report a Python program (PinMol) that designs molecular beacons best suited for live cell imaging by using structural information from secondary structures of the target RNA, predicted via energy minimization approaches. PinMol takes into account the accessibility of the targeted regions, as well as the inter- and intramolecular interactions of each selected probe. To demonstrate its applicability, we synthesized an oskar mRNA-specific molecular beacon (osk1236), which is selected by PinMol to target a more accessible region than a manually designed oskar-specific molecular beacon (osk2216). We previously demonstrated osk2216 to be efficient in detecting oskar mRNA in in vivo experiments. Here, we show that osk1236 outperformed osk2216 in live cell imaging experiments.

scholarly journals PinMol: Python application for designing molecular beacons for live cell imaging of endogenous mRNAs

RNA ◽  
2018 ◽  
Vol 25 (3) ◽  
pp. 305-318
Author(s):  
Livia V. Bayer ◽  
Omar S. Omar ◽  
Diana P. Bratu ◽  
Irina E. Catrina
Keyword(s):  
Live Cell Imaging ◽  
Cell Imaging ◽  
Live Cell ◽  
Molecular Beacons

Delivery of Molecular Beacons for Live-Cell Imaging and Analysis of RNA

2011 ◽  
pp. 159-174 ◽  
Author(s):  
Antony K. Chen ◽  
Won Jong Rhee ◽  
Gang Bao ◽  
Andrew Tsourkas
Keyword(s):  
Live Cell Imaging ◽  
Cell Imaging ◽  
Live Cell ◽  
Molecular Beacons
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