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.

A new visible-light-excitable ICT-CHEF-mediated fluorescence ‘turn-on’ probe for the selective detection of Cd2+ in a mixed aqueous system with live-cell imaging

2015 ◽  
Vol 44 (12) ◽  
pp. 5763-5770 ◽  
Author(s):  
Shyamaprosad Goswami ◽  
Krishnendu Aich ◽  
Sangita Das ◽  
Chitrangada Das Mukhopadhyay ◽  
Deblina Sarkar ◽  
...  
Keyword(s):  
Visible Light ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Aqueous System ◽  
Live Cell ◽  
Selective Detection ◽  
Turn On ◽  
Fluorescence Turn On

A new quinoline based sensor was developed and applied for the selective detection of Cd2+ both in vitro and in vivo.

scholarly journals tdLanYFP, a yellow, bright, photostable and pH insensitive fluorescent protein for live cell imaging and FRET-based sensing strategies

2021 ◽  
Author(s):  
Y. Bousmah ◽  
H. Valenta ◽  
G. Bertolin ◽  
U. Singh ◽  
V. Nicolas ◽  
...  
Keyword(s):  
Single Molecule ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Yellow Fluorescent Protein ◽  
Resonance Energy ◽  
Live Cell ◽  
Live Cells

AbstractYellow fluorescent proteins (YFP) are widely used as optical reporters in Förster Resonance Energy Transfer (FRET) based biosensors. Although great improvements have been done, the sensitivity of the biosensors is still limited by the low photostability and the poor fluorescence performances of YFPs at acidic pHs. In fact, today, there is no yellow variant derived from the EYFP with a pK1/2 below ∼5.5. Here, we characterize a new yellow fluorescent protein, tdLanYFP, derived from the tetrameric protein from the cephalochordate B. lanceolatum, LanYFP. With a quantum yield of 0.92 and an extinction coefficient of 133 000 mol−1.L.cm−1, it is, to our knowledge, the brightest dimeric fluorescent protein available, and brighter than most of the monomeric YFPs. Contrasting with EYFP and its derivatives, tdLanYFP has a very high photostability in vitro and preserves this property in live cells. As a consequence, tdLanYFP allows the imaging of cellular structures with sub-diffraction resolution with STED nanoscopy. We also demonstrate that the combination of high brightness and strong photostability is compatible with the use of spectro-microscopies in single molecule regimes. Its very low pK1/2 of 3.9 makes tdLanYFP an excellent tag even at acidic pHs. Finally, we show that tdLanYFP can be a FRET partner either as donor or acceptor in different biosensing modalities. Altogether, these assets make tdLanYFPa very attractive yellow fluorescent protein for long-term or single-molecule live-cell imaging that is also suitable for FRET experiment including at acidic pH.

scholarly journals CRISPR-mediated Multiplexed Live Cell Imaging of Nonrepetitive Genomic Loci

2020 ◽  
Author(s):  
Patricia A. Clow ◽  
Nathaniel Jillette ◽  
Jacqueline J. Zhu ◽  
Albert W. Cheng
Keyword(s):  
Live Cell Imaging ◽  
Cell Imaging ◽  
Repetitive Sequences ◽  
Binary Sequence ◽  
Three Dimensional ◽  
Live Cell ◽  
Live Cells ◽  
Imaging Method ◽  
Genomic Locus ◽  
Time Dynamics

AbstractThree-dimensional (3D) structures of the genome are dynamic, heterogeneous and functionally important. Live cell imaging has become the leading method for chromatin dynamics tracking. However, existing CRISPR- and TALE-based genomic labeling techniques have been hampered by laborious protocols and low signal-to-noise ratios (SNRs), and are thus mostly applicable to repetitive sequences. Here, we report a versatile CRISPR/Casilio-based imaging method, with an enhanced SNR, that allows for one nonrepetitive genomic locus to be labeled using a single sgRNA. We constructed Casilio dual-color probes to visualize the dynamic interactions of cohesin-bound elements in single live cells. By forming a binary sequence of multiple Casilio probes (PISCES) across a continuous stretch of DNA, we track the dynamic 3D folding of a 74kb genomic region over time. This method offers unprecedented resolution and scalability for delineating the dynamic 4D nucleome.One Sentence SummaryCasilio enables multiplexed live cell imaging of nonrepetitive DNA loci for illuminating the real-time dynamics of genome structures.

scholarly journals Regeneration of the neurogliovascular unit visualized in vivo by transcranial live-cell imaging

2020 ◽  
Vol 343 ◽  
pp. 108808 ◽  
Author(s):  
Margarita Arango-Lievano ◽  
Yann Dromard ◽  
Pierre Fontanaud ◽  
Chrystel Lafont ◽  
Patrice Mollard ◽  
...  
Keyword(s):  
Live Cell Imaging ◽  
Cell Imaging ◽  
Live Cell

scholarly journals CRISPR/dual-FRET molecular beacon for sensitive live-cell imaging of non-repetitive genomic loci

2019 ◽  
Vol 47 (20) ◽  
pp. e131-e131 ◽  
Author(s):  
Shiqi Mao ◽  
Yachen Ying ◽  
Xiaotian Wu ◽  
Christopher J Krueger ◽  
Antony K Chen
Keyword(s):  
Live Cell Imaging ◽  
Cell Imaging ◽  
Molecular Beacon ◽  
Fluorescent Protein ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Dynamic Imaging ◽  
Molecular Beacons ◽  
Imaging Systems ◽  
Guide Rna

Abstract Clustered regularly interspaced short palindromic repeats (CRISPR)-based genomic imaging systems predominantly rely on fluorescent protein reporters, which lack the optical properties essential for sensitive dynamic imaging. Here, we modified the CRISPR single-guide RNA (sgRNA) to carry two distinct molecular beacons (MBs) that can undergo fluorescence resonance energy transfer (FRET) and demonstrated that the resulting system, CRISPR/dual-FRET MB, enables dynamic imaging of non-repetitive genomic loci with only three unique sgRNAs.

scholarly journals Live Cell Imaging: 3-Dimensional Tracking of Non-blinking ‘Giant’ Quantum Dots in Live Cells (Adv. Funct. Mater. 30/2014)

2014 ◽  
Vol 24 (30) ◽  
pp. 4795-4795 ◽  
Author(s):  
Aaron M. Keller ◽  
Yagnaseni Ghosh ◽  
Matthew S. DeVore ◽  
Mary E. Phipps ◽  
Michael H. Stewart ◽  
...  
Keyword(s):  
Quantum Dots ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Live Cell ◽  
Live Cells ◽  
3 Dimensional

scholarly journals Label-free and live cell imaging by interferometric scattering microscopy

2018 ◽  
Vol 9 (10) ◽  
pp. 2690-2697 ◽  
Author(s):  
Jin-Sung Park ◽  
Il-Buem Lee ◽  
Hyeon-Min Moon ◽  
Jong-Hyeon Joo ◽  
Kyoung-Hoon Kim ◽  
...  
Keyword(s):  
Live Cell Imaging ◽  
Cell Imaging ◽  
Complex Structure ◽  
Live Cell ◽  
Fluorescent Label ◽  
Live Cells ◽  
Label Free ◽  
Cytoplasmic Organelles ◽  
Microscopic Techniques

Despite recent remarkable advances in microscopic techniques, it still remains very challenging to directly observe the complex structure of cytoplasmic organelles in live cells without a fluorescent label.

An aggregation-induced phosphorescence probe for calcium ion-specific detection and live-cell imaging in Arabidopsis thaliana

2019 ◽  
Vol 55 (33) ◽  
pp. 4841-4844 ◽  
Author(s):  
Guilin Chen ◽  
Zaicai Zhou ◽  
Hui Feng ◽  
Chenyan Zhang ◽  
Yifan Wang ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Calcium Ion ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Live Cell ◽  
Molecular Probe ◽  
Specific Detection ◽  
Phosphorescence Probe

A molecular probe with aggregation-induced phosphorescence (AIP) properties for calcium ion-specific detection and imaging in vivo was designed.

scholarly journals Detection and Characterization of Protein Interactions In Vivo by a Simple Live-Cell Imaging Method

PLoS ONE ◽  
2013 ◽  
Vol 8 (5) ◽  
pp. e62195 ◽  
Author(s):  
Oriol Gallego ◽  
Tanja Specht ◽  
Thorsten Brach ◽  
Arun Kumar ◽  
Anne-Claude Gavin ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Live Cell ◽  
Imaging Method
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