Tracking the Dynamic Folding and Unfolding of RNA G‐Quadruplexes in Live Cells

Chen, Xiu‐Cai; Chen, Shuo‐Bin; Dai, Jing; Yuan, Jiahao; Ou, Tian‐Miao; Huang, Zhi‐Shu; Tan, Jia‐Heng

doi:10.1002/ange.201801999

Cited by 50 publications

(51 citation statements)

References 43 publications

(13 reference statements)

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“…QUMA 1w as ah it that selectively stained RNA in HeLa cells duringa ne nzyme-digestion-based screening of an in-house compound library (Figure 10 c). [66] The hit compound exhibited desired (or more) properties that allowed the visualization of RNA G4 dynamics in live cells. ISCH-nras was uniquely developedf or the detection of ap articularR NA quadruplex (NRAS), based on the hybridization of at ail RNA sequence adjacent to aG -rich sequenceb yaDNA molecule connected to aq uadruplex-triggered fluorescent probe (Figure 10 d).…”

Section: Specific Targeting Of Telomere G4smentioning

confidence: 99%

“…Cell‐based screening of G4 ligands, as mentioned previously, was also effective in this case. QUMA 1 was a hit that selectively stained RNA in HeLa cells during an enzyme‐digestion‐based screening of an in‐house compound library (Figure c) . The hit compound exhibited desired (or more) properties that allowed the visualization of RNA G4 dynamics in live cells.…”

Section: Addressing the Specificity Of Ligands To Particular G4smentioning

confidence: 99%

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Ligand Design to Acquire Specificity to Intended G‐Quadruplex Structures

Asamitsu

Bando

Sugiyama

2018

Chemistry A European J

140

116

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A G-quadruplex is a nucleic acid secondary structure that is adopted by guanine-rich sequences, and is considered to be relevant in various pharmacological and biological contexts. G-Quadruplexes have also attracted great attention in the field of DNA nanotechnology because of their extremely high thermal stability and the availability of many defined structures. To date, a large repertory of DNA/RNA G-quadruplex-interactive ligands has been developed by numerous laboratories. Several relevant reviews have also been published that have helped researchers to grasp the full scope of G-quadruplex research from its outset to the present. This review focuses on the G-quadruplex ligands that allow targeting of specific G-quadruplexes. Moreover, unique ligands, successful methodologies, and future perspectives in relation to specific G-quadruplex recognition are also addressed.

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Section: Specific Targeting Of Telomere G4smentioning

confidence: 99%

Section: Addressing the Specificity Of Ligands To Particular G4smentioning

confidence: 99%

Ligand Design to Acquire Specificity to Intended G‐Quadruplex Structures

Asamitsu

Bando

Sugiyama

2018

Chemistry A European J

140

116

View full text Add to dashboard Cite

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“…G-quartets in G4s are additionally stabilized by monovalent cations, in which Li + < NH4 + < Na + < K +1 . RNA G4s (rG4s) have previously been visualized in both fixed and live cells using G4-specific antibodies and G4-specific fluorescence probes 4–7 . Numerous studies have suggested that rG4s regulate processes such as transcription, RNA splicing, translation and RNA metabolism 8 .…”

Section: Introductionmentioning

confidence: 99%

rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments

Chow

Lyu

Kwok

et al. 2020

Preprint

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ABSTRACTWe recently developed the rG4-seq method to detect and map in vitro RNA G-quadruplex (rG4s) structures on a transcriptome-wide scale. rG4-seq of purified human HeLa RNA has revealed many non-canonical rG4s and the effects adjacent sequences have on rG4 formation. In this study, we aimed to improve the outcomes and false-positive discrimination in rG4-seq experiments using a bioinformatic approach. By establishing connections between rG4-seq library preparation chemistry and the underlying properties of sequencing data, we identified how to mitigate indigenous sampling errors and background noise in rG4-seq. We applied these findings to develop a novel bioinformatics pipeline named rG4-seeker(https://github.com/TF-Chan-Lab/rG4-seeker), which uses tailored noise models to autonomously assess and optimize rG4 detections in a replicate-independent manner. Compared with previous methods, rG4-seeker exhibited better false-positive discrimination and improved sensitivity for non-canonical rG4s. Using rG4-seeker, we identified novel features in rG4 formation that were missed previously. rG4-seeker provides a reliable and sensitive approach for rG4-seq investigations, laying the foundations for further elucidation of rG4 biology.

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“…Meanwhile, to verify the Mito‐Cy‐involved mitochondria viscosity imaging, the fluorescence imaging experiments of Mito‐Cy‐stained MCF‐7 cells have been explored by introducing nystatin that increases the mitochondrial viscosity, or DNase I that degrades the intracellular DNA . Our mitochondria‐localized Mito‐Cy probe exhibits obvious red fluorescence enhancement in nystatin‐pretreated MCF‐7 cells, yet it shows negligible fluorescence changes after treatment with DNase I (Figure S7, Supporting Information).…”

Section: Resultsmentioning

confidence: 99%

Spatiotemporally Tracking the Programmable Mitochondrial Membrane Potential Evolutions by a Robust Molecular Rotor

Tan

Chen

et al. 2019

Small

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potential (MMP) is a vital parameter for reflecting the real-time status of mitochondrial function, and is thus closely correlated to cellular activities and functions. [3] Normal MMP maintains the efficient ATP synthesis and an appropriate proton gradient across the lipid bilayer, which plays a vital role in cell division and apoptosis. On the contrary, a minute MMP change could largely affect the mitochondrial functions. The aberrant MMP change has been frequently recognized as an early signal event for irreversible cell apoptosis, making the investigation of MMP variation a research focus in biological and biomedical researches. Moreover, the constant MMP fluctuations of intracellular physiological processes bring obstacles to the in situ MMP detection in living cells. Therefore, it is highly desirable and challenging to explore more robust and versatile approaches for monitoring the intracellular MMP fluctuations in realtime at a single-cell level.Fluorescent probes have attracted substantial attentions in biological researches for its high sensitivity and noninvasion capacity in combination with the real-time fluorescence imaging technique. [4] To date, plenty of fluorescence probes have been developed for monitoring MMP variations. [5] These probes are mainly based on the signal transduction between mitochondria and cytosol, such as rhodamine 123 (Rh 123), [5a] yet it is difficult to judge the decreased and vanished status of MMP just by fluorescence distribution owing to the ambiguous boundary between mitochondria and the surrounding cytosol. An alternative kind of fluorescent dichromatic probe JC-1, [6] with a moderate anti-interference feature, was then developed for discriminating these different MMP states based on an intramitochondria signal transduction mechanism, yet the inconvenient usage, low sensitivity, and limited photostability need to be solved before their extensive applications can be envisaged. Thus, it is essential to develop a robust and sensitive fluorescent probe for conveniently and accurately evaluating minute MMP fluctuations, such as normal, decreased, and vanished status.The ambiguous biointerface of mitochondria inspired us to utilize an alternative cellular compartment with distinct boundary for highly sensitive investigation of MMP variations. Considering that nucleus is spatially independent of cytosol, and thus there exists a distinct boundary between mitochondria Mitochondrial membrane potential (MMP) represents an essential parameter of cellular activities, and even a minute MMP variation could significantly affect the biological functions of living organisms. Thus, convenient and accurate MMP detection is highly desirable since conventional MMP probes are always constrained by photobleaching, inconvenience, and irreversibility. Herein, a spatial-dependent fluorescent molecular rotor Mito-Cy is introduced for efficiently tracking the varied MMP status through its restricted intramolecular rotation in mitochondria and nucleus compartments. Based on a systematic investig...

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Tracking the Dynamic Folding and Unfolding of RNA G‐Quadruplexes in Live Cells

Cited by 50 publications

References 43 publications

Ligand Design to Acquire Specificity to Intended G‐Quadruplex Structures

Ligand Design to Acquire Specificity to Intended G‐Quadruplex Structures

rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments

Spatiotemporally Tracking the Programmable Mitochondrial Membrane Potential Evolutions by a Robust Molecular Rotor

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