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Cotranscriptional RNA Chemical Probing
2022Cotranscriptional folding is a fundamental step in RNA biogenesis and the basis for many RNA-mediated gene regulation systems. Understanding how RNA folds as it is synthesized requires experimental methods that can systematically identify intermediate RNA structures that form during transcription.
Courtney E, Szyjka, Eric J, Strobel
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Nature Protocols, 2007
At the heart of microbial ecology lies a true scientific dichotomy. On the one hand, we know microbes are responsible for processes on which all other life on Earth is dependent; their removal would mean the cessation of all known life. However, in opposition, the majority of extant microbial species in natural environments have never been cultured or ...
Andrew S, Whiteley +3 more
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At the heart of microbial ecology lies a true scientific dichotomy. On the one hand, we know microbes are responsible for processes on which all other life on Earth is dependent; their removal would mean the cessation of all known life. However, in opposition, the majority of extant microbial species in natural environments have never been cultured or ...
Andrew S, Whiteley +3 more
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RNA imaging by chemical probes
Advanced Drug Delivery Reviews, 2019Sequence-specific detection of intracellular RNA is one of the most important approaches to understand life phenomena. However, it is difficult to detect RNA in living cells because of its variety and scarcity. In the last three decades, several chemical probes have been developed for RNA detection in living cells.
Fumiaki, Tomoike, Hiroshi, Abe
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RNA Stable Isotope Probing (RNA-SIP)
2019Stable isotope probing is a combined molecular and isotopic technique used to probe the identity and function of uncultivated microorganisms within environmental samples. Employing stable isotopes of common elements such as carbon and nitrogen, RNA-SIP exploits an increase in the buoyant density of RNA caused by the active metabolism and incorporation ...
Noor-Ul-Huda, Ghori +6 more
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Structural Probing of RNA Thermosensors
2009Chemical probing of RNA structure has become one of the most popular approaches to map the conformation of RNA molecules of various sizes under well-defined experimental conditions. The method monitors the sensitivity of each nucleotide to various chemicals, which reflects its hydrogen-bonding environment within the RNA molecule.
Chiaruttini, C. +2 more
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Probing the RNA–protein interface
Nature Reviews Genetics, 2020Corley et al. report fSHAPE, a simplified strategy for in vivo transcriptome-wide footprinting with SHAPE structure-probing techniques.
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RNA structure probing uncovers RNA structure-dependent biological functions
Nature Chemical Biology, 2021RNA molecules fold into complex structures that enable their diverse functions in cells. Recent revolutionary innovations in transcriptome-wide RNA structural probing of living cells have ushered in a new era in understanding RNA functions. Here, we summarize the latest technological advances for probing RNA secondary structures and discuss striking ...
Xi-Wen Wang +3 more
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Probing RNA Translocases with DNA
2014For some helicases, it is possible to investigate RNA translocase activity on DNA substrates because the enzyme acts on both substrates. Potassium permanganate (KMnO4) footprinting is a method used to chemically probe the conformation of DNA as well as the binding of proteins.
Kimberly A, Reynolds +2 more
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Probing RNA Structure Within Living Cells
2009RNA folding is the most fundamental process underlying RNA function. RNA structure and associated folding paradigms have been intensively studied in vitro. However, in vivo RNA structure formation has only been explored to a limited extent. To determine the influence of the cellular environment, which differs significantly from the in vitro refolding ...
Liebeg, Andreas, Waldsich, Christina
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