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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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In Situ Hybridization for RNA: Nonradioactive Probe: RNA Probe
2000Non-radioactive in situ hybridization method is now widely used to detect nucleic acid in tissue sections. However, the results for the detection of tissue mRNA are not always consistent. We have to consider several factors for this purpose. We describe our current methods for the most consistent detection.
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Chemical Probing of RNA and RNA/Protein Complexes
2009Chemical probing is widely used as a rapid approach for assessing RNA structure, folding, and function. In this chapter, we outline procedures for handling and using chemicals commonly used to probe nucleic acids. Detailed experimental conditions and design for footprinting and modification interference are presented herein.
Zhili, Xu, Gloria M, Culver
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Genetic probes of ribosomal RNA function
Biochemistry and Cell Biology, 1995We have used a genetic approach to uncover the functional roles of rRNA in protein synthesis. Mutations were constructed in a cloned rrn operon by site-directed mutagenesis or isolated by genetic selections following random mutagenesis. We have identified mutations that affect each step in the process of translation.
M, O'Connor +8 more
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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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Modern methods for probing RNA structure
Current Opinion in Biotechnology, 1998Molecular biologists have been remarkably successful in dividing large RNAs into small functional modules manageable for NMR and X-ray studies. At the same time biophysical, biochemical and genetic tools in RNA structure determination have reached a level of sophistication, at which we start to see a glimpse of molecular dynamics and the mechanism of ...
J, Kjems, J, Egebjerg
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Terbium as a solid-state probe for RNA
Bioinorganic Chemistry, 1978This paper continues previous work on the analysis of nucleic acid-terbium complexes in the solid state. The fluorescence excitation and emission spectra of the RNA-terbium(III) complex is reported. The fluorescence excitation and emission spectra of both the RNA-terbium(III) and DNA-terbium(III) complexes as trapped on millipore filters is reported ...
G, Yonuschot +4 more
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RNA Remodeling by RNA Chaperones Monitored by RNA Structure Probing
2019RNA structure probing enables the characterization of RNA secondary structures by established procedures such as the enzyme- or chemical-based detection of single- or double-stranded regions. A specific type of application involves the detection of changes of RNA structures and conformations that are induced by proteins with RNA chaperone activity ...
Susann, Friedrich +2 more
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Antisense probing of dynamic RNA structures
Methods, 2020RNA regulation is influenced by the dynamic changes in conformational accessibility on the transcript. Here we discuss the initial validation of a cell-free antisense probing method for structured RNAs, using the Tetrahymena group I intron as a control target.
Alexandra J, Lukasiewicz +1 more
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The RNA structurome: high-throughput probing
Nature Methods, 2010Novel deep-sequencing strategies are used to monitor, at the genomic scale, the structure of cellular RNAs using enzymatic probing.
Westhof, Eric, Romby, Pascale
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