Biomaterial Database

Probing RNA folding by hydroxyl radical footprinting. 2014

Maria Costa, and Dario Monachello

Centre de Génétique Moléculaire du C.N.R.S., Gif-sur-Yvette, France.

In recent years RNA molecules have emerged as central players in the regulation of gene expression. Many of these noncoding RNAs possess well-defined, complex, three-dimensional structures which are essential for their biological function. In this context, much effort has been devoted to develop computational and experimental techniques for RNA structure determination. Among available experimental tools to investigate the higher-order folding of structured RNAs, hydroxyl radical probing stands as one of the most informative and reliable ones. Hydroxyl radicals are oxidative species that cleave the nucleic acid backbone solely according to the solvent accessibility of individual phosphodiester bonds, with no sequence or secondary structure specificity. Therefore, the cleavage pattern obtained directly reflects the degree of protection/exposure to the solvent of each section of the molecule under inspection, providing valuable information about how these different sections interact together to form the final three-dimensional architecture. In this chapter we describe a robust, accurate and very sensitive hydroxyl radical probing method that can be applied to any structured RNA molecule and is suitable to investigate RNA folding and RNA conformational changes induced by binding of a ligand.

UI	MeSH Term	Description	Entries
D009690	Nucleic Acid Conformation	The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.	DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D004492	Edetic Acid	A chelating agent that sequesters a variety of polyvalent cations such as CALCIUM. It is used in pharmaceutical manufacturing and as a food additive.	EDTA,Edathamil,Edetates,Ethylenediaminetetraacetic Acid,Tetracemate,Calcium Disodium Edetate,Calcium Disodium Versenate,Calcium Tetacine,Chelaton 3,Chromium EDTA,Copper EDTA,Coprin,Dicobalt EDTA,Disodium Calcitetracemate,Disodium EDTA,Disodium Ethylene Dinitrilotetraacetate,Distannous EDTA,Edetate Disodium Calcium,Edetic Acid, Calcium Salt,Edetic Acid, Calcium, Sodium Salt,Edetic Acid, Chromium Salt,Edetic Acid, Dipotassium Salt,Edetic Acid, Disodium Salt,Edetic Acid, Disodium Salt, Dihydrate,Edetic Acid, Disodium, Magnesium Salt,Edetic Acid, Disodium, Monopotassium Salt,Edetic Acid, Magnesium Salt,Edetic Acid, Monopotassium Salt,Edetic Acid, Monosodium Salt,Edetic Acid, Potassium Salt,Edetic Acid, Sodium Salt,Ethylene Dinitrilotetraacetate,Ethylenedinitrilotetraacetic Acid,Gallium EDTA,Magnesium Disodium EDTA,N,N'-1,2-Ethanediylbis(N-(carboxymethyl)glycine),Potassium EDTA,Stannous EDTA,Versenate,Versene,Acid, Edetic,Acid, Ethylenediaminetetraacetic,Acid, Ethylenedinitrilotetraacetic,Calcitetracemate, Disodium,Dinitrilotetraacetate, Disodium Ethylene,Dinitrilotetraacetate, Ethylene,Disodium Versenate, Calcium,EDTA, Chromium,EDTA, Copper,EDTA, Dicobalt,EDTA, Disodium,EDTA, Distannous,EDTA, Gallium,EDTA, Magnesium Disodium,EDTA, Potassium,EDTA, Stannous,Edetate, Calcium Disodium,Ethylene Dinitrilotetraacetate, Disodium,Tetacine, Calcium,Versenate, Calcium Disodium
D005296	Ferrous Compounds	Inorganic or organic compounds that contain divalent iron.	Compounds, Ferrous
D012313	RNA	A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)	RNA, Non-Polyadenylated,Ribonucleic Acid,Gene Products, RNA,Non-Polyadenylated RNA,Acid, Ribonucleic,Non Polyadenylated RNA,RNA Gene Products,RNA, Non Polyadenylated
D014158	Transcription, Genetic	The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.	Genetic Transcription
D017665	Hydroxyl Radical	The univalent radical OH. Hydroxyl radical is a potent oxidizing agent.
D058645	Denaturing Gradient Gel Electrophoresis	Electrophoresis in which various denaturant gradients are used to induce nucleic acids to melt at various stages resulting in separation of molecules based on small sequence differences including SNPs. The denaturants used include heat, formamide, and urea.	Temperature Gradient Gel Electrophoresis
D059370	RNA Folding	The processes of RNA tertiary structure formation.	RNA Refolding,RNA Unfolding,Folding, RNA,Foldings, RNA,RNA Foldings,RNA Refoldings,RNA Unfoldings,Refolding, RNA,Refoldings, RNA,Unfolding, RNA,Unfoldings, RNA
D017931	DNA Primers	Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.	DNA Primer,Oligodeoxyribonucleotide Primer,Oligodeoxyribonucleotide Primers,Oligonucleotide Primer,Oligonucleotide Primers,Primer, DNA,Primer, Oligodeoxyribonucleotide,Primer, Oligonucleotide,Primers, DNA,Primers, Oligodeoxyribonucleotide,Primers, Oligonucleotide