Effect of hydrostatic pressure upon ethidium bromide association with transfer ribonucleic acid. 1980

P M Torgerson, and H G Drickamer, and G Weber

The binding of ethidium bromide to yeast phenylalanine-specific transfer ribonucleic acid (tRNAPhe) has been investigated in the pressure range from 1 atm to 9 kbar in the presence of 100 mM sodium chloride and 10 mM magnesium chloride, pH 7.7. One high-affinity binding site for ethidium is present, with a dissociation constant of 2.4 X 10(-6) M at 1 atm and 22 degrees C. Binding to this site is enhanced with increasing pressure, the dissociation constant reaching 2.9 X 10(-7) M at 2 kbar. Pressure also promotes the binding of ethidium to lower affinity sites of tRNAPhe. The standard volume change upon complex formation is found to be 25.6 +/- mL/mol for the first ethidium bound. If sodium is replaced by lithium in the buffer, the standard volume change is 23.3 +/- 0.5 mL/mol. We conclude that decrease of the electrostatic repulsion in the negatively charged tRNAPhe by binding of the positively charged ethidium is the main cause of the relatively large volume decrease upon complex formation. The electrostatic repulsion that must be present in this case, as well as in other nucleic acids, implies that intercalating binding sites are of the "soft" type as previously defined [Torgerson, P.M., Drickamer, H.G., & Weber, G. (1979) Biochemistry 18, 3079]. Model studies by others of the binding site characteristics are in agreement with this concept.

UI MeSH Term Description Entries
D007700 Kinetics The rate dynamics in chemical or physical systems.
D008274 Magnesium A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.
D008433 Mathematics The deductive study of shape, quantity, and dependence. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Mathematic
D011312 Pressure A type of stress exerted uniformly in all directions. Its measure is the force exerted per unit area. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Pressures
D002621 Chemistry A basic science concerned with the composition, structure, and properties of matter; and the reactions that occur between substances and the associated energy exchange.
D004996 Ethidium A trypanocidal agent and possible antiviral agent that is widely used in experimental cell biology and biochemistry. Ethidium has several experimentally useful properties including binding to nucleic acids, noncompetitive inhibition of nicotinic acetylcholine receptors, and fluorescence among others. It is most commonly used as the bromide. Ethidium Bromide,Homidium Bromide,Novidium,Bromide, Ethidium,Bromide, Homidium
D006874 Hydrostatic Pressure The pressure due to the weight of fluid. Hydrostatic Pressures,Pressure, Hydrostatic,Pressures, Hydrostatic
D012343 RNA, Transfer The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains. Suppressor Transfer RNA,Transfer RNA,tRNA,RNA, Transfer, Suppressor,Transfer RNA, Suppressor,RNA, Suppressor Transfer
D012965 Sodium Chloride A ubiquitous sodium salt that is commonly used to season food. Sodium Chloride, (22)Na,Sodium Chloride, (24)NaCl
D015636 Magnesium Chloride Magnesium chloride. An inorganic compound consisting of one magnesium and two chloride ions. The compound is used in medicine as a source of magnesium ions, which are essential for many cellular activities. It has also been used as a cathartic and in alloys. MgCl2,Chloride, Magnesium

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