Use of terbium(III) fluorescence enhancement to selectively monitor DNA and RNA guanine residues and their alteration by chemical modification

Ringer, David P.; Burchett, Stuart; Kizer, Donald E.

doi:10.1021/bi00615a032

Cited by 68 publications

(25 citation statements)

References 33 publications

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“…Thus far there has been no specific staining method for RNA in ultrastructural cytochemistry. Available data suggest that Tb ions in their oxidation form 3 ϩ can interact with single-stranded nucleic acids (Hörer et al 1977) at their guanine sites (Ringer et al 1978), at the phosphate in unpaired residues (Topal and Fresco 1980), and particularly with guanosine monophosphate in RNA (Ringer et al 1980).…”

Section: Discussionmentioning

confidence: 99%

“…Recently a renewed interest has characterized several studies involving the use of elements of the lanthanide family, such as europium and terbium. Data in the literature point out that these ions in their oxidation form 3 ϩ can interact with single-stranded nucleic acids (Hörer et al 1977) at their guanine sites (Ringer et al 1978), at the phosphate in unpaired residues (Topal and Fresco 1980), and especially with guanosine monophosphate in RNA (Ringer et al 1980). At the electron microscopic (EM) level, these ions (particularly lanthanum) have been known to precipitate in the presence of phosphate groups (Hayat 1993), and members of the family, such as cerium, are now routinely used for EM detection of phosphatase activity (Van Noorden and Frederiks 1993).…”

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Fine Structural Specific Visualization of RNA on Ultrathin Sections

Biggiogera

Fakan²

1998

J Histochem Cytochem.

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SUMMARYWe describe a new technique that allows specific visualization of RNA at the electron microscopic level by means of terbium citrate. Under the conditions presented here, terbium binds selectively to RNA and stains nucleoli, interchromatin granules, perichromatin fibrils, perichromatin granules, and coiled bodies in the cell nucleus, whereas ribosomes are the only contrasted structures in the cytoplasm. All the cell components contrasted by terbium are known to contain RNA. When ultrathin sections are pretreated with RNase A or nuclease S1 (specific for single-stranded nucleic acids), staining does not occur. Neither DNase nor pronase influences the reaction. We conclude that terbium staining is selective for RNA and especially for single-stranded RNA. The staining can be performed on thin sections of material embedded both in epoxy and in acrylic resins. The technique is not influenced by the aldehyde fixative used and can also be utilized after immunolabeling. The endproduct is very fine and, although weak in contrast, is suitable for high-resolution observations. (J Histochem Cytochem 46:389-395, 1998)

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Fine Structural Specific Visualization of RNA on Ultrathin Sections

Biggiogera

Fakan²

1998

J Histochem Cytochem.

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“…22,23 Also, their ability to substitute Zn(II) 24,25 and Mg(II) at their binding sites makes lanthanide luminescence a useful tool to study interaction between DNA and these ions. [26][27][28][29] In addition, polyelectrolyte/lanthanide ion systems are amenable to modeling by Monte Carlo and other techniques, which can help provide a more detailed understanding of the binding behavior. 30 The luminescence of the lanthanide ions arises from f f f electron transitions and this can give information on both the coordination environment 31,32 and degree of hydration of these ions.…”

Section: Introductionmentioning

confidence: 99%

Changes in Hydration of Lanthanide Ions on Binding to DNA in Aqueous Solution

2005

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The interaction of the trivalent lanthanides Ce(III), Eu(III), and Tb(III) with sodium deoxyribonucleic acid (DNA) in aqueous solution has been studied using their luminescence spectra and decays. Complexation with DNA is indicated by changes in luminescence intensity. In the system terbium(III)-DNA, changes in luminescence with pH are suggested to be due to the protonation of phosphate groups. The degree of hydration of Tb(III) on binding to DNA is followed by luminescence lifetime measurements in water and deuterium oxide solutions, and it is found that the lanthanide ion loses at least one hydration water on binding to long double stranded DNA at pH 4.7 and pH 7. Rather different behavior is observed on binding to long or short single stranded DNA, where six water molecules are lost, independent of pH. It is suggested that in this case the lanthanide probably binds to the bases of the DNA backbone. The DNA conformation seems to be an important factor in the binding. In addition, the isotopic effect on terbium luminescence lifetime may provide a useful method to distinguish between single and double stranded DNA. DSC results are consistent with cleavage of the double helix of DNA at pH 9 in the presence of terbium.

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“…Guanine and poly-guanines in both DNA and RNA have been shown to have high affinity towards lanthanides. [31][32][33] In the hammerhead ribozyme, the binding of Tb 3+ also points to a single guanine residue. 15 In this work, we compared the relative binding strength of different lanthanides.…”

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The group trend of lanthanides binding to DNA and DNAzymes with a complex but symmetric pattern

et al. 2014

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Using sensitized Tb 3+ luminescence spectroscopy as a tool, binding of 14 lanthanides to a lanthanide-dependent DNAzyme is studied, where the binding affinity is symmetric cross the series and the tightest binding occurs with Nd 3+ and Ho 3+ . This trend does not correlate with DNAzyme activity, suggesting that metal binding may not be the rate-limiting step of the DNAzyme catalysis.Lanthanides refer to the elements in the periodic table from La to Lu. Beyond their critical roles in modern technologies, lanthanides also emerge as important probes for biology and medicine. 1,2 In particular, they have been extensively used to study the structure and function of nucleic acids. These applications take advantage of a few of their unique properties. First, lanthanides and their complexes can efficiently cleave nucleic acids, 3 and thus are used as RNA structural probes 4 and DNA cleaving agents. 5 In addition, a number of in vitro selection experiments were carried out using lanthanides as metal cofactors to obtain DNA-based catalysts (so called DNAzymes 6-12 ) for RNA or DNA cleavage. 13,14 Second, a few lanthanides (especially Tb 3+ ) are luminescent and DNA can act as an antenna to increase their light absorption and thus emission intensity. This is useful for probing metal binding sites, 15 and for developing biosensors. 16 Third, lanthanides are hard Lewis acids and some have a similar size as Ca 2+ . Lanthanides can compete with other metal ions in enzymes and act as enzyme inhibitors. For example, both the 17E DNAzyme and the hammerhead ribozyme are inhibited by lanthanides. 15,17 On the other hand, the Leadzyme and a DNA-based ligase are accelerated by lanthanides. [18][19][20] All these examples suggest strong interactions between lanthanides and nucleic acids. Finally, nucleotides and lanthanides can form coordination complexes with useful luminescence and DNA binding properties. [21][22][23][24] Given these progresses, few studies explored the binding of the whole lanthanide series with DNA or correlated metal binding with enzyme activity. Such studies are important for revealing the coordination chemistry of lanthanides, and for DNA bioinorganic chemistry in general. 25,26 We recently performed an in vitro selection experiment using Ce 4+ as the intended metal cofactor. The selected DNAzyme (named Ce13d) was found to have similar activity with all trivalent lanthanides. 14 Therefore, Ce13d must bind all the lanthanides and this DNAzyme might provide a good scaffold for studying lanthanide binding. Herein, we employed Tb 3+ luminescence as a tool to study lanthanide binding to DNAzymes and its relation to catalytic activity. The secondary structure of the Ce13d DNAzyme complex is shown in Figure 1A. It consists of a substrate strand named Sub-rA with a single RNA linkage (rA, ribo-adenosine), and an enzyme strand named Ce13d. In the presence of a trivalent lanthanide, the substrate is cleaved into two fragments at the position pointed by the arrowhead. Lanthanides alone can catalyze the reaction and no div...

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Use of terbium(III) fluorescence enhancement to selectively monitor DNA and RNA guanine residues and their alteration by chemical modification

Cited by 68 publications

References 33 publications

Fine Structural Specific Visualization of RNA on Ultrathin Sections

Fine Structural Specific Visualization of RNA on Ultrathin Sections

Changes in Hydration of Lanthanide Ions on Binding to DNA in Aqueous Solution

The group trend of lanthanides binding to DNA and DNAzymes with a complex but symmetric pattern

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