The Experts below are selected from a list of 123 Experts worldwide ranked by ideXlab platform

Claude Hélène - One of the best experts on this subject based on the ideXlab platform.

  • Intercalation of Ethidium bromide into a triple-stranded oligonucleotide
    Nucleic acids research, 1991
    Co-Authors: Jean-louis Mergny, David A. Collier, Michel Rougee, Thérèse Montenay-garestier, Claude Hélène
    Abstract:

    We have examined the ability of a cationic planar chromophore, Ethidium bromide, to intercalate into a short, defined triple helix. Using UV absorption, fluorescence spectroscopy and a gel retardation assay we demonstrate that Ethidium bromide is able to bind to a triple helix with a lower affinity than to the corresponding duplex. Energy transfer from base triplets to Ethidium shows that Ethidium is intercalated into the triple helix. The spectroscopic characteristics of Ethidium intercalated into a triplex are similar to those observed for intercalation into duplex DNA.

  • Theoretical study of Ethidium intercalation in triple-stranded DNA and at triplex-duplex junctions.
    J Biomol Struct Dyn, 1991
    Co-Authors: Js Sun, Thérèse Montenay-garestier, R. Lavery, J. Chomilier, K. Zakrzewska, Claude Hélène
    Abstract:

    The contribution of different factors in the interaction of Ethidium intercalated into various sequences of a triple helix, or in the region of the junction between the double- and triple-stranded DNA has been studied by energy minimization. It is found that in the total energy of the Ethidium- triple helix complexes, a particular electrostatic contribution emerges due to the presence of protonated cytosines in the triple helix. This parameters is determinant in the sequence-specificity of Ethidium binding to the triple helix. The preferred intercalation sites of Ethidium in the triple helix are proposed. The interaction of Ethidium at the triplex-duplex junction, and its effects are also discussed. This study is aimed at searching for new drugs specific for the triple helix, or for the triplex-duplex junctions.The contribution of different factors in the interaction of Ethidium intercalated into various sequences of a triple helix, or in the region of the junction between the double- and triple-stranded DNA has been studied by energy minimization. It is found that in the total energy of the Ethidium- triple helix complexes, a particular electrostatic contribution emerges due to the presence of protonated cytosines in the triple helix. This parameters is determinant in the sequence-specificity of Ethidium binding to the triple helix. The preferred intercalation sites of Ethidium in the triple helix are proposed. The interaction of Ethidium at the triplex-duplex junction, and its effects are also discussed. This study is aimed at searching for new drugs specific for the triple helix, or for the triplex-duplex junctions.

  • Theoretical Study of Ethidium Intercalation in Triple-Stranded DNA and at Triplex-Duplex Junctions
    Journal of biomolecular structure & dynamics, 1991
    Co-Authors: Jian-sheng Sun, Thérèse Montenay-garestier, R. Lavery, J. Chomilier, K. Zakrzewska, Claude Hélène
    Abstract:

    Abstract The contribution of different factors in the interaction of Ethidium intercalated into various sequences of a triple helix, or in the region of the junction between the double- and triple-stranded DNA has been studied by energy minimization. It is found that in the total energy of the Ethidium - triple helix complexes, a particular electrostatic contribution emerges due to the presence of protonated cytosines in the triple helix. This parameter is determinant in the sequence-specificity of Ethidium binding to the triple helix. The preferred intercalation sites of Ethidium in the triple helix are proposed. The interaction of Ethidium at the triplex-duplex junction, and its effects are also discussed. This study is aimed at searching for new drugs specific for the triple helix, or for the triplex-duplex junctions.

Walter C Prozialeck - One of the best experts on this subject based on the ideXlab platform.

  • A novel method for the evaluation of proximal tubule epithelial cellular necrosis in the intact rat kidney using Ethidium homodimer
    BMC Physiology, 2007
    Co-Authors: Joshua R Edwards, Evangelos A Diamantakos, Jacob D Peuler, Peter C Lamar, Walter C Prozialeck
    Abstract:

    Background Ethidium homodimer is a cell-membrane impermeant nuclear fluorochrome that has been widely used to identify necrotic cells in culture. Here, we describe a novel technique for evaluating necrosis of epithelial cells in the proximal tubule that involves perfusing Ethidium homodimer through the intact rat kidney. As a positive control for inducing necrosis, rats were treated with 3.5, 1.75, 0.87 and 0.43 mg/kg mercuric chloride (Hg^2+, intraperitoneal), treatments which have previously been shown to rapidly cause dose-dependent necrosis of the proximal tubule. Twenty-four h after the administration of Hg^2+, Ethidium homodimer (5 μM) was perfused through the intact left kidney while the animal was anesthetized. The kidney was then removed, placed in embedding medium, frozen and cryosectioned at a thickness of 5 μm. Sections were permeabilized with -20°C methanol and then stained with 4',6-diamidino-2-phenylindole (DAPI) to label total nuclei. Total cell number was determined from the DAPI staining in random microscopic fields and the number of necrotic cells in the same field was determined by Ethidium homodimer labeling. Results The Hg^2+-treated animals showed a dose-dependent increase in the number of Ethidium labeled cells in the proximal tubule, but not in other segments of the nephron. Other results showed that a nephrotoxic dose of gentamicin also caused a significant increase in the number of Ethidium labeled cells in the proximal tubule. Conclusion These results indicate that this simple and sensitive perfusion technique can be used to evaluate cellular necrosis in the proximal tubule with the three-dimensional cyto-architecture intact.

  • a novel method for the evaluation of proximal tubule epithelial cellular necrosis in the intact rat kidney using Ethidium homodimer
    BMC Physiology, 2007
    Co-Authors: Joshua R Edwards, Evangelos A Diamantakos, Jacob D Peuler, Peter C Lamar, Walter C Prozialeck
    Abstract:

    Ethidium homodimer is a cell-membrane impermeant nuclear fluorochrome that has been widely used to identify necrotic cells in culture. Here, we describe a novel technique for evaluating necrosis of epithelial cells in the proximal tubule that involves perfusing Ethidium homodimer through the intact rat kidney. As a positive control for inducing necrosis, rats were treated with 3.5, 1.75, 0.87 and 0.43 mg/kg mercuric chloride (Hg2+, intraperitoneal), treatments which have previously been shown to rapidly cause dose-dependent necrosis of the proximal tubule. Twenty-four h after the administration of Hg2+, Ethidium homodimer (5 μM) was perfused through the intact left kidney while the animal was anesthetized. The kidney was then removed, placed in embedding medium, frozen and cryosectioned at a thickness of 5 μm. Sections were permeabilized with -20°C methanol and then stained with 4',6-diamidino-2-phenylindole (DAPI) to label total nuclei. Total cell number was determined from the DAPI staining in random microscopic fields and the number of necrotic cells in the same field was determined by Ethidium homodimer labeling. The Hg2+-treated animals showed a dose-dependent increase in the number of Ethidium labeled cells in the proximal tubule, but not in other segments of the nephron. Other results showed that a nephrotoxic dose of gentamicin also caused a significant increase in the number of Ethidium labeled cells in the proximal tubule. These results indicate that this simple and sensitive perfusion technique can be used to evaluate cellular necrosis in the proximal tubule with the three-dimensional cyto-architecture intact.

Joshua R Edwards - One of the best experts on this subject based on the ideXlab platform.

  • A novel method for the evaluation of proximal tubule epithelial cellular necrosis in the intact rat kidney using Ethidium homodimer
    BMC Physiology, 2007
    Co-Authors: Joshua R Edwards, Evangelos A Diamantakos, Jacob D Peuler, Peter C Lamar, Walter C Prozialeck
    Abstract:

    Background Ethidium homodimer is a cell-membrane impermeant nuclear fluorochrome that has been widely used to identify necrotic cells in culture. Here, we describe a novel technique for evaluating necrosis of epithelial cells in the proximal tubule that involves perfusing Ethidium homodimer through the intact rat kidney. As a positive control for inducing necrosis, rats were treated with 3.5, 1.75, 0.87 and 0.43 mg/kg mercuric chloride (Hg^2+, intraperitoneal), treatments which have previously been shown to rapidly cause dose-dependent necrosis of the proximal tubule. Twenty-four h after the administration of Hg^2+, Ethidium homodimer (5 μM) was perfused through the intact left kidney while the animal was anesthetized. The kidney was then removed, placed in embedding medium, frozen and cryosectioned at a thickness of 5 μm. Sections were permeabilized with -20°C methanol and then stained with 4',6-diamidino-2-phenylindole (DAPI) to label total nuclei. Total cell number was determined from the DAPI staining in random microscopic fields and the number of necrotic cells in the same field was determined by Ethidium homodimer labeling. Results The Hg^2+-treated animals showed a dose-dependent increase in the number of Ethidium labeled cells in the proximal tubule, but not in other segments of the nephron. Other results showed that a nephrotoxic dose of gentamicin also caused a significant increase in the number of Ethidium labeled cells in the proximal tubule. Conclusion These results indicate that this simple and sensitive perfusion technique can be used to evaluate cellular necrosis in the proximal tubule with the three-dimensional cyto-architecture intact.

  • a novel method for the evaluation of proximal tubule epithelial cellular necrosis in the intact rat kidney using Ethidium homodimer
    BMC Physiology, 2007
    Co-Authors: Joshua R Edwards, Evangelos A Diamantakos, Jacob D Peuler, Peter C Lamar, Walter C Prozialeck
    Abstract:

    Ethidium homodimer is a cell-membrane impermeant nuclear fluorochrome that has been widely used to identify necrotic cells in culture. Here, we describe a novel technique for evaluating necrosis of epithelial cells in the proximal tubule that involves perfusing Ethidium homodimer through the intact rat kidney. As a positive control for inducing necrosis, rats were treated with 3.5, 1.75, 0.87 and 0.43 mg/kg mercuric chloride (Hg2+, intraperitoneal), treatments which have previously been shown to rapidly cause dose-dependent necrosis of the proximal tubule. Twenty-four h after the administration of Hg2+, Ethidium homodimer (5 μM) was perfused through the intact left kidney while the animal was anesthetized. The kidney was then removed, placed in embedding medium, frozen and cryosectioned at a thickness of 5 μm. Sections were permeabilized with -20°C methanol and then stained with 4',6-diamidino-2-phenylindole (DAPI) to label total nuclei. Total cell number was determined from the DAPI staining in random microscopic fields and the number of necrotic cells in the same field was determined by Ethidium homodimer labeling. The Hg2+-treated animals showed a dose-dependent increase in the number of Ethidium labeled cells in the proximal tubule, but not in other segments of the nephron. Other results showed that a nephrotoxic dose of gentamicin also caused a significant increase in the number of Ethidium labeled cells in the proximal tubule. These results indicate that this simple and sensitive perfusion technique can be used to evaluate cellular necrosis in the proximal tubule with the three-dimensional cyto-architecture intact.

Thérèse Montenay-garestier - One of the best experts on this subject based on the ideXlab platform.

  • Intercalation of Ethidium bromide into a triple-stranded oligonucleotide
    Nucleic acids research, 1991
    Co-Authors: Jean-louis Mergny, David A. Collier, Michel Rougee, Thérèse Montenay-garestier, Claude Hélène
    Abstract:

    We have examined the ability of a cationic planar chromophore, Ethidium bromide, to intercalate into a short, defined triple helix. Using UV absorption, fluorescence spectroscopy and a gel retardation assay we demonstrate that Ethidium bromide is able to bind to a triple helix with a lower affinity than to the corresponding duplex. Energy transfer from base triplets to Ethidium shows that Ethidium is intercalated into the triple helix. The spectroscopic characteristics of Ethidium intercalated into a triplex are similar to those observed for intercalation into duplex DNA.

  • Theoretical study of Ethidium intercalation in triple-stranded DNA and at triplex-duplex junctions.
    J Biomol Struct Dyn, 1991
    Co-Authors: Js Sun, Thérèse Montenay-garestier, R. Lavery, J. Chomilier, K. Zakrzewska, Claude Hélène
    Abstract:

    The contribution of different factors in the interaction of Ethidium intercalated into various sequences of a triple helix, or in the region of the junction between the double- and triple-stranded DNA has been studied by energy minimization. It is found that in the total energy of the Ethidium- triple helix complexes, a particular electrostatic contribution emerges due to the presence of protonated cytosines in the triple helix. This parameters is determinant in the sequence-specificity of Ethidium binding to the triple helix. The preferred intercalation sites of Ethidium in the triple helix are proposed. The interaction of Ethidium at the triplex-duplex junction, and its effects are also discussed. This study is aimed at searching for new drugs specific for the triple helix, or for the triplex-duplex junctions.The contribution of different factors in the interaction of Ethidium intercalated into various sequences of a triple helix, or in the region of the junction between the double- and triple-stranded DNA has been studied by energy minimization. It is found that in the total energy of the Ethidium- triple helix complexes, a particular electrostatic contribution emerges due to the presence of protonated cytosines in the triple helix. This parameters is determinant in the sequence-specificity of Ethidium binding to the triple helix. The preferred intercalation sites of Ethidium in the triple helix are proposed. The interaction of Ethidium at the triplex-duplex junction, and its effects are also discussed. This study is aimed at searching for new drugs specific for the triple helix, or for the triplex-duplex junctions.

  • Theoretical Study of Ethidium Intercalation in Triple-Stranded DNA and at Triplex-Duplex Junctions
    Journal of biomolecular structure & dynamics, 1991
    Co-Authors: Jian-sheng Sun, Thérèse Montenay-garestier, R. Lavery, J. Chomilier, K. Zakrzewska, Claude Hélène
    Abstract:

    Abstract The contribution of different factors in the interaction of Ethidium intercalated into various sequences of a triple helix, or in the region of the junction between the double- and triple-stranded DNA has been studied by energy minimization. It is found that in the total energy of the Ethidium - triple helix complexes, a particular electrostatic contribution emerges due to the presence of protonated cytosines in the triple helix. This parameter is determinant in the sequence-specificity of Ethidium binding to the triple helix. The preferred intercalation sites of Ethidium in the triple helix are proposed. The interaction of Ethidium at the triplex-duplex junction, and its effects are also discussed. This study is aimed at searching for new drugs specific for the triple helix, or for the triplex-duplex junctions.

Gopinatha Suresh Kumar - One of the best experts on this subject based on the ideXlab platform.

  • binding of dna binding alkaloids berberine and palmatine to trna and comparison to Ethidium spectroscopic and molecular modeling studies
    Journal of Molecular Structure, 2008
    Co-Authors: Md Maidul Islam, Prateek Pandya, Sebanti Roy Chowdhury, Surat Kumar, Gopinatha Suresh Kumar
    Abstract:

    Abstract The interaction of two natural protoberberine plant alkaloids berberine and palmatine with tRNA phe was studied using various biophysical techniques and molecular modeling and the data were compared with the binding of the classical DNA intercalator, Ethidium. Circular dichroic studies revealed that the tRNA conformation was moderately perturbed on binding of the alkaloids. The cooperative binding of both the alkaloids and Ethidium to tRNA was revealed from absorbance and fluorescence studies. Fluorescence quenching studies advanced a conclusion that while berberine and palmatine are partially intercalated, Ethidium is fully intercalated on the tRNA molecule. The binding of the alkaloids as well as Ethidium stabilized the tRNA melting, and the binding constant evaluated from the averaged optical melting temperature data was in agreement with fluorescence spectral-binding data. Differential scanning calorimetry revealed that the tRNA melting showed three close transitions that were affected on binding of these small molecules. Molecular docking calculations performed showed the preferred regions of binding of these small molecules on the tRNA. Taken together, the results suggest that the binding of the alkaloids berberine and palmatine on the tRNA structure appears to be mostly by partial intercalation while Ethidium intercalates fully on the tRNA. These results further advance our knowledge on the molecular aspects on the interaction of these alkaloids to tRNA.

  • rna binding small molecules studies on t rna binding by cytotoxic plant alkaloids berberine palmatine and the comparison to Ethidium
    Biophysical Chemistry, 2007
    Co-Authors: Md Maidul Islam, Rangana Sinha, Gopinatha Suresh Kumar
    Abstract:

    Abstract The interaction of two natural protoberberine plant alkaloids berberine and palmatine with t-RNAphe was studied using various biophysical techniques and the data was compared with the binding of the classical DNA intercalator, Ethidium. The results of optical thermal melting, differential scanning calorimetry and circular dichroism characterized the native cloverleaf structure of t-RNA under the conditions of the study. The strong binding of the alkaloids and Ethidium to t-RNA was revealed from the absorption and fluorescence studies. The salt dependence of the binding constants enabled the dissection of the binding free energy to electrostatic and non-electrostatic contributions. This analysis revealed a surprisingly large favourable component of the non-electrostatic contribution to the binding of these charged alkaloids and Ethidium to t-RNA. Isothermal titration calorimetric studies revealed that the binding of both the alkaloids is driven by a moderately favourable enthalpy decrease and a moderately favourable entropy increase while that of Ethidium is driven by a large favourable enthalpy decrease. Taken together, the results suggest that the binding of these alkaloid molecules on the t-RNA structure appears to be mostly by partial intercalation while Ethidium intercalates to the t-RNA. These results reveal the molecular aspects on the interaction of these alkaloids to t-RNA.