Different bindings of the minor groove ligands DAPI and Hoechst 33258 to multimers of the curved (CA4T4G) and noncurved (CT4A4G) DNA sequences

Caneva, R.; Simoni, Alessandro; Mayol, Luciano; Rossetti, Luigi; Savino, M.

doi:10.1016/s0167-4781(97)00091-2

Cited by 12 publications

(9 citation statements)

References 28 publications

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“…Comparative studies of Caneva et al indicate that DAPI may also bind to other AT rich sequences. DAPI was found to slightly prefer binding to the (CT 4 A 4 G) n compared with the (CA 4 T 4 G) n DNA sequence motif (Caneva et al, 1997).…”

Section: Introductionmentioning

confidence: 95%

DAPI binding to the DNA minor groove: a continuum solvent analysis

Castro¹,

Zacharias²

2002

J of Molecular Recognition

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A continuum solvent model based on the generalized Born (GB) or finite-difference Poisson-Boltzmann (FDPB) approaches has been employed to compare the binding of 4'-6-diamidine-2-phenyl indole (DAPI) to the minor groove of various DNA sequences. Qualitative agreement between the results of GB and FDPB approaches as well as between calculated and experimentally observed trends regarding the sequence specificity of DAPI binding to B-DNA was obtained. Calculated binding energies were decomposed into various contributions to solvation and DNA-ligand interaction. DNA conformational adaptation was found to make a favorable contribution to the calculated total interaction energy but did not change the DAPI binding affinity ranking of different DNA sequences. The calculations indicate that closed complex formation is mainly driven by nonpolar contributions and was found to be disfavored electrostatically due to a desolvation penalty that outbalances the attractive Coulomb interaction. The calculated penalty was larger for DAPI binding to GC-rich sequences compared with AT-rich target sequences and generally larger for the FDPB vs the GB continuum model. A radial interaction profile for DAPI at different distances from the DNA minor groove revealed an electrostatic energy minimum a few Angstroms farther away from the closed binding geometry. The calculated electrostatic interaction up to this distance is attractive and it may stabilize a nonspecific binding arrangement.

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Section: Introductionmentioning

confidence: 95%

DAPI binding to the DNA minor groove: a continuum solvent analysis

Castro¹,

Zacharias²

2002

J of Molecular Recognition

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“…The isotherms were fitted using the following equation:

where r is the concentration of bound EthBr molecules per nucleotide, C f is the molar concentration of free EthBr, while K i and N i , the association constant and the number of sites excluded per 1 mole of bound EthBr, respectively, are the free parameters. This is a standard method for the best fit procedure [18,19] and results are summarized in Table 2 . Subsequent experiments, where the ion strength was increased, were performed to elucidate the nature of the weak binding site.…”

Section: Resultsmentioning

confidence: 99%

Biophysical study of a molecular intermediate preceding collapse of tight couple and Kaltschmidt–Wittmann ribosomes

Bonincontro¹,

Nierhaus²,

Ortore³

et al. 2002

FEBS Letters

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In previous works we evidenced, by di¡erent biophysical approaches, two levels of structural organization in Escherichia coli ribosomal particles. Thermal treatment up to a de¢ned and non-denaturing temperature causes demolition of only one level of structural complexity. By consequence the ribosomal particle exists in an intermediate state between the native form and the completely collapsed one. In this communication we report on a structural comparison of this intermediate state in Kaltschmidt^Wittmann (LC) and 'tight couple' (TC) ribosomes. Three di¡erent biophysical approaches were adopted : dielectric spectroscopy, £uorescence and light scattering. Di¡er-ential responses to thermal treatment are evidenced in the two ribosomal species. In particular TC show a more compact structure and the overall particle population is more homogeneous than LC in the native state. On the other hand, LC particles after thermal treatment undergo major alterations of geometry and/or phenomena of supra-particle aggregation. ß

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“…Thus, DAPI has been used as a specific aptamer for DNA labelling. DNA curvature has a main role in the recognition of both regulatory and structural proteins, as demonstrated by a number of studies on the molecular aspects of fundamental biological processes such as transcription and chromatin assembly 33 . Thus, the presence of charged ions and amino acids in the isolated bioactive compound may go and bind to DNA thus influencing the DNA curvatures and stability.…”

Section: A B Fig 6: (A) Effect Of the Purified Bioactive Protein On mentioning

confidence: 99%

Untitled

2018

IJPSR

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Cancer, the uncontrolled growth of cells, has been estimated as a major cause of death among human population. Although there are many potential drugs, a much effective bioactive drug with less side effects are still in its pioneer stage of research. The aim of the study was to isolate, purify and characterize the anticancer muscle protein from edible marine catfish, Tachysaurus dussumieri, so as to project it as an alternative medicine for cancer. The anticancer muscle protein was purified to its homogeneity from the edible marine catfish Tachysurus dussumieri through ammonium sulphate fractionation and ion exchange chromatography. Both partially purified crude fractions and isolated purified muscle protein were screened for its anticancer activity by MTT assay. The fraction III revealed prominent anti-cancer activity which was subjected to MALDI-TOF MS analysis for its molecular weight confirmation. Further, Peptide Mass Finger printing analysis (PMF) was executed to reveal its nature. To reconfirm its anticancer action, DAPI, PI staining and Comet assay were executed. The purified dimer having 13.285 kDa weight was homologous to Tumor Necrosis Factor (TNF)-3a. The Purified protein showed a remarkable inhibitory effect on the proliferation of human colon adenocarcinoma cell line (HT 29) at a concentration of 20 µg/ml. Comet assay and fluorescence microscopic analysis also confirmed the significant increase in DNA fragmentation and cellular degradation of HT 29 cells, when treated with isolated protein. These results indicated the potentiality of the protein as a colorectal cancer therapeutic agent. INTRODUCTION: Cancer death worldwide is projected to rise continuously with an estimated 11.5 million deaths in 2030 and about 1,660,290 new cancer cases every year 1 .

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Different bindings of the minor groove ligands DAPI and Hoechst 33258 to multimers of the curved (CA4T4G) and noncurved (CT4A4G) DNA sequences

Cited by 12 publications

References 28 publications

DAPI binding to the DNA minor groove: a continuum solvent analysis

DAPI binding to the DNA minor groove: a continuum solvent analysis

Biophysical study of a molecular intermediate preceding collapse of tight couple and Kaltschmidt–Wittmann ribosomes

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