Ionic Strength Dependence of the Binding of Methylene Blue to Chromatin and Calf Thymus DNA

Abstract

The binding of the intercalating dye methylene blue (MB) to chromatin and to free DNA has been studied as a function of ionic strength at very low binding ratios (1 MB/400 DNA bases) using absorption spectroscopy. With increasing salt concentration MB is displaced from chromatin to a higher extent than from DNA. The free energy change for MB binding to chromatin is found to be approximately 5 kJ/mole lower than for binding to DNA. This difference can be explained by the reduced number of high affinity binding sites in chromatin due to the presence of histone proteins. The difference in binding energy is virtually independent of the degree of chromatin condensation and also of the valence of counter ions, suggesting that neither the affinity for, nor the number of intercalation sites in the linker DNA is markedly changed upon the salt-induced condensation. The unaffected thermodynamics of the linker binding suggests that factors such as DNA superhelicity and the electrostatic influence from the chromatosomes remain unchanged during chromatin condensation.

Use of competition dialysis in the discovery of G-quadruplex selective ligands

“…Ethidium bromide binds to DNA via an intercalation mode, usually to double stranded DNA, with preference for alternating purine-pyrimidine sequences (37), but can also bind single-stranded DNA, triplex, quadruplex and DNA-RNA hybrid structures;. Methylene blue is another intercalator with unknown structural preferences (38,39). Berberine (40) is an alkaloid derived from traditional Chinese herbal remedies; it proved to have binding activity towards triplex DNA and in a minor extent to quadruplex DNA.…”

Synthesis, characterization and DNA-binding properties of rac-[Ru(5,6-dmp)2(dppz)]2+ – Enantiopreferential DNA binding and co-ligand promoted exciton coupling

“…It is often very useful to study the effect of varying the ionic strength and temperature on the CD spectra [58] keeping the mixing ratio constant (R = 2). Thus, when the ionic strength of the buffer is varied from 0.05 to 4 M by increasing the concentration of NaCl in the buffer, the intensities of both the positive and negative extremas of the ICD decrease with a blue-shift from 278 to 270 nm in the zero cross-over (8 nm) and become constant at 2.5 M NaCl (Fig.…”

Complex of Osmium Tetroxide with 1,10-Phenanthroline Binds Covalently to Double-Stranded DNA

“…Ethidium bromide-induced binding of Os,bipy to dsDNA was inhibited by MgC1 2 (Figure 7, lanes 6, 7) suggesting that the strong inhibitory effect of MgC1 2 may be connected with ability of Mg2+ to prevent intercalation. The Mg2+-induced dissociation of intercalators from DNA was described (35,36). (d) Preference for TA and AT steps (Table I, Figure 8) was also observed with psoralens which intercalate prior to their covalent bind-…”