Intercalation of small molecules into DNA in chromatin is primarily controlled by superhelical constraint

Abstract

The restricted access of regulatory factors to their binding sites on DNA wrapped around the nucleosomes is generally interpreted in terms of molecular shielding exerted by nucleosomal structure and internucleosomal interactions. Binding of proteins to DNA often includes intercalation of hydrophobic amino acids into the DNA. To assess the role of constrained superhelicity in limiting these interactions, we studied the binding of small molecule intercalators to chromatin in close to native conditions by laser scanning cytometry. We demonstrate that the nucleosome-constrained superhelical configuration of DNA is the main barrier to intercalation. As a result, intercalating compounds are virtually excluded from the nucleosome-occupied regions of the chromatin. Binding of intercalators to extranucleosomal regions is limited to a smaller degree, in line with the existence of net supercoiling in the regions comprising linker and nucleosome free DNA. Its relaxation by inducing as few as a single nick per ~50 kb increases intercalation in the entire chromatin loop, demonstrating the possibility for long-distance effects of regulatory potential.

Epigenetic Modulation via the C-Terminal Tail of H2A.Z

“…These architectural differences are reflected in global effects of functional consequences, as shown below. As compared to DKO H2A.Z nuclei, those of the DKO H2A.ZΔC line stained much more readily with intercalator dyes used at such low concentrations where dye binding is DNA topology dependent (54), and were much more readily digested using MNase, nickase and DNAse I (Fig. 3), suggesting major H2A.Z C-terminal tail-dependent overall differences in chromatin structure.…”

“…The large difference between the staining of the DKO H2A.Z and H2A.ZΔC nuclei with the two intercalating dyes would be unexpected if the dyes were applied at the usual concentration allowing for stoichiometric binding to the DNA. However, they were added at a lower concentration where their binding to the DNA is highly sensitive to the constrtained nucleosomal and to the plectonemic internucleosomal superhelicity (54). The H2A.ZΔC levels expressed in the nuclei of these DKO DT40 cells are about half of the H2A.Z levels in the same DKO background, but the total number of H3K9me3, H3K27me3, H2B nucleosomes and also the amount of DNA in the nuclei of the two cell types are similar (Suppl.…”

Virtual Screening of Phenylenediamine Schiff`s Base Derivatives as Possible DNA Intercalating Agents

“…Lipophilicity (LogP o/w) values of all synthesized compounds were in the range from 1.83 to 3.44 for mono-substituted compounds, and 3.10 to 6.31 for disubstituted compounds while their molecular weights are generally within the accepted range-with a few exceptions. The compounds were found with optimum number of hydrogen bonding donors (0-4) and hydrogen bonding acceptors (1)(2)(3)(4)(5)(6)(7)(8). The achieved results indicate that most of the compounds follow Lipinski rule and have a good partition coefficient.…”

Profound Nanoscale Structural and Biomechanical Changes in DNA Helix upon Treatment with Anthracycline Drugs

“…In previous experiments, we demonstrated a number of nanoscale disturbances of dsDNA properties caused by anthracycline antibiotics. It has been suggested that the superhelical twist and higher order structures can prevent the DNA intercalation, and thus can serve as a natural barrier against some molecules [29]. It is always the question if and how these effects could have been observed in nanoscale, very often in an isolated experimental setup, and whether they reflect microscale properties of DNA.…”