Analysis of the effects of antibiotics on the structure of nucleosome core particles determined by DNAase I cleavage

Role of structure-proteins in the porphyrin-DNA interaction

We studied the complexation of meso-tetrakis(4-N-methylpyridyl)porphyrin (TMPyP) with HeLa nucleosomes and compared it to our earlier results on T7 phage nucleoprotein complex (NP) and isolated DNA. To identify binding modes and relative concentrations of the bound TMPyP forms, the porphyrin absorption spectra were analyzed at various base pair/porphyrin ratios. Spectral decomposition and circular dichroism measurements proved that the two main binding modes of TMPyP, i.e., external binding and intercalation occur also in the nucleosomes. The DNA superstructure maintained by the proteins decreases its accessibility for TMPyP similarly in both nucleoproteins. A difference is observed between the partitioning of the two binding modes: in the case of nucleosome the ratio of intercalation to groove-binding is changed from 60/40 to 40/60 as determined for T7 NP and for isolated DNA-s. Using UV and CD melting studies, we revealed that TMPyP destabilizes the DNA-protein interaction in the nucleosomes but not in the T7 phage. Lastly, photoinduced reaction of bound TMPyP caused alterations in DNA structures and DNA-protein interactions within both nucleoprotein complexes; the nucleosomes were found to be more sensitive to the photoreaction.

Nuclear condensation and free radical scavenging: a dual mechanism of bisbenzimidazoles to modulate radiation damage to DNA

The complexing of histones with DNA and the resulting condensation of chromatin protects mammalian cell, from radiation-induced strand breakage. In the present study, benzimidazoles DMA and TBZ showed marked radioprotection through drug-induced compaction of chromatin and direct quenching of free radicals generated by radiation. The mammalian cells were incubated with 100 microM concentration of DMA and TBZ and irradiated at 5 Gy; both the ligands showed nuclei condensation suggesting a probable mechanism to protect DNA from radiation damage. The bisubstituted analogs of Hoechst 33342 are found to be better free radical scavengers and protect DNA against radiation-induced damage at a lower concentration than the parent molecule. Both the ligands also quenched free radicals in isolated free radical system suggesting their dual mode of action against radiation-induced damage to DNA. Molecules binding to the chromatin alter gene expression, whereas in this study both the ligands have not shown any profound effect on the nucleosome assembly and gene expression in vitro and in vivo. Both ligands afford a 2-fold protection by altering DNA structure as well as through direct free radical quenching in bulk solution in comparison to the parent ligand, which acts only through quenching of free radicals.

The anthracycline antibiotics: antitumor drugs that alter chromatin structure

Anthracycline antibiotics are an important group of antitumor drugs widely used in cancer chemotherapy. However, despite the increasing interest in these chemotherapeutic agents, their mechanism of action is not yet completely understood. Here, we review what is currently known about the molecular mechanisms involved with special emphasis on the interaction of these drugs with chromatin and its constitutive components: DNA and histones. The evidence suggests that one very important component of the activity of these drugs is the result of these manifold interactions that lead to a chromatin unfolding and aggregation. This chromatin structural disruption is likely to interfere with the metabolic processes of DNA (replication and transcription) and it may play an important role in the apoptosis undergone by the cells upon treatment with these drugs.

Visualising DNA: Footprinting and 1-2D Gels

The study of molecular recognition of DNA by natural and synthetic ligands has made enormous progress due in large part to the discovery and development of methods for separating DNA fragments by gel electrophoresis in one and two dimensions, and for characterizing DNA-ligand complexes by footprinting techniques.

Drug-RNA footprinting

RNase I and RNase T1 can be used to obtain high-quality footprinting information for paromomycin binding to a 176-mer RNA from the packaging region of HIV-1 (LAI). Controls and scanning procedures are necessary for quantitation of autoradiographic data, so that footprinting plots showing cutting behavior as a function of drug concentration can be used to identify binding sites and regions of altered structure on the 176-mer. From the RNase I footprinting results the primary paromomycin binding sites on the 176-mer are on the main stem and on the stem of SL1, but noncontiguous sequences may be involved in the same binding event. Strong enhancements in cleavage with added drug are also observed, indicating drug-induced structural changes. Drug binding may cause linker regions between stem-loops of the 176-mer to change structure, possibly providing a site or sites for additional drug binding. Because drug binding changes the structure of the packaging region, which may alter its function, paromomycin analogs with enhanced specificity for HIV psi RNA have potential as a new class of agent for treating AIDS.

Effects of cycloheximide on B-chronic lymphocytic leukaemic and normal lymphocytes in vitro: induction of apoptosis

A number of reports indicate that protein synthesis is a requirement for the occurrence of apoptosis. In this study, the effect of the protein synthesis inhibitor cycloheximide (CHM) on spontaneous apoptosis of B-chronic lymphocytic leukaemia (B-CLL) cells, previously shown to occur when they are cultured in RPMI-1640 medium with autologous or heterologous serum, was examined. No definite inhibition of apoptosis was observed. Indeed, CHM-treatment augmented apoptosis in the B-CLL cultures and also induced apoptosis of cultured normal peripheral blood lymphocytes. Augmentation was dose-dependent for B-CLL cells over the concentration range 10(-6) M (0.28 micrograms ml-1) to 10(-2) M (2800 micrograms ml-1), resulting in 9% to 98% apoptosis respectively by 24 h of culture (r = 0.619, P = 0.0008). Normal lymphocytes were affected by CHM over the range 10(-4) M to 10(-2) M, resulting in 7% to 74% apoptosis respectively (r = 0.794, P = 0.0001). Inhibition of protein synthesis in these cells by CHM was virtually complete at a concentration of 10(-3) M. The findings are in accord with some recent reports indicating that suppression of protein synthesis by CHM does not inhibit apoptosis in all circumstances. They also illustrate the marked susceptibility of B-CLL cells, compared with normal lymphocytes, to the induction of apoptosis by this drug. The manner in which CHM triggers apoptosis of some cell types is at present uncertain.

Molecular modelling study of changes induced by netropsin binding to nucleosome core particles

It is well known that certain sequence-dependent modulators in structure appear to determine the rotational positioning of DNA on the nucleosome core particle. That preference is rather weak and could be modified by some ligands as netropsin, a minor-groove binding antibiotic. We have undertaken a molecular modelling approach to calculate the relative energy of interaction between a DNA molecule and the protein core particle. The histones particle is considered as a distribution of positive charges on the protein surface that interacts with the DNA molecule. The molecular electrostatic potentials for the DNA, simulated as a discontinuous cylinder, were calculated using the values for all the base pairs. Computing these parameters, we calculated the relative energy of interaction and the more stable rotational setting of DNA. The binding of four molecules of netropsin to this model showed that a new minimum of energy is obtained when the DNA turns toward the protein surface by about 180 degrees, so a new energetically favoured structure appears where netropsin binding sites are located facing toward the histones surface. The effect of netropsin could be explained in terms of an induced change in the phasing of DNA on the core particle. The induced rotation is considered to optimize non-bonded contacts between the netropsin molecules and the DNA backbone.

Chemical and photochemical probing of DNA complexes

An overview of the chemical and photochemical probes which over the past ten years have been used in studies of DNA/ligand complexes and of non-B-form DNA conformations is presented with emphasis on the chemical reactions of the probes with DNA and on their present 'use-profile'. The chemical probes include: dimethyl sulfate, ethyl nitroso urea, diethyl pyrocarbonate, osmium tetroxide, permanganate, aldehydes, methidiumpropyl-EDTA-Fell (MPE), phenanthroline metal complexes and EDTA/FeII. The photochemical probes that have been used include: psoralens, UVB, acridines and uranyl salts. The biological systems analysed by use of these probes are reviewed by tabulation.

Footprinting analysis of sequence-specific DNA-drug interactions

Footprinting is a technique widely used in the analysis of sequence-specificity of proteins and drugs which bind to DNA in an equilibrium manner. Footprinting studies combine the enzymatic or chemical cleavage of DNA with the analysis of the resulting products by sequencing gels, thus revealing the position and length of individual binding sites. This review compares the information that can be obtained by using different footprinting agents and the characteristics of DNA-drug interactions that can be inferred from footprinting results.