Involvement of H1 and other chromatin proteins in the formation of DNA-protein cross-links induced by visible light in the presence of methylene blue

Visible-Light-Mediated Modification and Manipulation of Biomacromolecules

Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.

Influence of distamycin, chromomycin, and UV-irradiation on extraction of histone H1 from rat liver nuclei by polyglutamic acid

Rat liver nucleus histone H1 was fractionated by polyglutamic acid (PG) in the presence of distamycin A (DM) or chromomycin A(3) (CM). In the absence of the antibiotics, PG extracts from the nuclei about half of the nuclear H1. DM or CM added to the nuclei in saturating concentrations weakens the binding potential of most of H1. Titration of nuclei with DM shows that the number of binding sites for DM in the nuclei is less than in isolated DNA by only 20-25%, and this difference disappears after treatment of nuclei with PG. The lower CD value of DM complexes with nuclei compared to that of DM complexes with free DNA is evidence of a change in the DM-DNA binding mode in nuclear chromatin. About 25% of total histone H1 is sensitive only to DM and ~5% is sensitive only to CM. Half of the DM-sensitive H1 fraction seems to have a different binding mode in condensed compared relaxed chromatin. A small part of H1 (~3%) remains tightly bound to the nuclear chromatin independent of the presence of the antibiotics. Subfraction H1A is more DM-sensitive and H1B is more CM-sensitive. UV irradiation of nuclei results in dose-dependent cross-linking of up to 50% of total H1, which is neither acid-extractable nor recovered during SDS electrophoresis. PG with DM extracts only about 3% of H1 from UV-stabilized chromatin. DM treatment of the nuclei before UV irradiation results in extraction of the whole DM-sensitive H1 fraction (~25%), which in this case is not stabilized in the nucleus. A hypothesis on possible roles of the found H1 fractions in chromatin structural organization is discussed.

Cross-linking of histone proteins to DNA by UV illumination of chromatin stained with Hoechst 33342

The photochemical effects of near-UV light on chromatin labeled with the vital DNA dye Hoechst 33342 (H33342) are studied. Several types of experiments demonstrate that illumination at both 365 and 410 nm results in significant cross-linking of proteins with the DNA. Fluorescence microscopy of dye-stained Xenopus XTC-2 nuclei shows that UV illumination has effects similar to chemical fixation by formaldehyde. At 365 nm a dose of approximately 70 J/cm2 results in 50% of the DNA being cross-linked, as measured by chloroform-sodium dodecyl sulfate extraction. At 410 nm the efficiency of cross-linking was smaller by a factor of 3. Gel electrophoresis of the cross-linked proteins shows them to be predominantly core histones. The implications of these results for experiments on live cells stained with H33342, for example, fluorescence microscopy of nuclear dynamics or cell sorting, are discussed.

Visible Light Irradiation of Ethidium Bromide–stained Interphase Nuclei Causes DNA–Protein Linking and Structural Stabilization of Nucleoprotein Complexes¶

Fixation of DNA and proteins in the isolated rat hepatocyte nuclei stained with ethidium bromide and irradiated with visible light was analyzed in this study. It was shown that irradiation results in the following modifications of higher-level nucleoprotein complexes of interphase chromatin: (1) the complexes acquire resistance to decondensing treatments, which may be indicative of the formation of links between proteins or proteins and DNA in the chromatin; (2) the linking rate for both DNA and proteins is dose dependent; (3) the irradiation induces intermolecular link formation between DNA molecules, which brings about an increase in the average molecular weight of DNA fragments; (4) some modifications (dimerization, etc.) of histones and nonhistone proteins occur; and (5) histone proteins are not effectively cross-linked to DNA. The structural stabilization of interphase chromatin is possibly mediated by free radical-based mechanisms, whereas disulfide bonds seem to play no significant role in the cross-linking.

Phenothiazines: potential alternatives for the management of antibiotic resistant infections of tuberculosis and malaria in developing countries

The in vitro and in vivo activity of phenothiazines against antibiotic susceptible and antibiotic resistant Mycobacterium tuberculosis and malaria-causing Plasmodia is reviewed. Given the facts that pulmonary tuberculosis and malaria are the major causes of death in developing countries, that both of these infections continue to escalate in their resistance to antibiotics, that the cost for the management of these infections is beyond that afforded by most developing nations, and lastly, that new and effective agents are not forthcoming from the pharmaceutical industry, the scientific rationale for the potential use of select phenothiazines for the management of these infections is presented.

Simultaneous photoconjugation of methylene blue and cis-Rh(phen)2Cl2+ to DNA via a synergistic effect

Irradiation of the red-light absorbing dye, methylene blue (MB), in the presence of the metal complex, cis-Rh(phen)2Cl2+ (BISPHEN), leads to irreversible photobinding of both reagents to DNA. Evidence from absorption and emission spectroscopy indicates that the dye is strongly complexed to the DNA at the concentrations used in the experiments and that this complex is unaffected by the presence of BISPHEN. The level of covalent binding is proportional to the absorbed light dose, with the quantum efficiency for covalent binding of BISPHEN to the DNA with 633 nm light equal to 3.5 x 10(-4). Electrospray ionization mass spectrum of a mixture of DNA fragments created by enzymatic degradation of DNA isolated following irradiation indicates that purine adducts are formed with both BISPHEN and the dye. In addition, UV-Vis and high-performance liquid chromatography analyses of the irradiated MB/BISPHEN/DNA mixture and isolated adducts show extensive conversion of the dye and metal complex to the corresponding N-demethylated and aquated derivatives, respectively. Triplet quenchers for MB, for example oxygen and benzoquinone, inhibit both the photoconjugation and the photochemistry of BISPHEN. A mechanism for the synergistic interaction is proposed that involves photoconjugation of both partners to the DNA following oxidation and reduction via electron transfer between 1MB*/DNA and 3MB*/BISPHEN.

DNA damage induced by 4,6,8,9-tetramethyl-2H-furo[2,3-h]quinolin-2-one, a new furocoumarin analog: biological consequences

4,6,8,9-Tetramethyl-2H-furo[2,3-h]quinolin-2-one (HFQ) and its isomer FQ (1,4,6,8-tetramethyl-2H-furo[2,3-h]quinolin-2-one) showed very strong antiproliferative activity in mammalian cells, about two times greater than 8-methoxypsoralen (8-MOP). Both compounds induced DNA-protein cross-links (DPC) but not interstrand cross-links. The FQ generated DPC in a biphotonic process, yielding a new kind of diadduct, whereas HFQ induced DPC by a monophotonic one, probably without its physical participation in the covalent bridge. These lesions gave different toxic responses. Sensitization of FQ led to extensive DNA fragmentation and to a number of chromosomal aberrations. Conversely, HFQ seemed to be completely inactive and 8-MOP gave intermediate results. A strict relationship between DPC formation and induction of chromosomal aberrations was observed. The HFQ did not induce light skin erythemas, whereas FQ was more phototoxic than 8-MOP, thus suggesting that FQ lesions, DPC in particular, may be implicated in skin phototoxicity. Ehrlich ascites cells, a transplantable mouse tumor, inactivated by furoquinolinone sensitization and injected into healthy mice, protected them from a successive challenge by viable tumor cells. This response appeared to be based on an immune mechanism. Comparable amounts of base substitution revertants were scored when testing furoquinolinones and 8-MOP in bacteria but no DPC were detected. This suggests that classic mutagenesis tests on bacteria are insufficient to give adequate information on furocoumarin genotoxicity. Given its features, HFQ can be regarded as an interesting new agent for psoralen plus UVA photochemotherapy and photopheresis.

Photodynamic crosslinking of proteins. I. Model studies using histidine- and lysine-containing N-(2-hydroxypropyl)methacrylamide copolymers

One of the mechanisms by which cells might be damaged during the photodynamic therapy (PDT) of tumors is via the covalent crosslinking of proteins to proteins or to other molecules in the cell. It has been suggested that photodynamically generated singlet oxygen interacts with photo-oxidizable amino acid residues such as His, Cys, Trp and Tyr in one protein molecule to generate reactive species, which in turn interact non-photochemically with residues of these types or with free amino groups in another protein molecule to form a crosslink. In some cases, photochemically generated free radicals may be involved in crosslinking. This paper describes studies on the use of N-(2-hydroxypropyl)methacrylamide (HPMA) copolymers containing epsilon-aminocaproic acid side chains terminating in His (P-Acap-His) or Lys (P-Acap-Lys) as models for the photodynamic crosslinking of proteins. The model copolymer P-Acap-His had a weight-averaged molecular weight of about 22,000 and contained four to five His residues per copolymer molecule. The model copolymer P-Acap-Lys had a weight average molecular weight of about 18,000 and contained four to five Lys residues per copolymer molecule. The extent of photocrosslinking, as sensitized by rose bengal, was estimated by measuring the increase in the viscosity of model copolymer solution after various periods of illumination. The extent of intermolecular crosslinking was estimated from the changes in molecular weight distribution of samples before and at the end of illumination as determined by size exclusion chromatography. Photodynamic crosslinking occurred between P-Acap-His molecules and between P-Acap-His and P-Acap-Lys molecules. The higher the concentration of macromolecules in the solution, the higher is the yield of intermolecular crosslinking. Oxygen was necessary for crosslinking, and azide inhibition studies indicated the involvement of singlet oxygen.