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The Single-Stranded DNA Binding Protein of Bacteriophage T4
Published in James F. Kane, Multifunctional Proteins: Catalytic/Structural and Regulatory, 2019
Daniel H. Doherty, Peter Gauss, Larry Gold
The central protein in the T4 replication complex is the T4 DNA polymerase, the product of gene 43. We have noted that gp32 stimulates DNA synthesis by the T4 DNA polymerase when assayed on a single-stranded DNA template.19 Conversely, the E. coli and bacteriophage T7 single-stranded DNA binding proteins do not stimulate DNA synthesis by the T4 DNA polymerase. 58,60 As we have noted, the lack of stimulation by heterologous single-stranded DNA binding proteins might be a consequence of the different geometry of the complexes between the various binding proteins and DNA. More interestingly, one can imagine that the homologous reaction involves a protein-protein contact between gp43 and gp32. Such a complex has been isolated and studied.19,59 Purified T4 DNA polymerase will co-migrate with gp32 multimers in a sucrose gradient at high gp32 concentrations. The formation of this complex is dependent on the presence of the T4 DNA polymerase; no associations are observed between gp32 and E. coli DNA polymerase I or II. This association of polymerase and gp32 has been shown to require an intact carboxyterminus of the gene 32 protein.59
DNA-Binding Proteins and DNA-Synthesizing Enzymes in Eukaryotes
Published in Lubomir S. Hnilica, Chromosomal Nonhistone Proteins, 2018
The mechanism of these proteins involving in DNA replication is not known. However, a detailed analysis of the interaction of the E. coli DNA binding protein with DNA polymerase II has suggested a model to account for these various observations. E. coli DNA binding protein interacts with E. coli DNA polymerase II to form a protein-protein complex in the absence of DNA. DNA-binding protein, when bound to DNA, retains its ability to interact with DNA polymerase II and to form a ternary complex between DNA-binding protein, DNA polymerase II, and DNA. Neither E. coli DNA polymerase I nor DNA polymerase III nor phage T4-induced DNA polymerase interacts with DNA-binding protein. Thus, it appears that the specific stimulation is due to complex formation. The stimulation rate and extent of synthesis seen when the DNA-binding protein is added can be explained by destabilizing the double helix of DNA template as well as by binding to the polymerase during DNA synthesis, such that the polymerase does not dissociate from the template during processing.
Role of Nonhistone Chromosomal Proteins in Selective Gene Expression
Published in Gerald M. Kolodny, Eukaryotic Gene Regulation, 2018
I.R. Phillips, E.A. Shephard, J.L. Stein, G.S. Stein
Specific DNA-binding nonhistone proteins have been isolated by several groups of workers, and the techniques used, together with their associated problems, were described in the section on fractionating the nonhistone chromosomal proteins by DNA affinity techniques. In this section, we will discuss some of the properties of these DNA-binding proteins which may have a bearing on their postulated role in the control of gene expression.
Epigenetic modulations in cancer: predictive biomarkers and potential targets for overcoming the resistance to topoisomerase I inhibitors
Published in Annals of Medicine, 2023
Moustafa M. Madkour, Wafaa S. Ramadan, Ekram Saleh, Raafat El-Awady
DNA methylation is known to affect the interaction with certain DNA-binding proteins including DNA Tops. The role of DNA methylation in controlling the response of cancer cells to drugs including Top I inhibitors was identified by the use of the hypomethylating cytidine analogue 5-azacytidine (5-azaC). The pre-treatment of Chinese hamster ovary cells with 5-azaC was demonstrated to increase their sensitivity to CPT and to result in a strong synergistic effect on chromosomal damage. This could be premised on the idea that changing chromosome replication timing after DNA hypomethylation increases the number of replication forks in early S phase, which subsequently increases the likelihood of collision between a blocked DNA-Top I-CPT cleavage complex and the replication fork [61]. In addition, the cytotoxicity of irinotecan was demonstrated to be increased by 5-azaC in colorectal cancer cells via at least one of the following mechanisms: (a) demethylation of the Top I promoter, (b) indirect stimulation of Top I expression, and (c) amendment of cell cycle progression and/or apoptosis following DNA damage [62,63] (Figure 2(A)). Interestingly, the combination of 5-azaC and irinotecan resulted in a synergistic response with considerable improvement in survival and tumor regression in human colon cancer xenograft mice [64,65]. In pheochromocytoma/paraganglioma, the intermittent coadministration of 5-azaC also increased the efficacy of low doses of CPT and other Top I inhibitors in in vitro and in vivo settings [66].
Immunogenic cell death in a combined synergic gene- and immune-therapy against cancer
Published in OncoImmunology, 2019
Benjamin Nayagom, Ikrame Amara, Meryem Habiballah, Floriane Amrouche, Philippe Beaune, Isabelle de Waziers
HMGB1 is the most abundant non-histone, nuclear protein. It acts as a DNA-binding protein in the nucleus to sustain chromatin structure and it regulates DNA repair. The function of HMGB1 depends upon its localization.28 In the extracellular medium, HMGB1 operates as a potent pro-inflammatory stimulus.29 HMGB1 release was observed when TC1 cells were treated with oxaliplatin (positive control for immunogenic cell death30) and this release was more important when cells were treated with the supernatant of MSC-CYP2B6* treated with CPA. No HMGB1 release was observed in untreated TC1 cells or in TC1 cells incubated with docetaxel or with the supernatant of MSC-NI treated with CPA (Figure 6).
Ternary complex of plasmid DNA with NLS-Mu-Mu protein and cationic niosome for biocompatible and efficient gene delivery: a comparative study with protamine and lipofectamine
Published in Artificial Cells, Nanomedicine, and Biotechnology, 2018
Mohammad Hadi Nematollahi, Masoud Torkzadeh-Mahanai, Abbas Pardakhty, Hossein Ali Ebrahimi Meimand, Gholamreza Asadikaram
EtBr is a universal DNA intercalation dye and its fluorescence intensity increases substantially after binding to DNA. In the presence of another molecule, there would be competition between the new molecule and EtBr for binding to DNA. Such competitive binding studies have been used to identify the new DNA binding protein or drug. Our result confirmed that NMM similar to protamine has the ability to displace EtBr (Figure 4). Therefore, NMM protein is likely to be an intercalator of DNA. Although, the NMM was also able to induce a decrease in EtBr fluorescence but this effect was more obvious in presence of protamine. Similar results regarding protamine EtBr exclusion are also reported by De Ilarduya et al. [39].