Different Effects of Cisplatin and Transplatin on the Higher-Order Structure of DNA and Gene Expression

Despite the effectiveness of cisplatin as an anticancer agent, its trans-isomer, transplatin, is clinically ineffective. Although both isomers target nuclear DNA, there is a large difference in the magnitude of their biological effects. Here, we compared their effects on gene expression in an in vitro luciferase assay and quantified their effects on the higher-order structure of DNA using fluorescence microscopy (FM) and atomic force microscopy (AFM). The inhibitory effect of cisplatin on gene expression was about 7 times that of transplatin. Analysis of the fluctuation autocorrelation function of the intrachain Brownian motion of individual DNA molecules showed that cisplatin increases the spring and damping constants of DNA by one order of magnitude and these visco-elastic characteristics tend to increase gradually over several hours. Transplatin had a weaker effect, which tended to decrease with time. These results agree with a stronger inhibitory effect of cisplatin on gene expression. We discussed the characteristic effects of the two compounds on the higher-order DNA structure and gene expression in terms of the differences in their binding to DNA.

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Effects of Structural Isomers of Spermine on the Higher-Order Structure of DNA and Gene Expression

International Journal of Molecular Sciences ◽

10.3390/ijms22052355 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2355

Author(s):

Tomoki Kitagawa ◽

Takashi Nishio ◽

Yuko Yoshikawa ◽

Naoki Umezawa ◽

Tsunehiko Higuchi ◽

...

Keyword(s):

Gene Expression ◽

Luciferase Assay ◽

Order Structure ◽

Structural Isomers ◽

Force Microscopy ◽

Atomic Force ◽

A Cell ◽

Expression Activity ◽

High Concentrations ◽

Differentiation Gene

Polyamines are involved in various biological functions, including cell proliferation, differentiation, gene regulation, etc. Recently, it was found that polyamines exhibit biphasic effects on gene expression: promotion and inhibition at low and high concentrations, respectively. Here, we compared the effects of three naturally occurring tetravalent polyamines, spermine (SPM), thermospermine (TSPM), and N4-aminopropylspermidine (BSPD). Based on the single DNA observation with fluorescence microscopy together with measurements by atomic force microscopy revealed that these polyamines induce shrinkage and then compaction of DNA molecules, at low and high concentrations, respectively. We also performed the observation to evaluate the effects of these polyamine isomers on the activity of gene expression by adapting a cell-free luciferase assay. Interestingly, the potency of their effects on the DNA conformation and also on the inhibition of gene expression activity indicates the highest for TSPM among spermine isomers. A numerical evaluation of the strength of the interaction of these polyamines with negatively charged double-strand DNA revealed that this ordering of the potency corresponds to the order of the strength of the attractive interaction between phosphate groups of DNA and positively charged amino groups of the polyamines.

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Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro

Nucleic Acids Research ◽

10.1093/nar/gkaa479 ◽

2020 ◽

Vol 48 (12) ◽

pp. 6458-6470

Author(s):

Xiaonong Zhang ◽

Yingqi Zhang ◽

Wenke Zhang

Keyword(s):

Single Molecule ◽

Tandem Repeats ◽

Structural Information ◽

Higher Order ◽

Single Wall Carbon Nanotubes ◽

Order Structure ◽

Telomeric Dna ◽

Force Microscopy ◽

Order Structures

Abstract The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to synthesize long-chain double-stranded tandem repeats of telomeric DNA. Using mechanical manipulation assays based on single-molecule atomic force microscopy, we found that mechanical force can trigger the melting of double-stranded telomeric DNA and the formation of higher-order structures (G-quadruplexes or i-motifs). Our results show that only when both the G-strand and C-strand of double-stranded telomeric DNA form higher-order structures (G-quadruplexes or i-motifs) at the same time (e.g. in the presence of 100 mM KCl under pH 4.7), that the higher-order structure(s) can remain after the external force is removed. The presence of monovalent K+, single-wall carbon nanotubes (SWCNTs), acidic conditions, or short G-rich fragments (∼30 nt) can shift the transition from dsDNA to higher-order structures. Our results provide a new way to regulate the topology of telomeric DNA.

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Higher-order structure of the 5.8 S rRNA sequence within the yeast 35 S precursor ribosomal RNA synthesized in vitro

Journal of Molecular Biology ◽

10.1016/0022-2836(91)90523-9 ◽

1991 ◽

Vol 217 (4) ◽

pp. 649-659 ◽

Cited By ~ 9

Author(s):

Lee-Chuan C. Yeh ◽

John C. Lee

Keyword(s):

Ribosomal Rna ◽

Higher Order ◽

Order Structure ◽

Rrna Sequence

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Yy1 regulates Senp1 contributing to AMPA receptor GluR1 expression following neuronal depolarization

Journal of Biomedical Science ◽

10.1186/s12929-019-0582-1 ◽

2019 ◽

Vol 26 (1) ◽

Cited By ~ 2

Author(s):

Tao Wu ◽

Mary E. Donohoe

Keyword(s):

Gene Expression ◽

Ampa Receptor ◽

Neuronal Activity ◽

Cortical Neurons ◽

Expression Patterns ◽

Luciferase Assay ◽

Regulation Mechanism ◽

Phosphatase Inhibitors ◽

Ampa Receptor Subunit

Abstract Background Neuronal activity-induced changes in gene expression patterns are important mediators of neuronal plasticity. Many neuronal genes can be activated or inactivated in response to neuronal depolarization. Mechanisms that activate gene transcription are well established, but activity-dependent mechanisms that silence transcription are less understood. It is also not clear what is the significance of inhibiting these genes during neuronal activity. Methods Quantitative Real Time-PCR, western blot and immunofluorescence staining were performed to examine the expression of Senp1 and GluR1 in mouse cortical neurons. The alterations of Yy1 phosphorylation upon neuronal depolarization and the interaction of Yy1 with Brd4 were studied by protein co-immunoprecipitation. The regulators of Yy1 phosphorylation were identified by phosphatase inhibitors. Chromatin immunoprecipitation, in vitro DNA binding assay, luciferase assay and gene knockdown experiments were used to validate the roles of Yy1 and its phosphorylation as well as Brd4 in regulating Senp1 expression. Results We report that neuronal depolarization deactivates the transcription of the SUMO protease Senp1, an important component regulating synaptic transmission, scaling, and plasticity, through Yy1. In un-stimulated neurons, Senp1 transcription is activated by a Yy1-Brd4 transcription factor protein complex assembled on the Senp1 promoter. Upon membrane depolarization, however, Yy1 is dephosphorylated and the Yy1-Brd4 complex is evicted from the Senp1 promoter, reducing Senp1 transcription levels. Both Yy1 and Senp1 promote the expression of AMPA receptor subunit GluR1, a pivotal component in learning and memory. Conclusions These results reveal an axis of Yy1/Brd4-Senp1 which regulates the expression of GluR1 during neuronal depolarization. This implicates a regulation mechanism in silencing gene expression upon neuronal activity.

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In Vitro Cytological Responses against Laser Photobiomodulation for Periodontal Regeneration

International Journal of Molecular Sciences ◽

10.3390/ijms21239002 ◽

2020 ◽

Vol 21 (23) ◽

pp. 9002

Author(s):

Yujin Ohsugi ◽

Hiromi Niimi ◽

Tsuyoshi Shimohira ◽

Masahiro Hatasa ◽

Sayaka Katagiri ◽

...

Keyword(s):

Gene Expression ◽

Endothelial Cells ◽

Laser Irradiation ◽

Biological Effects ◽

Periodontal Regeneration ◽

Chronic Inflammatory Disease ◽

Periodontal Ligament Cells ◽

Positive Effects ◽

Periodontal Tissues

Periodontal disease is a chronic inflammatory disease caused by periodontal bacteria. Recently, periodontal phototherapy, treatment using various types of lasers, has attracted attention. Photobiomodulation, the biological effect of low-power laser irradiation, has been widely studied. Although many types of lasers are applied in periodontal phototherapy, molecular biological effects of laser irradiation on cells in periodontal tissues are unclear. Here, we have summarized the molecular biological effects of diode, Nd:YAG, Er:YAG, Er,Cr:YSGG, and CO2 lasers irradiation on cells in periodontal tissues. Photobiomodulation by laser irradiation enhanced cell proliferation and calcification in osteoblasts with altering gene expression. Positive effects were observed in fibroblasts on the proliferation, migration, and secretion of chemokines/cytokines. Laser irradiation suppressed gene expression related to inflammation in osteoblasts, fibroblasts, human periodontal ligament cells (hPDLCs), and endothelial cells. Furthermore, recent studies have revealed that laser irradiation affects cell differentiation in hPDLCs and stem cells. Additionally, some studies have also investigated the effects of laser irradiation on endothelial cells, cementoblasts, epithelial cells, osteoclasts, and osteocytes. The appropriate irradiation power was different for each laser apparatus and targeted cells. Thus, through this review, we tried to shed light on basic research that would ultimately lead to clinical application of periodontal phototherapy in the future.

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Succinic and Cytochrome Oxidase Activity of Rat Liver Mitochondria After in Vitro Irradiation With Ultraviolet Light

American Journal of Physiology-Legacy Content ◽

10.1152/ajplegacy.1957.188.3.547 ◽

1957 ◽

Vol 188 (3) ◽

pp. 547-549 ◽

Cited By ~ 5

Author(s):

Attilio Canzanelli ◽

Rhea Sossen ◽

David Rapport

Keyword(s):

Cytochrome Oxidase ◽

Ultraviolet Light ◽

Rat Liver ◽

Oxidase Activity ◽

Biological Effects ◽

Liver Mitochondria ◽

Rat Liver Mitochondria ◽

Cytochrome Oxidase Activity ◽

Order Of Magnitude

Five per cent suspensions of rat liver mitochondria were irradiated with ultraviolet light for varying periods of time and the succinoxidase and cytochrome oxidase activity were determined. Both succinoxidase and cytochrome oxidase activity were reduced by irradiation with ultraviolet. The order of magnitude of the ultraviolet energy necessary to produce such changes is much less than that necessary to produce chemical changes in nucleic acid derivatives, and approaches the amount which has been shown to produce lethal and other biological effects.

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Natural chromatin is heterogeneous and self-associates in vitro

Molecular Biology of the Cell ◽

10.1091/mbc.e17-07-0449 ◽

2018 ◽

Vol 29 (13) ◽

pp. 1652-1663 ◽

Cited By ~ 12

Author(s):

Shujun Cai ◽

Yajiao Song ◽

Chen Chen ◽

Jian Shi ◽

Lu Gan

Keyword(s):

Divalent Cations ◽

Large Mass ◽

Higher Order ◽

Linker Histone ◽

Order Structure ◽

Face To Face ◽

Chromatin Packing ◽

Electron Cryotomography

The 30-nm fiber is commonly formed by oligonucleosome arrays in vitro but rarely found inside cells. To determine how chromatin higher-order structure is controlled, we used electron cryotomography (cryo-ET) to study the undigested natural chromatin released from two single-celled organisms in which 30-nm fibers have not been observed in vivo: picoplankton and yeast. In the presence of divalent cations, most of the chromatin from both organisms is condensed into a large mass in vitro. Rare irregular 30-nm fibers, some of which include face-to-face nucleosome interactions, do form at the periphery of this mass. In the absence of divalent cations, picoplankton chromatin decondenses into open zigzags. By contrast, yeast chromatin mostly remains condensed, with very few open motifs. Yeast chromatin packing is largely unchanged in the absence of linker histone and mildly decondensed when histones are more acetylated. Natural chromatin is therefore generally nonpermissive of regular motifs, even at the level of oligonucleosomes.

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Enhancing the regeneration of bone defects by alkalizing the peri-implant zone – an in vitro approach

Current Directions in Biomedical Engineering ◽

10.1515/cdbme-2016-0121 ◽

2016 ◽

Vol 2 (1) ◽

pp. 547-551 ◽

Cited By ~ 1

Author(s):

Anne-Marie Galow ◽

Philipp Wysotzki ◽

Werner Baumann ◽

Jan Gimsa

Keyword(s):

Gene Expression ◽

Pure Titanium ◽

Force Microscopy ◽

Cell Counts ◽

Initial Adhesion ◽

Entire Experiment ◽

Titanium Surfaces ◽

Coated Surfaces ◽

Cell Force

AbstractThe effects of alkaline pH on the initial adhesion of osteoblasts to titanium surfaces was analyzed by single cell force microscopy (SCFM). In the SCFM measurements, the same cells were used to compare their unspecific adhesion to uncoated titanium with their specific adhesion to collagen coated titanium. When the maximum detachment forces (MDFs) were compared at pH 7.4 and 8.0, only slight differences were found on pure titanium, while the MDFs were significantly increased at collagen coated surfaces at pH 8.0. Effects on the subsequent proliferation and gene expression were investigated in an in vitro model system consisting of an alkalizing polyvinyl alcohol (PVA) matrix and a perforated titanium disc. The sodium hydroxide releasing matrix maintained the medium pH between pH 7.6 and pH 8.4 during the entire experiment. Under these conditions, cell counts were significantly increased with respect to the control system after 7 days in culture. These results were supported by gene expression analyses, which showed an upregulation of proliferation-controlling genes of the EGFR1 and PI3K/AKT pathways after 14 days in culture. The SCFM data were complemented by findings of an intensive regulation of genes known to be associated with focal adhesion such as Itga8 and Tnn.

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