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

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

International Journal of Molecular Sciences ◽

10.3390/ijms21010034 ◽

2019 ◽

Vol 21 (1) ◽

pp. 34 ◽

Cited By ~ 2

Author(s):

Toshifumi Kishimoto ◽

Yuko Yoshikawa ◽

Kenichi Yoshikawa ◽

Seiji Komeda

Keyword(s):

Gene Expression ◽

Nuclear Dna ◽

Biological Effects ◽

Inhibitory Effect ◽

Higher Order ◽

Luciferase Assay ◽

Order Structure ◽

Force Microscopy ◽

Order Of Magnitude

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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Optical, Structural and Electrical Properties of Electrochemical Synthesis of Thin Film of Polyaniline

Baghdad Science Journal ◽

10.21123/bsj.15.1.73-80 ◽

2018 ◽

Vol 15 (1) ◽

pp. 73-80 ◽

Cited By ~ 1

Author(s):

Baghdad Science Journal

Keyword(s):

X Ray Diffraction ◽

X Ray ◽

Force Microscopy ◽

Morphological Studies ◽

Atomic Force ◽

Vis Spectroscopy ◽

Structural And Electrical Properties ◽

A Cell ◽

Ft Ir ◽

Ir And Raman

Polyaniline membranes of aniline were produced using an electrochemical method in a cell consisting of two poles. The effect of the vaccination was observed on the color of membranes of polyaniline, where analysis as of blue to olive green paints. The sanction of PANI was done by FT-IR and Raman techniques. The crystallinity of the models was studied by X-ray diffraction technique. The different electronic transitions of the PANI were determined by UV-VIS spectroscopy. The electrical conductivity of the manufactured samples was measured by using the four-probe technique at room temperature. Morphological studies have been determined by Atomic force microscopy (AFM). The structural studies have been measured by (SEM).

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Improved unroofing protocols for cryo-electron microscopy, atomic force microscopy and freeze-etching electron microscopy and the associated mechanisms

Microscopy ◽

10.1093/jmicro/dfaa028 ◽

2020 ◽

Vol 69 (6) ◽

pp. 350-359

Author(s):

Nobuhiro Morone ◽

Eiji Usukura ◽

Akihiro Narita ◽

Jiro Usukura

Keyword(s):

Electron Microscopy ◽

Atomic Force Microscopy ◽

Cell Membrane ◽

Apical Cell ◽

Force Microscopy ◽

Atomic Force ◽

Cryo Electron Microscopy ◽

Cytoplasmic Surface ◽

A Cell ◽

Freeze Etching

Abstract Unroofing, which is the mechanical shearing of a cell to expose the cytoplasmic surface of the cell membrane, is a unique preparation method that allows membrane cytoskeletons to be observed by cryo-electron microscopy, atomic force microscopy, freeze-etching electron microscopy and other methods. Ultrasound and adhesion have been known to mechanically unroof cells. In this study, unroofing using these two means was denoted sonication unroofing and adhesion unroofing, respectively. We clarified the mechanisms by which cell membranes are removed in these unroofing procedures and established efficient protocols for each based on the mechanisms. In sonication unroofing, fine bubbles generated by sonication adhered electrostatically to apical cell surfaces and then removed the apical (dorsal) cell membrane with the assistance of buoyancy and water flow. The cytoplasmic surface of the ventral cell membrane remaining on the grids became observable by this method. In adhesion unroofing, grids charged positively by coating with Alcian blue were pressed onto the cells, thereby tightly adsorbing the dorsal cell membrane. Subsequently, a part of the cell membrane strongly adhered to the grids was peeled from the cells and transferred onto the grids when the grids were lifted. This method thus allowed the visualization of the cytoplasmic surface of the dorsal cell membrane. This paper describes robust, improved protocols for the two unroofing methods in detail. In addition, micro-unroofing (perforation) likely due to nanobubbles is introduced as a new method to make cells transparent to electron beams.

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A New Drug Vehicle - Lipid Coated Biodegradable Nanoparticles

Advances in Science and Technology ◽

10.4028/www.scientific.net/ast.57.148 ◽

2008 ◽

Vol 57 ◽

pp. 148-153 ◽

Cited By ~ 10

Author(s):

J. Schäfer ◽

Johannes Sitterberg ◽

C. Ehrhardt ◽

M.N.V. Ravi Kumar ◽

Udo Bakowsky

Keyword(s):

Plga Nanoparticles ◽

Correlation Spectroscopy ◽

Cell Culture Model ◽

Supported Lipid Bilayer ◽

Photon Correlation ◽

Force Microscopy ◽

Coated Nanoparticles ◽

Atomic Force ◽

Culture Model ◽

A Cell

The preparation and charactersiation of novel lipid coated PLGA nanoparticles was investigated in the presented study. The size of the pure nanoparticles could be adjusted in dependence on the stabilizer content. The supported lipid bilayer surrounding the nanoparticles was formed by the liposome spreading technique. The Lipid- coated nanoparticles were characterised using Photon Correlation Spectroscopy (PCS) and atomic force microscopy (AFM) investigations. The bioadhesive properties was proofed in a cell culture model.

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Motion of a Cell Wall Polysaccharide Observed by Atomic Force Microscopy

Macromolecules ◽

10.1021/ma000331w ◽

2000 ◽

Vol 33 (15) ◽

pp. 5680-5685 ◽

Cited By ~ 18

Author(s):

A. Patrick Gunning ◽

Alan R. Mackie ◽

Andrew R. Kirby ◽

Paul Kroon ◽

Gary Williamson ◽

...

Keyword(s):

Atomic Force Microscopy ◽

Cell Wall ◽

Cell Wall Polysaccharide ◽

Force Microscopy ◽

Atomic Force ◽

A Cell

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Deposition of Lipid Bilayers with Atomic Force Microscopy

Microscopy and Microanalysis ◽

10.1017/s1431927605050853 ◽

2005 ◽

Vol 11 (S03) ◽

pp. 44-47 ◽

Cited By ~ 1

Author(s):

G. D. Tavares ◽

M. C. de Oliveira ◽

J. M. C. Vilela ◽

M. S. Andrade

Keyword(s):

Lipid Bilayers ◽

Lipid Membranes ◽

Force Microscopy ◽

Langmuir Blodgett ◽

Flat Substrate ◽

Atomic Force ◽

Lipid Mixtures ◽

A Cell ◽

Integral Proteins ◽

Spherical Vesicles

Biological membranes are constituted of lipids organized as a two dimensional bilayer supporting peripheral and integral proteins, providing a barrier between the inside and the outside of a cell [1]. Similar membranes can be prepared from the lipid mixtures forming liposomes. The liposomes are multi or unilamellar spherical vesicles in which an aqueous volume is enclosed and can be used to encapsulate some drugs [2]. In order to better expose the details of their structure, these membranes are generally deposited on the surface of a flat substrate. These supported planar lipid membranes can also provide a model system for investigating the properties and functions of the complex cell membrane and membrane mediated processes such as recognition events and biological signal transduction. Various methods have been used to create artificial lipid membranes supported on a solid surface, being the most used the Langmuir-Blodgett monolayers formation [3], the vesicle fusion or liposome adsorption [4] and the solution spreading [5].

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A Comparison of Uric Acid Optical Detection Using as Sensitive Materials an Amino-Substituted Porphyrin and Its Nanomaterials with CuNPs, PtNPs and Pt@CuNPs

Processes ◽

10.3390/pr9112072 ◽

2021 ◽

Vol 9 (11) ◽

pp. 2072

Author(s):

Camelia Epuran ◽

Ion Fratilescu ◽

Diana Anghel ◽

Mihaela Birdeanu ◽

Corina Orha ◽

...

Keyword(s):

Atomic Force Microscopy ◽

Uric Acid ◽

Copper Nanoparticles ◽

Hybrid Material ◽

Human Environment ◽

Detection Range ◽

Force Microscopy ◽

Atomic Force ◽

High Concentrations ◽

Very High

Hybrid nanomaterials consisting in 5,10,15,20-tetrakis(4-amino-phenyl)-porphyrin (TAmPP) and copper nanoparticles (CuNPs), platinum nanoparticles (PtNPs), or both types (Pt@CuNPs) were obtained and tested for their capacity to optically detect uric acid from solutions. The introduction of diverse metal nanoparticles into the hybrid material proved their capacity to improve the detection range. The detection was monitored by using UV-Vis spectrophotometry, and differences between morphology of the materials were performed using atomic force microscopy (AFM). The hybrid material formed between porphyrin and PtNPs hasthe best and most stable response for uric acid detection in the range of 6.1958 × 10−6–1.5763 × 10−5 M, even in the presence of very high concentrations of the interference species present in human environment.

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Pathway Complexity in Supramolecular Porphyrin Self-Assembly at an Immiscible Liquid|Liquid Interface

10.26434/chemrxiv.14170202 ◽

2021 ◽

Author(s):

Iván Robayo-Molina ◽

Andrés F. Molina-Osorio ◽

Luke Guinane ◽

Syed A.M. Tofail ◽

Micheal D. Scanlon

Keyword(s):

Self Assembly ◽

Immiscible Liquid ◽

Bulk Solution ◽

Time Resolved ◽

Force Microscopy ◽

Atomic Force ◽

Aggregate Growth ◽

High Concentrations ◽

Thermodynamic Processes

<p>Nanostructures that are inaccessible through spontaneous thermodynamic processes may be formed by supramolecular self-assembly under kinetic control. In the past decade, the dynamics of pathway complexity in self-assembly have been elucidated through kinetic models based on aggregate growth by sequential monomer association and dissociation. Immiscible liquid|liquid interfaces are an attractive platform to develop well-ordered self-assembled nanostructures, unattainable in bulk solution, due to the templating interaction of the interface with adsorbed molecules. Here, we report time-resolved <i>in situ</i> UV/vis spectroscopic observations of the self-assembly of zinc(II) meso-tetrakis(4-carboxyphenyl)porphyrin (ZnTPPc) at an immiscible aqueous|organic interface. We show that the kinetically favoured metastable J-type nanostructures form quickly, but then transform into stable thermodynamically favoured H-type nanostructures. Numerical modelling revealed two parallel and competing cooperative pathways leading to the different porphyrin nanostructures. These insights demonstrate that pathway complexity is not unique to self-assembly processes in bulk solution, and equally valid for interfacial self-assembly. Subsequently, the interfacial electrostatic environment was tuned using a kosmotropic anion (citrate) in order to control the influence the pathway selection. At high concentrations, interfacial nanostructure formation was forced completely down the kinetically favoured pathway and only J-type nanostructures were obtained. Furthermore, we found by atomic force microscopy (AFM) and scanning electron microscopy (SEM) that the J- and H-type nanostructures obtained at low and high citric acid concentrations, respectively, are morphologically distinct, which illustrates the pathway-dependent material properties.</p>

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Determining Mechanical Properties of Escherichia Coli by Nanoindentation

MRS Proceedings ◽

10.1557/opl.2012.233 ◽

2012 ◽

Vol 1424 ◽

Author(s):

C. A. Wright ◽

C.J. Sullivan ◽

B. Crawford ◽

L.D. Britt ◽

M.A. Mamun ◽

...

Keyword(s):

Escherichia Coli ◽

Mechanical Properties ◽

Cell Wall ◽

Contact Area ◽

Solute Concentration ◽

Force Microscopy ◽

E Coli ◽

Atomic Force ◽

A Cell ◽

Afm Cantilever

ABSTRACTEscherichia coli, like other gram-negative bacteria, is protected from the surrounding harsh environment by a cell wall consisting of the peptidoglycan and outer membrane. Whereas the cytoplasmic membrane is the selective barrier, the cell wall provides mechanical strength for the cell. As bacteria navigate various environments, osmotic pressure can change dramatically due to changes in local solute concentration. The peptidoglycan together with the cellular proteins mitigates the osmotic stress that would otherwise cause lysis. The mechanical properties of E. coli cells and its individual layers have been largely indeterminable until the recent development of probe-based measurement tools. Since their invention, scientists have reported significant data measuring elasticity, modulus, and stiffness using atomic force microscopy (AFM). Fundamentally, in order to determine these mechanical properties through probe-based techniques, the contact area and load should be well defined. The load can be precisely calculated through the AFM cantilever spring constant. However, the silicon tip contact area can only be estimated, potentially leading to compounding uncertainties. Therefore, we developed a methodology to determine nanomechanical properties of E. coli using a nanoindenter.

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Protein Adsorption to Titanium and Zirconia Using a Quartz Crystal Microbalance Method

BioMed Research International ◽

10.1155/2017/1521593 ◽

2017 ◽

Vol 2017 ◽

pp. 1-8 ◽

Cited By ~ 12

Author(s):

You Kusakawa ◽

Eiji Yoshida ◽

Tohru Hayakawa

Keyword(s):

Surface Roughness ◽

Protein Adsorption ◽

Quartz Crystal Microbalance ◽

Quartz Crystal ◽

Adsorption Rate ◽

Force Microscopy ◽

Atomic Force ◽

A Cell ◽

Addition Amount

Protein adsorption onto titanium (Ti) or zirconia (ZrO2) was evaluated using a 27 MHz quartz crystal microbalance (QCM). As proteins, fibronectin (Fn), a cell adhesive protein, and albumin (Alb), a cell adhesion-inhibiting protein, were evaluated. The Ti and ZrO2 sensors for QCM were characterized by atomic force microscopy and electron probe microanalysis observation, measurement of contact angle against water, and surface roughness. The amounts of Fn and Alb adsorbed onto the Ti and ZrO2 sensors and apparent reaction rate were obtained using QCM measurements. Ti sensor showed greater adsorption of Fn and Alb than the ZrO2 sensor. In addition, amount of Fn adsorbed onto the Ti or ZrO2 sensors was higher than that of Alb. The surface roughness and hydrophilicity of Ti or ZrO2 may influence the adsorption of Fn or Alb. With regard to the adsorption rate, Alb adsorbed more rapidly than Fn onto Ti. Comparing Ti and ZrO2, Alb adsorption rate to Ti was faster than that to ZrO2. Fn adsorption will be effective for cell activities, but Alb adsorption will not. QCM method could simulate in vivo Fn and Alb adsorption to Ti or ZrO2.

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