Time-resolved chloroquine-induced relaxation of supercoiled plasmid DNA

Herein, we report on the in vitro change of DNA conformation of plasmids bound to a 3-aminopropyl-modified mica surface and monitoring the events by atomic force microscopy (AFM) imaging under near physiological conditions. In our study, we used an intercalating drug, chloroquine, which is known to decrease the twist of the double helix and thus altered the conformation of the whole DNA. During our experiments, a chloroquine solution was added while imaging a few highly condensed plasmid nanoparticles in solution. AFM images recorded after the drug addition clearly show a time-resolved relaxation of these bionanoparticles into a mixture of loose DNA strands.     

Atomic force microscopy study of the adsorption and electrostatic self-organization of poly(amidoamine) dendrimers on mica

The adsorption behavior of poly(amidoamine) dendrimers to mica surfaces was investigated as a function of ionic strength and pH. The conformation and lateral distribution of the adsorbed dendrimers of generations G8 and G10 were obtained ex situ by tapping mode atomic force microscopy (AFM). The deposition kinetics of the dendrimers was found to follow a diffusion-limited process. Fractional surface coverage and pair correlation functions of the adsorbed dendrimers were obtained from the AFM images. The data are interpreted in terms of the random sequential adsorption (RSA) model, where electrostatic repulsion due to overlapping double layers is considered. Although the general trends typical for an RSA-determined process are well-reproduced, quantitative agreement is lacking at low ionic strengths.     

Synthesis and property of helical poly(phenylacetylene)s bearing chiral ruthenium complexes and real space imaging of meso- and nanoscopic structures by atomic force microscopy

Novel sets of helical poly(phenylacetylene)s bearing a chiral ruthenium (Ru) complex with opposite chirality (Δ and Λ forms) as a bulky pendant (poly- 1 and poly- 2 ) were synthesized through the polymerization of the corresponding optically pure phenylacetylenes with a rhodium catalyst, and their structures in solution and morphology on solid substrates were investigated with NMR, ultraviolet–visible, and circular dichroism (CD) spectroscopies and with atomic force microscopy (AFM), respectively. The obtained cis–transoidal polymers (poly- 1 and poly- 2 ) showed characteristic Cotton effects in the region of metal-to-ligand charge transfer of the chiral Ru pendants. Poly- 1 and poly- 2 were thought to have a predominantly one-handed helical conformation induced by the chiral pendants. However, the apparent Cotton effects derived from the helically twisted π-conjugated polymer backbone could not be observed, probably because of the strong chiral chromophoric pendants. However, in the AFM images, the helical polymers adsorbed on mica could be easily discerned as isolated strands, and the visualization and discrimination of the right- and left-handed helical structures of the chiral polymers were achieved by high-resolution AFM imaging. On the basis of the AFM observations together with the CD measurements and computational calculation results, possible structures of poly- 1 and poly- 2 were examined. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4621–4640, 2004     

DNA共价结合在化学修饰云母片上的AFM研究

原子力显微镜(AFM)自1986年发明以来,已经成为生物学研究领域中的一个有效工具,尤其在核酸及其它生物大分子结构方面的应用已成为普遍关注的热点.原子力显微镜要求基底达到原子级平整,硅片和玻璃表面的起伏很大,因而原子级平整的云母具有重要的价值.     

Interaction of human plasma fibrinogen with commercially pure titanium as studied with atomic force microscopy and X-ray photoelectron spectroscopy

The surface of a biomaterial interacts with the body fluid upon implantation in the human body. The biocompatibility of a material is strongly influenced by the adsorption of proteins onto the surface. Titanium is frequently used as a biomaterial for implants in orthopedics and cardiovascular devices. Understanding the biocompatibility is very important to improve implants. The surface chemistry of an implant material and its influence on the interaction with body fluid is crucial in that perspective. The main goal of this study was to investigate the conformation of human plasma fibrinogen (HPF) adsorbed on commercially pure titanium (CP Ti) on a molecular level by means of ex situ atomic force microscopy (AFM). With X-ray photoelectron spectroscopy combined with argon ion beam depth profiling, it was shown that the oxide layer present at the surface was mainly composed of TiO2, with a small percentage of Ti2O3. Ex situ AFM imaging showed the conformation of HPF on CP Ti. Single molecules and aggregates of fibrinogen were observed. The trinodular structure of single HPF molecules (two spherical D domains at the distal ends of the extended molecule and the central spherical E domain) adsorbed onto CP Ti was visualized. Aggregate formation through the connection of the D domains of the HPF molecules was observed on CP Ti. The alphaC domains of HPF were not visible on CP Ti. The ex situ AFM images indicated conformational changes of HPF upon adsorption onto CP Ti. The conformation of the adsorbed HPF molecules was different on mica and titanium. The difference in wettability between both substrates caused a larger spread of the protein on the CP Ti surface and thus resulted in a larger perturbation to the native structure of HPF as compared to mica.     

Dewetting pattern and stability of thin xyloglucan films adsorbed on silicon and mica

Thin polysaccharide films prepared with xyloglucan (XG), a neutral polysaccharide extracted from the seeds of Guibourtia hymenifolia were prepared by spin-coating and drop deposition under pH3, pH5 and pH12, on silicon and mica substrates. Atomic force microscopy (AFM) images show flat nanoporous matrices with additional grain-like structures on both mica and silicon for pH 3 and pH 5. However, X-ray photoelectron spectroscopy (XPS) and Auger spectra of these adsorbed biopolymers prepared under alkaline condition (pH 12) reveal that Na⁺ ions from the solution interact with the mica substrate surface and with XG forming chemical bonds. Both XPS and Auger results suggest XG depolymerisation during adsorption, caused by an alkaline ß-base catalyzed degradation mechanism, which is consistent with the more basic character of the mica surface under these conditions. Thus, the polysaccharide diffusion is inhibited during dewetting due to the surface bonding. On the other hand, the interaction of Na⁺ in solution with the silicon surface is weaker, favoring its interaction with the polysaccharide, conserving the overall polymer structure of XG and allowing the biopolymer to slip and diffuse during dewetting, forming the final branched fractal structure.     

The breakage and damage of plasmid DNA photocatalized by TiO2/carbon nanotube composites

In this paper, the plasmid DNA was used as a target to evaluate the bioeffect of TiO₂/Carbon Nanotube (CNT) composites. The conformational change and breakage of DNA induced by the composites were characterized by the integrated tools of electrochemistry, circular dichroism (CD), atomic force microscopy (AFM), and DNA electrophoresis. At the early stage of incubation, the DNA double helix conformation was substantially changed by TiO₂/CNT composites. Both electrophoresis and electrochemistry results suggested the breakage and damage appeared on the native DNA molecules. When DNA was treated longer by TiO₂/CNT, DNA molecules were broken into fragment. AFM images confirmed the process. The DNA damage was deemed to be a gradual process: supercoiled plasmid DNA was first damaged to nicked‐circle structure, then further to linear form, and then DNA fragment. Copyright © 2011 John Wiley & Sons, Ltd.     

Adsorption and desorption of polymer/surfactant mixtures at solid-liquid interfaces: substitution experiments

The adsorption of mixtures of aqueous solutions of cationic hydroxyethylcellulose polymer JR400 and anionic surfactant, sodium dodecyl sulfate, using atomic force microscopy (AFM) has been studied. Samples with various compositions from different regions of the ternary phase diagram presented in our previous work were imaged by atomic force microscopy on freshly cleaved mica, and hydrophobically modified mica and silica in soft-contact mode. A series of "washing" (subsequent injection of compositions with gradually decreasing polymer/surfactant ratio) and "scratching" (mechanical agitation of the surface material with an AFM tip) experiments were performed. It was revealed that the morphology of the adsorbed layer altered in a manner following the changes in morphology in the bulk solution. These changes were evidenced in cluster formation in the layer. The results suggest that the influence of the surface was limited to the formation of the adsorbed layer where the local concentrations of polymer and surfactant were higher than those in the bulk. All further modifications were driven by changes in the mixture composition in bulk. Force measurements upon retraction reveal the formation of network structures within the surface aggregates that will greatly slow structural reequilibration.     

AFM诱导正十八硫醇在金基底上的选择性生长

扫描探针显微镜（SCCnningPF0boMICCOSCOPy,SPM）由于其极高的空间分辨能力和高度的可控性,已成为纳米尺度加工的有力工具［‘·’j．自Schneir等［’j报道原子级平整金基底的制备和用装备An针尖的扫描隧道显微镜（ScanningTunnelingMicroscoPy,STM）在基底上制备金纳米点以来,有关在All和HOPG等基底上制备由金点构成的任意图案的方法及用导电原子力显微镜（AtomicForceM卜roscopy,AFM）在HOPG和St基底上制备金点阵的工作已有许多报道［‘·’‘．用导电AFM和TaPPingmodeAFM”,’‘对St进行直接氧化可在其表面加…     

Conformational change in an isolated single synthetic polymer chain on a mica surface observed by atomic force microscopy

The random coil conformation of an isolated conventional synthetic polymer chain was clearly imaged by atomic force microscopy (AFM). The sample used was a poly(styrene)-block-poly(methyl methacrylate) diblock copolymer. A very dilute solution of the copolymer with benzene was spread on a water surface. The structure thus formed on water was subsequently transferred and deposited onto mica at various surface pressures and observed under AFM. The AFM images obtained with films deposited at a low surface pressure (<0.1 mN/m) showed a single polystyrene (PS) block chain aggregated into a single PS particle with a single poly(methyl methacrylate) (PMMA) block chain emanating from the particle. Immediately after the deposition, the single PMMA block chain aggregated to form a condensed monolayer around the polystyrene particles. However, after exposing the deposited film to highly humid air for 1 day, the PMMA chains spread out so that the single PMMA block chain could be identified as a random coil on the substrate. The thin water layer formed on the mica substrate in humid air may enable the PMMA block chain to be mobilized on the substrate, leading to the conformational rearrangement from the condensed monolayer conformation to an expanded and elongated coil. The elongation of the PMMA chain was highly sensitive to the humidity; the maximum elongation was obtained at 79% relative humidity. The elongation was a slow process and took about 20 h.     

DNA分子结构的多态性研究 (Ⅱ) 吖啶橙凝聚体变化诱导的质粒DNA大分子构象的研究

利用吸收光谱和荧光光谱方法,研究了吖啶橙（ＡＯ）与质粒ＤＮＡ水溶液、以及含胶束介质的吖啶橙与质粒ＤＮＡ溶液体系的相互结合作用及减色效应。结果表明：吖啶橙对质粒ＤＮＡ的吸收光谱有减色效应;含十二烷基硫酸钠（ＳＤＳ）的ＡＯ水溶液体系中,随着ＳＤＳ浓度的增加,其光谱结果表现为由凝聚态向单体的转化。而在含十二烷基硫酸钠（ＳＤＳ）的ＡＯ与质粒ＤＮＡ溶液体系中,吖啶橙凝聚态随ＳＤＳ浓度的增加,对ＡＯ与质粒ＤＮＡ相互结合产生协同的减色效应,使质粒ＤＮＡ空间结构发生缩拢。进一步采用电泳法研究了ＡＯ凝聚态可能对质粒ＤＮＡ构象的影响,结果表明：在ＡＯ与质粒ＤＮＡ溶液体系中,ＡＯ浓度的增加对质粒ＤＮＡ构象未产生影响;而在含有ＳＤＳ的ＡＯ与质粒ＤＮＡ的溶液体系中,由于ＳＤＳ对ＡＯ凝聚态的解聚作用,以及ＳＤＳ对质粒ＤＮＡ减色效应的协同作用,使得质粒ＤＮＡ的构象发生变化,诱导质粒ＤＮＡ形成超螺旋构象     

Formation of aminosilane-functionalized mica for atomic force microscopy imaging of DNA

Factors affecting the functionalization of mica with aminosilanes, in particular, aminopropyltriethoxysilane (APTES-mica), formed from the vapor phase have been systematically studied. The relative humidity (RH) during vapor deposition has been varied, and postdeposition treatment through baking has been used, as well as the comparison of mono and trifunctionality, to investigate how optimal surfaces for AFM imaging of DNA are formed. It is found that the stability of the APTES layers is a consequence of lateral polymerization and not covalent attachment to the mica substrate. At low RH (<25%), DNA adopts an open, well-resolved conformation, whereas at >25% RH, DNA surface-induced condensation occurs. Contact mode AFM scratching experiments show that two main structures of the silane layer exist at different humidity: a monolayer exists at RH < 25%, and a bilayer structure exists at RH > 25%. Finally, structural changes that these two layer types undergo after baking at 150 degrees C were investigated by AFM and X-ray photoelectron spectroscopy (XPS), and these now prevented DNA from binding to the APTES-mica, except in the presence of Mg(II) ions.     

Construction and control of plasmid DNA network

The influences of different cations on plasmid DNA network structures on a mica substrate were investigated by atomic force microscopy (AFM). Interactions between the DNA strands and mica substrate, and between the DNA strands themselves were more strongly influenced by the complex cations (Fe(phen)3(2+), Ni(phen)3(2+), and Co(phen)3(3+)) than by the simple cations (Mg2+, Mn2+, Ni2+, Ca2+, Co3+). The mesh height of the plasmid DNA network was higher when the complex cations were added to DNA samples. The mesh size decreased with increasing DNA concentration and increased with decreasing DNA concentration in the same cation solution sample. Hence, plasmid DNA network height can be controlled by selecting different cations, and the mesh size can be controlled by adjusting plasmid DNA concentration.     

Dissimilar pH-dependent adsorption features of bovine serum albumin and α-chymotrypsin on mica probed by AFM

We studied bovine serum albumin (BSA) and α-chymotrypsin adsorption onto mica surfaces over a large pH range by atomic force microscopy (AFM) measurements in liquid. Data analyses (height, roughness and roughness factor) brought new insights on the conformation of proteins in soil environments, with mica as a model of soil phyllosilicates and non-hydrophobic surfaces. Validation of AFM approach was performed on BSA, whose behavior was previously described by nuclear magnetic resonance and infra-red spectroscopic methods. Maximum adsorption was observed near the isoelectric point (IEP). A stronger interaction and a lower amount of adsorbed proteins were observed below the IEP, which contrasted with the progressive decrease of adsorption above the IEP. We then studied the adsorption of α-chymotrypsin, a proteolytic enzyme commonly found in soils. AFM pictures demonstrated a complete coverage of the mica surface at the IEP in contrast to the BSA case. Comparison of the AFM data with other indirect methods broadened the understanding of α-chymotrypsin adsorption process through the direct display of the protein adsorption patterns as a function of pH.     

Template-directed self-assembly of a designed amphiphilic hexapeptide on mica surface

Self-assembly of small molecules into highly ordered nanostructures offers many important potential applications in science research and industry. Precise self-assembling with the assistance of inorganic substrate is considered as an ideal strategy. In this experiment, the highly ordered mica surface was used to template the assembling of a novel designed amphiphilic hexapeptide to form orderly parallel fibers. The nanostructure and the self-assembly mechanism were investigated by atomic force microscopy (AFM), transmission electron microscopy, Fourier transform infrared spectroscopy, and circular dichroism techniques. By the experimental results, a dramatic conformation transition from random coil and/or α-helix into β-sheet was found after the peptide assembled on the mica surface under certain conditions, which was considered as a key factor for the ordered nanostructure. Finally, according to the AFM images and the simulated length of peptide molecules, a trilaminar β-sheet structure model was proposed to explain the hierarchical self-assembly mechanism.     

Self-organization of a wedge-shaped surfactant in monolayers and multilayers

The self-organization behavior of a wedge-shaped surfactant, disodium-3,4,5-tris(dodecyloxy)phenylmethylphosphonate, was studied in Langmuir monolayers (at the air-water interface), Langmuir-Blodgett (LB) monolayers and multilayers, and films adsorbed spontaneously from isooctane solution onto a mica substrate (self-assembled films). This compound forms an inverted hexagonal lyotropic liquid crystal phase in the bulk and in thick adsorbed films. Surface pressure isotherm and Brewster angle microscope (BAM) studies of Langmuir monolayers revealed three phases: gas (G), liquid expanded (LE), and liquid condensed (LC). The surface pressure-temperature phase diagram was determined in detail; a triple point was found at approximately 10 degrees C. Atomic force microscope (AFM) images of LB monolayers transferred from various regions of the phase diagram were consistent with the BAM images and indicated that the LE regions are approximately 0.5 nm thinner than the LC regions. AFM images were also obtained of self-assembled films after various adsorption times. For short adsorption times, when monolayer self-assembly was incomplete, the film topography indicated the coexistence of two distinct monolayer phases. The height difference between these two phases was again 0.5 nm, suggesting a correspondence with the LE/LC coexistence observed in the Langmuir monolayers. For longer immersion times, adsorbed multilayers assembled into highly organized periodic arrays of inverse cylindrical micelles. Similar periodic structures, with the same repeat distance of 4.5 nm, were also observed in three-layer LB films. However, the regions of organized periodic structure were much smaller and more poorly correlated in the LB multilayers than in the films adsorbed from solution. Collectively, these observations indicate a high degree of similarity between the molecular organization in Langmuir layers/LB films and adsorbed self-assembled films. In both cases, monolayers progress through an LE phase, into LE/LC coexistence, and finally into LC phase as surface density increases. Following the deposition of an additional bilayer, the film reorganizes to form an array of inverted cylindrical micelles.     

Anthracycline-dependent heat-induced transition from positive to negative supercoiled DNA

The conformational stability of individual DNA topoisomers depends on the concentration of DNA intercalating drugs. To study the DNA-drug interaction, we used ethidium bromide (EtBr) and negative supercoiled pUC19 as a model system. The effects of two anthracyclines widely used in cancer therapy, daunorubicin (Dau) and doxorubicin (Doxo), and EtBr were compared. In spite of their different chemical structures and intercalation mode, all intercalating agents show similar effects on the conformational stability of supercoiled DNA. Our observations show that the studied intercalators have at least two main effects on the supercoiled DNA: (i) they decrease the level of negative supercoiling and, at certain concentrations, they may induce positive supercoiling in DNA; (ii) a temperature increase can cause a recovery of negative supercoiling in DNA. The conformational stability of plasmid DNA-drug complexes has been investigated by temperature gradient gel electrophoresis (TGGE). We demonstrate the suitability of TGGE for this purpose, because it offers a global view on DNA-drug complexes over a continuous range of temperature. Images of DNA plasmids adsorbed onto a substrate at different temperatures and drug concentrations were acquired by atomic force microscopy (AFM), allowing us to distinguish directly the conformation chirality assumed by the plasmid under different conditions confirming TGGE results. Our detection system allows to characterize unknown drugs and to determine their intercalating properties.     

Adsorption of plasmid DNA to a natural organic matter-coated silica surface: kinetics, conformation, and reversibility

A quartz crystal microbalance with dissipation (QCM-D) has been used to determine the adsorption rate of ampicillin-resistant linear and supercoiled plasmid DNA onto a silica surface coated with natural organic matter (NOM). The structure of the resulting adsorbed DNA layer was determined by analyzing the viscoelastic properties of the adsorbed DNA layers as they formed and were then exposed to solutions of different ionic composition. The QCM-D data were complemented by dynamic light scattering measurements of diffusion coefficients of the DNA molecules as a function of solution ionic composition. The obtained results suggest that electrostatic interactions control the adsorption and structural changes of the adsorbed plasmid DNA on the NOM-coated silica surface. The adsorption of DNA molecules to the NOM layer took place at moderately high monovalent (sodium) electrolyte concentrations. A sharp decrease in solution ionic strength did not result in the release of the adsorbed DNA, indicating that DNA adsorption on the NOM-coated silica surface is irreversible under the studied solution conditions. However, the decrease in electrolyte concentration influenced the structure of the adsorbed layer, causing the adsorbed DNA to adopt a less compact conformation. The linear and supercoiled DNA had similar adsorption rates, but the linear DNA formed a thicker and less compact adsorbed layer than the supercoiled DNA.     

AFM imaging of adsorbed Nafion polymer on mica and graphite at molecular level

Perfluorosulfonic acid ionomer (PFSA, specifically Nafion at EW = 975 g/mol) was visualized at the single molecule level using atomic force microscopy (AFM) in liquid. The diluted commercial Nafion dispersion shows an apparent M(w) = 1430 kg/mol and M(w)/M(n) = 3.81, which is assigned to chain aggregation. PFSA aggregates, imaged on mica and HOPG during adsorption from EtOH-H(2)O solvent at pH(e) 3.0 (below isoelectric point), showed a stable, segmented rod-like conformation. This structure is consistent with earlier NMR, SAXS/SANS, and TEM results that support a stiff helical Nafion conformation with long persistence length, a sharp solvent-polymer interface, and an extension of the sulfonated side chain into solution. Adsorption of Nafion structures on HOPG was observed at even higher pH(e) from EtOH due to screening of the repulsive electrostatic interaction in lower dielectric constant solvent, while the chain adopted an expanded coil conformation. These measurements provided direct evidence of the chain aggregation in EtOH-H(2)O solution and revealed their equilibrium conformations for adsorption on two model surfaces, highly ordered pyrolitic graphite (HOPG) and mica. The commercial Nafion dispersion was autoclaved at 0.10% w/w in nPrOH/H(2)O = 4:1 v/v solvent at 230 °C for 6 h to give a single-chain dispersion with M(w) = 310 kg/mol and M(w)/M(n) = 1.60. The autoclaved chains adopt an electrostatically stabilized compact globule conformation as observed by AFM imaging of the single PFSA molecules after rapid deposition on mica and HOPG at a low surface coverage.     

Anionic polyelectrolyte adsorption on mica mediated by multivalent cations: a solution to DNA imaging by atomic force microscopy under high ionic strengths

Adsorption of DNA molecules on mica, a highly negatively charged surface, mediated by divalent or trivalent cations is considered. By analyzing atomic force microscope (AFM) images of DNA molecules adsorbed on mica, phase diagrams of DNA molecules interacting with a mica surface are established in terms of concentrations of monovalent salt (NaCl) and divalent (MgCl2) or multivalent (spermidine, cobalt hexamine) salts. These diagrams show two transitions between nonadsorption and adsorption. The first one arises when the concentration of multivalent counterions is larger than a limit value, which is not sensitive to the monovalent salt concentration. The second transition is due to the binding competition between monovalent and multivalent counterions. In addition, we develop a model of polyelectrolyte adsorption on like-charged surfaces with multivalent counterions. This model shows that the correlations of the multivalent counterions at the interface between DNA and mica play a critical role. Furthermore, it appears that DNA adsorption takes place when the energy gain in counterion correlations overcomes an energy barrier. This barrier is induced by the entropy loss in confining DNA in a thin adsorbed layer, the entropy loss in the interpenetration of the clouds of mica and DNA counterions, and the electrostatic repulsion between DNA and mica. The analysis of the experimental results provides an estimation of this energy barrier. We then discuss some important issues, including DNA adsorption under physiological conditions.