Assembling and imaging of his-tag green fluorescent protein on mica surfaces studied by atomic force microscopy and fluorescence microscopy

Study on the Interactions Between Cisplatin and Cadherin by Fluorescence Spectrometry and Atomic Force Microscopy

Cisplatin is an important platinum drug in cancer chemotherapy in clinical practice. It is well established that the main target of cisplatin is nuclear DNA. However, recent studies have demonstrated that platinum drugs may act on some important functional proteins in the human body. E-cadherin is a newly discovered glycoprotein that has been regarded as an important sign of the occurrence and development of some tumors. This study examines the interactions between cisplatin and E-cadherin by fluorescence spectrometry and atomic force microscopy (AFM). The fluorescence spectrometry results indicated that cisplatin can efficiently quench the fluorescence of E-cadherin. The calculated binding constant Kb was 3.20 × 106 (25 ℃), 1.36 × 106(31 ℃), and 8.22 × 105 L mol-1 (37 ℃). These results reveal that the fluorescence quenching effect of cisplatin on E-cadherin is static quenching. The obtained thermodynamic parameters ΔH < 0, ΔS < 0, and ΔG < 0, indicate that the binding of cisplatin on E-cadherin is a spontaneous process dominated by hydrogen bonds and Van der Waals forces. The AFM results revealed that E-cadherins are interlaced with each other to form a spherical-chain structure. The addition of cisplatin can significantly disrupt the interlaced structure of the E-cadherin molecules.

Influenza A virus hemagglutinin prevents extensive membrane damage upon dehydration

While the molecular mechanisms of virus infectivity are rather well known, the detailed consequences of environmental factors on virus biophysical properties are poorly understood. Seasonal influenza outbreaks are usually connected to the low winter temperature, but also to the low relative air humidity. Indeed, transmission rates increase in cold regions during winter. While low temperature must slow degradation processes, the role of low humidity is not clear. We studied the effect of relative humidity on a model of Influenza A H1N1 virus envelope, a supported lipid bilayer containing the surface glycoprotein hemagglutinin (HA), which is present in the viral envelope in very high density. For complete cycles of hydration, dehydration and rehydration, we evaluate the membrane properties in terms of structure and dynamics, which we assess by combining confocal fluorescence microscopy, raster image correlation spectroscopy, line-scan fluorescence correlation spectroscopy and atomic force microscopy. Our findings indicate that the presence of HA prevents macroscopic membrane damage after dehydration. Without HA, fast membrane disruption is followed by irreversible loss of lipid and protein mobility. Although our model is principally limited by the membrane composition, the macroscopic effects of HA under dehydration stress reveal new insights on the stability of the virus at low relative humidity.

DNA-Directed Assembly of Carbon Nanotube-Protein Hybrids

Here, we report the controlled assembly of SWCNT–GFP hybrids employing DNA as a linker. Two distinct, enriched SWCNTs chiralities, (6,5), (7,6), and an unsorted SWCNT solution, were selectively functionalized with DNA and hybridized to a complementary GFP^DNA conjugate. Atomic force microscopy images confirmed that GFP attachment occurred predominantly at the terminal ends of the nanotubes, as designed. The electronic coupling of the proteins to the nanotubes was confirmed via in-solution fluorescence spectroscopy, that revealed an increase in the emission intensity of GFP when linked to the CNTs.

Spatially selective binding of green fluorescent protein on designed organosilane nanopatterns prepared with particle lithography

A practical approach for preparing protein nanopatterns has been to design surface templates of nanopatterns of alkanethiols or organosilanes that will selectively bind and localize the placement of biomolecules. Particle lithography provides a way to prepare millions of protein nanopatterns with a few basic steps. For our nanopatterning strategy, organosilanes with methoxy and sulfhydryl groups were chosen as a surface template. Green fluorescent protein (GFP) was selected as a model for patterning. Areas of 2-[methoxy (polyethyleneoxy)6-9propyl]trichlorosilane (MPT-silane) are effective as a matrix for resisting the attachment of proteins, whereas nanopatterns with sulfur groups provide reactive sites for binding linker groups to connect proteins. A protocol with particle lithography was designed to make a surface template of nanopatterns of (3-mercaptopropyl)trimethoxysilane (MPTMS) surrounded by a methoxy terminated matrix. The sulfhydryl groups of the MPTMS nanopatterns were activated with a sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate linker. The activated regions of MPTMS furnished sites for binding GFP. Samples were characterized with atomic force microscopy after successive steps of the patterning protocol to evaluate the selectivity of protein binding. Direct views of the protein bound selectively to designated sites of MPTMS are presented, as evidence of robust and reproducible patterning. Nanoscale patterns of proteins can be used for surfaces of biochips and biosensors, and also for immunochemistry test platforms.

Structural study on the interactions of oxaliplatin and linear DNA

Damage to cellular DNA is believed to determine the cytotoxicity of oxaliplatin. However, high resolution structures formed by oxaliplatin and different linear DNA remain unclear. This study characterized, the key structures of different linear DNA in the platination process by UV absorption spectra and atomic force microscopy (AFM). Bathochromic shift and hyperchromicity in UV spectra after addition of oxaliplatin revealed that it can disrupt base stacking of DNA in the platination process. AFM results of different linear DNA indicated that, the platination process can induce DNA change from an extended conformation to the network structure with many kinks and finally to the compact particles, or toroids with increasing the incubation time. All AFM results confirmed that, platination of different linear DNA by oxaliplatin is a time depended process. The present AFM results provide, structural evidence about the interactions between oxaliplatin and different linear DNA containing multiple targets. SCANNING 38:880-888, 2016. © 2016 Wiley Periodicals, Inc.

Site-specific immobilization of protein layers on gold surfaces via orthogonal sortases

We report a site-specific, sortase-mediated ligation to immobilize proteins layer-by-layer on a gold surface. Recombinant fluorescent proteins with a Sortase A recognition tag at the C-terminus were immobilized on peptide-modified gold surfaces. We used two sortases with different substrate specificities (Streptococcus pyogenes Sortase A and Staphylococcus aureus Sortase A) to immobilize layers of GFP and mCherry site-specifically on the gold surface. Surfaces were characterized using fluorescence and atomic force microscopy after immobilizing each layer of protein. Fluorescent micrographs showed that both protein immobilization on the modified gold surface and protein oligomerization are sortase-dependent. AFM images showed that either homogenous protein monolayers or layers of protein oligomers can be generated using appropriately tagged substrate proteins. Using Sortase A variants with orthogonal peptide substrate specificities, site-specific immobilization of appropriately tagged GFP onto a layer of immobilized mCherry was achieved without disruption of the underlying protein layer.

Adsorption of human serum albumin onto highly orientated pyrolytic graphite surface studied by atomic force microscopy

It is important to know the adsorption behavior and assembly structure of human serum albumin (HSA) molecules onto a carbonaceous substrate for further application of carbon nanomaterials in biomedical field. Individual HSA molecules and oligmers (dimer and trimer) adsorbed onto HOPG surface have been imaged by atomic force microscopy (AFM). Individual HSA molecule appeared as an ellipsoid on HOPG surface with average length of 12.6, width of 6.5, and height of 1.9 nm when they were incubated at the physiological condition (pH 7.4). HSA molecules also can form the interconnected chains, uniform network, and monolayer by tuning the initial concentrations and adsorption time. Furthermore, HSA molecules can assemble into quite different network structures and irregular chains at pH of 2, 5, and 10. This study could expand our knowledge of the interactions between protein and carbonaceous surfaces.

Toward structurally defined carbon dots as ultracompact fluorescent probes

There has been much discussion on the need to develop fluorescent quantum dots (QDs) as ultracompact probes, with overall size profiles comparable to those of the genetically encoded fluorescent tags. In the use of conventional semiconductor QDs for such a purpose, the beautifully displayed dependence of fluorescence color on the particle diameter becomes a limitation. More recently, carbon dots have emerged as a new platform of QD-like fluorescent nanomaterials. The optical absorption and fluorescence emissions in carbon dots are not bandgap in origin, different from those in conventional semiconductor QDs. The absence of any theoretically defined fluorescence color-dot size relationships in carbon dots may actually be exploited as a unique advantage in the size reduction toward having carbon dots serve as ultracompact QD-like fluorescence probes. Here we report on carbon dots of less than 5 nm in the overall dot diameter with the use of 2,2'-(ethylenedioxy)bis(ethylamine) (EDA) molecules for the carbon particle surface passivation. The EDA-carbon dots were found to be brightly fluorescent, especially over the spectral range of green fluorescent protein. These aqueous soluble smaller carbon dots also enabled more quantitative characterizations, including the use of solution-phase NMR techniques, and the results suggested that the dot structures were relatively simple and better-defined. The potential for these smaller carbon dots to serve as fluorescence probes of overall sizes comparable to those of fluorescent proteins is discussed.

Unusual DNA structures formed on bare highly oriented pyrolytic graphite surfaces studied by atomic force microscopy

It is important to know the detailed DNA structure on carbonaceous surfaces for further application of DNA-functionalized carbonaceous materials in diverse research areas. In this study, the topographic and structural characteristics of the separated single DNA molecules and their assembly on highly oriented pyrolytic graphite (HOPG) surfaces have been investigated by atomic force microscopy (AFM). AFM results indicate that both circular and linear DNA molecules tend to form hexagonal patterns along with some unusual structures that include node, protrusion, cruciform, parallel single-stranded DNA (ssDNA), and compact zigzag. Furthermore, parallel ssDNA patterns and their crossed structures have been obtained under high-temperature conditions. Our AFM results reveal that a bare HOPG surface can induce DNA molecules to form various unusual structures. This finding is helpful for understanding the adsorption behavior of DNA on other carbonaceous surfaces such as carbon nanotubes and graphene. In addition, the hexagonal DNA patterns in this study are similar to those formed on the alkylamine-modified HOPG surface, which implies that a bare HOPG, without any chemical modification, has a strong ability to align biomolecules. This study could expand our knowledge of the diversities of DNA structures and the aligning ability of carbonaceous surfaces.

Fluorescent protein senses and reports mechanical damage in glass-fiber-reinforced polymer composites

Yellow fluorescent protein (YFP) is used as a mechanoresponsive layer at the fiber/resin interface in glass-fiber-reinforced composites. The protein loses its fluorescence when subjected to mechanical stress. Within the material, it reports interfacial shear debonding and barely visible impact damage by a transition from a fluorescent to a non-fluorescent state.

Analysis of DNA interactions using single-molecule force spectroscopy

Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.

Electrodeposition of polymer nanodots with controlled density and their reversible functionalization by polyhistidine-tag proteins

We present a simple and rapid procedure for producing polymer-coated substrates that can be easily functionalized by ion-chelating proteins. The procedure consists of depositing 18 nm metal-chelating cyclam-modified polymer nanoparticles (cyclam-nps) onto a conductive substrate (an Indium Tin Oxide (ITO) electrode) from an aqueous dispersion of Cu(2+)-loaded cyclam-nps while being subjected to a direct current (DC) field. The density of deposited nps as measured by AFM is shown to be in direct correlation to the concentration of nps in the dispersion with deposition of the particles taking less than 5 s. Because of the functionalization of the nps with cyclam groups, they can be used as anchoring sites for 6-Histidine (6-His) tagged proteins through complexation with divalent metal ions. In this work 6-His Green Fluorescent Protein (6-His GFP) is used as a model protein. The characterization by fluorescence microscopy clearly shows that the protein affinity was ion dependent and that the 6-His GFP density can be controlled by np density, which is itself easily tunable. AFM observations confirmed the immobilization of 6-His GFP onto cyclam-nps and its subsequent removal by treatment with ethylenediaminetetraacetic acid (EDTA).

Imaging and studying human topoisomerase I on mica surfaces in air and in liquid by atomic force microscopy

In this study, the topography of human topoisomerase I (TOPO I) on mica surfaces in air and in liquid has been studied by atomic force microscopy (AFM). The average height of TOPO I on mica surface in air measured by AFM was 2.59+/-0.32 nm. After adsorption of the 0.3 U/microl TOPO I on mica surfaces for 2 h, and then imaged in liquid by AFM, well-separated single TOPO I was observed. The average height of TOPO I on mica surfaces in liquid measured by AFM was 2.93+/-0.42 nm. After adsorption of the 4 U/microl TOPO I on mica surfaces for 1.5 h, TOPO I monolayer can be formed. The produced TOPO I monolayer on mica was flat and exhibited good stability.