Investigations of DNA-mediated protein oxidation

DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA π-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt π-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA π-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]^3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins.

Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding E. coli Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.

Further work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)₂, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)₂ is substituted with poly(dAdT)₂, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species.

We have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in E. coli Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at g = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate.

DNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.

While the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]^3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]³⁺ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells.

In conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.

Thin film shape memory alloys and microactuators

For Micro-electro-mechanical System (MEMS) applications, TiNi-based thin film Shape Memory Alloys (SMAs) possess many desirable properties, such as high power density, large transformation stress and strain upon heating and cooling, superelasticity and biocompatibility. In this paper, recent development in TiNi-based thin film SMA and microactuator applications is discussed. The topics related to film deposition and characterisation is mainly focused on crystal nucleation and growth during annealing, film thickness effect, film texture, stress induced surface relief, wrinkling and trenches as well as Temperature Memory Effect (TME). The microactuator applications are mainly focused on microvalve and microcage for biological applications, micromirror for optical applications and data storage using nanoindentation method. Copyright © 2009, Inderscience Publishers.

Gas-phase production of multifunctional composite nanoparticles by photoinduced chemical vapor deposition

As these results indicate, photo-CVD coating is a robust process that allows for the creation of core-shell nanoparticles. In the present work we demonstrated that photo-CVD can effectively coat Fe2O3 particles with silica for purposes of biological applications. TDMA results combined with TEM images indicate that all particles are effectively coated and that particle coating thicknesses can be tuned to desired thickness depending on the application. In addition, the ability to vary coating properties and to coat high concentrations of particles makes this technique of interest for industrial production where uniform properties are needed for large quantities of particles [2]. Copyright © 2010 by ASME.

Viscoelastic analysis of single-component and composite PEG and alginate hydrogels

Hydrogels, three-dimensional hydrophilic polymer networks, are appealing candidate materials for studying the cellular microenvironment as their substantial water content helps to better mimic soft tissue. However, hydrogels can lack mechanical stiffness, strength, and toughness. Composite hydrogel systems have been shown to improve upon mechanical properties compared to their singlecomponent counterparts. Poly (ethylene glycol) dimethacrylate (PEGDMA) and alginate are polymers that have been used to form hydrogels for biological applications. Singlecomponent and composite PEGDMA and alginate systems were fabricated with a range of total polymer concentrations. Bulk gels were mechanically characterized using spherical indentation testing and a viscoelastic analysis framework. An increase in shear modulus with increasing polymer concentration was demonstrated for all systems. Alginate hydrogels were shown to have a smaller viscoelastic ratio than the PEGDMA gels, indicating more extensive relaxation over time. Composite alginate and PEGDMA hydrogels exhibited a combination of the mechanical properties of the constituents, as well as a qualitative increase in toughness. Additionally, multiple hydrogel systems were produced that had similar shear moduli, but different viscoelastic behaviors. Accurate measurement of the mechanical properties of hydrogels is necessary in order to determine what parameters are key in modeling the cellular microenvironment. © 2014 The Chinese Society of Theoretical and Applied Mechanics; Institute of Mechanics, Chinese Academy of Sciences and Springer-Verlag Berlin Heidelberg.

Synthesis and identification of Heterocyclic derivatives of fullerene C-60: Unexpected reaction of anionic C-60 with benzonitrile

During the reaction of reduced C-60 with benzyl bromide in benzonitrile, a novel cis-1 C-60 adduct, 1,4-dibenzyl-2,3-cyclic phenylimidate C-60 (1), Was obtained rather than the expected product of 1,4-dibenzyl C-60. The structure of compound 1 was analyzed by X-ray single-crystal diffraction, identifying the presence of a five-membered heterocycle at a [5,6] bond of C-60. One of the heteroatoms is assigned as a nitrogen atom; however, the identity of the other heteroatom cannot be determined unambiguously by crystallography due to similarity between the nitrogen and oxygen atoms.

Water-Soluble Graphene Covalently Functionalized by Biocompatible Poly-L-lysine

Graphene sheets functionalized covalently with biocompatible poly-L-lysine (PLL) were first synthesized in all alkaline solution. PLL-functionalized graphene is water-soluble and biocompatible, which makes it a novel material promising for biological applications. Graphene sheets played an important role as connectors to assemble these active amino groups Of Poly-L-lysine, which provided a very biocompatible. environment for further functionalization, such as attaching bioactive molecules. As an example, an amplified biosensor toward H2O2 based on linking peroxidase onto PLL-functionalized graphene was investigated.

Gold nanoparticle probes

Depending on their size, shape. degree of aggregation and nature of the protecting organic shells on their surface, gold nanoparticles (AuNPs) can appear red, blue and other colors and emit bright resonance light scattering of various wavelengths. Because of this unique optical property. AuNPs have been extensively explored as probes for sensing/imaging a wide range of analytes/targets, such as heavy metallic cations, nucleic acids, proteins, cells, etc. Since their initial discovery, novel synthetic methods have led to precise control over particle size, shape and stability, thus allowing the modification of a wide variety of ligands on the AuNP surfaces to meet different experimental conditions. This review discusses the synthesis and applications of functionalized AuNPs in chemical sensing and imaging.

Design of polymeric stabilizers for size-controlled synthesis of monodisperse gold nanoparticles in water

A new methodology is described for the one-step aqueous preparation of highly monodisperse gold nanoparticles with diameters below 5 nm using thioether- and thiol-functionalized polymer ligands. The particle size and size distribution was controlled by subtle variation of the polymer structure. It was shown that poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA) were the most effective stabilizing polymers in the group studied and that relatively low molar mass ligands (similar to 2500 g/mol) gave rise to the narrowest particle size distributions. Particle uniformity and colloidal stability to changes in ionic strength and pH were strongly affected by the hydrophobicity of the ligand end group. "Multidentate" thiol-terminated ligands were produced by employing dithiols and tetrathiols as chain-transfer agents, and these ligands gave rise to particles with unprecedented control over particle size and enhanced colloidal stability. It was found throughout that dynamic light scattering (DLS) is a very useful corroboratory technique for characterization of these gold nanoparticles in addition to optical spectroscopy and TEM.

Carbon nanotubes selective destabilization of duplex and triplex DNA and inducing B-A transition in solution

Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nano-device applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mechanism. We report here, for the first time, that DNA destabilization and conformational transition induced by SWNTs are sequence-dependent. Contrasting changes for SWNTs binding to poly[dGdC]:poly[dGdC] and poly[dAdT]:poly[dAdT] were observed. For GC homopolymer, DNA melting temperature was decreased 40 degrees C by SWNTs but no change for AT-DNA. SWNTs can induce B-A transition for GC-DNA but AT-DNA resisted the transition. Our circular dichroism, competitive binding assay and triplex destabilization studies provide direct evidence that SWNTs induce DNA B-A transition in solution and they bind to the DNA major groove with GC preference.

Fabrication of cerium oxide nanoparticles: Characterization and optical properties

Ceria (CeO2) is a technologically important rare earth material because of its unique properties and various engineering and biological applications. A facile and rapid method has been developed to prepare ceria nanoparticles using microwave with the average size 7 nm in the presence of a set of ionic liquids based on the bis (trifluoromethylsulfonyl) imide anion and different cations of 1-alkyl-3-methyl-imidazolium. The structural features and optical properties of the nanoparticles were determined in depth with X-ray powder diffraction, transmission electron microscope, N-2 adsorption-desorption technique, dynamic light scattering (DLS) analysis, FTIR spectroscopy, Raman spectroscopy, UV-vis absorption spectroscopy, and Diffuse reflectance spectroscopy. The energy band gap measurements of nanoparticles of ceria have been carried out by UV-visible absorption spectroscopy and diffuse reflectance spectroscopy. The surface charge properties of colloidal ceria dispersions in ethylene glycol have been also studied. To the best of our knowledge, this is the first report on using this type of ionic liquids in ceria nanoparticle synthesis. (C) 2011 Elsevier Inc. All rights reserved.

Electrical methods of controlling bacterial adhesion and biofilm on device surfaces.

This review will summarize the significant body of research within the field of electrical methods of controlling the growth of microorganisms. We examine the progress from early work using current to kill bacteria in static fluids to more realistic treatment scenarios such as flow-through systems designed to imitate the human urinary tract. Additionally, the electrical enhancement of biocide and antibiotic efficacy will be examined alongside recent innovations including the biological applications of acoustic energy systems to prevent bacterial surface adherence. Particular attention will be paid to the electrical engineering aspects of previous work, such as electrode composition, quantitative electrical parameters and the conductive medium used. Scrutiny of published systems from an electrical engineering perspective will help to facilitate improved understanding of the methods, devices and mechanisms that have been effective in controlling bacteria, as well as providing insights and strategies to improve the performance of such systems and develop the next generation of antimicrobial bioelectric materials.

Preparation of Highly Stable OEG derivatives-functionalized AuNPs and Its Application in LSPR-based Detection of PSA/ACT Complex

The zero-length crosslinker EDC has been widely used to make amide bonds between carboxylic acid and amine groups for bioconjugation because no residues remain in the crosslinked protein. During the conjugation process, EDC activates the carboxyl groups (negatively charged) and forms an unstable amine-reactive intermediate (positively charged). However, the process turns to be a problematic issue if it is applied to modify carboxyl-functionalized and –stabilized Au nanoparticles (AuNPs) due to the fact that the negatively repulsive forces which help to stabilize the AuNPs were disrupted leading to the colloid aggregation. Therefore, to modify the negatively carboxyl-terminated AuNPs while their stability can be maintained yet, we assume that functionalization of the AuNPs using 02 kinds of negatively charged groups which one serves as a linking agent, and the other one plays a role of negative charge maintainer could overcome the impediment.

In this study, the colloidal gold nanoparticles were synthesized by Turkevitch’s method, and then their surface was rationally functionalized with different molar ratios of HS(CH2)11(OCH2CH2)6OCH2COOH and HS(CH2)11(OCH2CH2)3OH (OEG6-COOH/OEG3-OH) by self assembling technique. As a result, the most appropriate molar ratio was found to be 1:10, and the AuNP aggregation was prevented not only in the activation process by EDC but also in the present of high concentration of NaCl as well as over in a wide pH range. This is the first time that extremely stable OEG derivatives-functionalized Au nanoparticles for protein bioconjugation using EDC chemistry is reported, and the results open the door for covalent bioconjugation of AuNPs in biological applications.

In vitro mesenchymal stem cell responses on laser-welded NiTi alloy

The biocompatibility of NiTi after laser welding was studied by examining the in vitro (mesenchymal stem cell) MSC responses at different sets of time varying from early (4 to 12 h) to intermediate phases (1 and 4 days) of cell culture. The effects of physical (surface roughness and topography) and chemical (surface Ti/Ni ratio) changes as a consequence of laser welding in different regions (WZ, HAZ, and BM) on the cell morphology and cell coverage were studied. The results in this research indicated that the morphology of MSCs was affected primarily by the topographical factors in the WZ: the well-defined and directional dendritic pattern and the presence of deeper grooves. The morphology of MSCs was not significantly modulated by surface roughness. Despite the possible initial Ni release in the medium during the cell culture, no toxic effect seemed to cause to MSCs as evidenced by the success of adhesion and spreading of the cells onto different regions in the laser weldment. The good biocompatibility of the NiTi laser weldment has been firstly reported in this study.