Adsorption of homopolypeptides on gold investigated using atomistic molecular dynamics

We investigate the role of dynamics on adsorption of peptides to gold surfaces using all-atom molecular dynamics simulations in explicit solvent. We choose six homopolypeptides [Ala(10), Ser(10), Thr(10), Arg(10), Lys(10), and Gln(10)], for which experimental surface coverages are not correlated with amino acid level affinities for gold, with the idea that dynamic properties may also play a role. To assess dynamics we determine both conformational movement and flexibility of the peptide within a given conformation. Low conformational movement indicates stability of a given conformation and leads to less adsorption than homopolypeptides with faster conformational movement. Likewise, low flexibility within a given conformation also leads to less adsorption. Neither amino acid affinities nor dynamic considerations alone predict surface coverage; rather both quantities must be considered in peptide adsorption to gold surfaces.     

Adsorption of DNA onto gold nanoparticles and graphene oxide: surface science and applications

The interaction between DNA and inorganic surfaces has attracted intense research interest, as a detailed understanding of adsorption and desorption is required for DNA microarray optimization, biosensor development, and nanoparticle functionalization. One of the most commonly studied surfaces is gold due to its unique optical and electric properties. Through various surface science tools, it was found that thiolated DNA can interact with gold not only via the thiol group but also through the DNA bases. Most of the previous work has been performed with planar gold surfaces. However, knowledge gained from planar gold may not be directly applicable to gold nanoparticles (AuNPs) for several reasons. First, DNA adsorption affinity is a function of AuNP size. Second, DNA may interact with AuNPs differently due to the high curvature. Finally, the colloidal stability of AuNPs confines salt concentration, whereas there is no such limit for planar gold. In addition to gold, graphene oxide (GO) has emerged as a new material for interfacing with DNA. GO and AuNPs share many similar properties for DNA adsorption; both have negatively charged surfaces but can still strongly adsorb DNA, and both are excellent fluorescence quenchers. Similar analytical and biomedical applications have been demonstrated with these two surfaces. The nature of the attractive force however, is different for each of these. DNA adsorption on AuNPs occurs via specific chemical interactions but adsorption on GO occurs via aromatic stacking and hydrophobic interactions. Herein, we summarize the recent developments in studying non-thiolated DNA adsorption and desorption as a function of salt, pH, temperature and DNA secondary structures. Potential future directions and applications are also discussed.     

Determination of Saxitoxin by Aptamer-Based Surface-Enhanced Raman Scattering

Saxitoxin is one of the most harmful paralytic shellfish toxins due to its high toxicity and adverse effects on the environment and human health. Aptasensors provide simple detection procedures because they have the advantages of chemical stability, easy synthesis and modification, and high convenience in signal transformation. Surface-enhanced Raman scattering (SERS) is an analytical technique that amplifies the analytical signals of molecules at extremely low concentrations, or even at the single molecule level, when the analyte is very close to rough metal surfaces or nanostructures. In this study, an SERS aptasensor is reported for the determination of saxitoxin for the first time. The optimized saxitoxin aptamer (M-30f) was modified on gold nanoparticles and served as the recognition element. Crystal violet was used as the Raman reporter without chemical bounding. The analytical principles of the aptasensor are that saxitoxin destabilized the conformations of the aptamer at high temperature conditions and altered the binding of crystal violet on the gold nanoparticles. In the presence of saxitoxin, the conformation of aptamer containing the G-quadruplex that selectively bound crystal violet unfolded to a large extent and hence the crystal violet molecules were released from gold nanoparticles with a reduced SERS signal. The effects of the gold nanoparticle size, the amount of DNA, aptamer density, sodium chloride concentration, and operation temperature upon the SERS determination were optimized. The resulting simple SERS aptasensor was developed with a satisfactory limit of detection (11.7?nM) and selectivity. The application for the analysis of real shellfish samples with simple procedures demonstrates that this SERS aptasensor is promising for on-site applications.     

Facile Electrochemical Hydrogenation and Chlorination of Glassy Carbon to Produce Highly Reactive and Uniform Surfaces for Stable Anchoring of Thiolated Molecules

Carbon is a highly adaptable family of materials and is one of the most chemically stable materials known, providing a remarkable platform for the development of tunable molecular interfaces. Herein, we report a two‐step process for the electrochemical hydrogenation of glassy carbon followed by either chemical or electrochemical chlorination to provide a highly reactive surface for further functionalization. The carbon surface at each stage of the process is characterized by AFM, SEM, Raman, attenuated total reflectance (ATR) FTIR, X‐ray photoelectron spectroscopy (XPS), and electroanalytical techniques. Electrochemical chlorination of hydrogen‐terminated surfaces is achieved in just 5 min at room temperature with hydrochloric acid, and chemical chlorination is performed with phosphorus pentachloride at 50 °C over a three‐hour period. A more controlled and uniform surface is obtained using the electrochemical approach, as chemical chlorination is observed to damage the glassy carbon surface. A ferrocene‐labeled alkylthiol is used as a model system to demonstrate the genericity and potential application of the highly reactive chlorinated surface formed, and the methodology is optimized. This process is then applied to thiolated DNA, and the functionality of the immobilized DNA probe is demonstrated. XPS reveals the covalent bond formed to be a C?S bond. The thermal stability of the thiolated molecules anchored on the glassy carbon is evaluated, and is found to be far superior to that on gold surfaces. This is the first report on the electrochemical hydrogenation and electrochemical chlorination of a glassy carbon surface, and this facile process can be applied to the highly stable functionalization of carbon surfaces with a plethora of diverse molecules, finding widespread applications.     

Effects of gold nanoparticle and electrode surface properties on electrocatalytic silver deposition for electrochemical DNA hybridization detection

In this paper we report the catalytic effects of various gold nanoparticles for silver electrodeposition on indium tin oxide (ITO)-based electrodes, and successfully apply this methodology for signal amplification of the hybridization assay. The most widely used gold nanoparticle-based hybridization indicators all promote silver electrodeposition on the bare ITO electrodes, with decreasing catalytic capability in order of 10 nm gold, DNA probe-10 nm gold conjugate, streptavidin-5 nm gold, and streptavidin-10 nm gold. Of greater importance, these electrocatalytic characteristics are affected by any surface modifications of the electrode surfaces. This is illustrated by coating the ITO with an electroconducting polymer, poly(2-aminobenzoic acid)(PABA), as well as avidin molecules, which are promising immobilization platforms for DNA biosensors. The catalytic silver electrodeposition of the gold nanoparticles on the PABA-coated ITO surfaces resembles that on the bare surfaces. With avidin covalently bound to the PABA, it is interesting to note that the changes in electrocatalytic performance vary for different types of gold nanoparticles. For the streptavidin-5 nm gold, the silver electrodeposition profile is unaffected by the presence of the avidin layer, whereas for both the 10 nm Au and DNA probe-10 nm gold conjugate, the deposition profiles are suppressed. The streptavidin-5 nm gold is employed as the hybridization indicator, with avidin-modified (via PABA) ITO electrode as the immobilization platform, to enable signal amplification by the silver electrodeposition process. Under the conditions, this detection strategy offers a signal-to-noise ratio of 20. We believe that this protocol has great potential for simple, reproducible, highly selective and sensitive DNA detection on fully integrated microdevices in clinical diagnostics and environmental monitoring applications.     

Solid-state bonding technique for template-stripped ultraflat gold substrates

A simple procedure using gold diffusion bonding for the preparation of template-stripped gold (TSG) surfaces is described. TSG surfaces are useful for surface studies because a very consistent flat gold surface with few defects can be easily prepared. We have developed a method of producing TSG surfaces that relies only on gold diffusion bonding rather than epoxies. The resulting substrates are free from concerns of solvent compatibility, heat stability, and impurities. Bonding of centimeter-sized substrates is performed at 300 degrees C for 2 h using a vise and aluminum foil.     

Methylene blue as an electrochemical discriminator of single- and double-stranded oligonucleotides immobilised on gold substrates.

Self-assembly of thiol-terminated oligonucleotides on gold substrates provides a convenient and versatile route to DNA-functionalised surfaces. Here we show that the square-wave voltammetric peak position of methylene blue complexed to thiol-terminated single-stranded oligonucleotides immobilised on gold electrodes differs from that of methylene blue complexed to thiol-terminated double-stranded oligonucleotides immobilised on gold electrodes. The peak potential of methylene blue at the single-stranded oligonucleotide array was consistently found to occur at potentials ca. 10-15 mV more positive than that at double-stranded oligonucleotide arrays, the precise difference being dependent on the direction of the voltammetry. This voltammetric behaviour mirrors that found for methylene blue bound to freely diffusing single- and double-stranded calf thymus DNA and suggests that the immobilised oligonucleotides retain the methylene blue binding properties of their freely diffusing counterparts. Thus methylene blue provides a simple electrochemical indicator for the status of oligonucleotide-functionalised gold surfaces.     

DNA-controlled assembly of soft nanoparticles

Immobilization of DNA (encoding) on solid nanoparticles requires surface chemistry, which is well established for gold surfaces but often tedious and not generally applicable for many other inorganic surface materials. While substantial effort has been devoted to expanding surface chemistry techniques for solid nanoparticles, considerably less attention has been given to the development of noncovalent attachment of DNA to soft nanoparticles, like liposomes. Here we report a DNA-controlled assembly of liposomes in solution and on solid supported membranes, this process displays remarkably sharp thermal transitions from an assembled to a disassembled state, allowing application of DNA-controlled liposome assembly for the detection of polynucleotides (e.g., DNA) with single mismatch discrimination power. The method is based on a single DNA strand (contains two lipid membrane anchors), which is able to noncovalently attach to a liposome surface. This design enables detection of biological polynucleotide targets as the complementary strand can be unmodified DNA and RNA strands.     

The role of surface charging during the coadsorption of mercaptohexanol to DNA layers on gold: direct observation of desorption and layer reorientation

We study the coadsorption of mercaptohexanol onto preimmobilized oligonucleotide layers on gold. Monitoring the position of the DNA relative to the surface by optical means directly shows the mercaptohexanol-induced desorption of DNA and the reorientation of surface-tethered strands in situ and in real time. By simultaneously recording the electrochemical electrode potential, we are able to demonstrate that changes in the layer conformation are predominantly of electrostatic origin and can be reversed by applying external bias to the substrate.     

Non‐B DNA Structures Show Diverse Conformations and Complex Transition Kinetics Comparable to RNA or Proteins—A Perspective from Mechanical Unfolding and Refolding Experiments

With the firm demonstration of the in vivo presence and biological functions of many non‐B DNA structures, it is of great significance to understand their physiological roles from the perspective of structural conformation, stability, and transition kinetics. Although relatively simple in primary sequences compared to proteins, non‐B DNA species show rather versatile conformations and dynamic transitions. As the most‐studied non‐B DNA species, the G‐quadruplex displays a myriad of conformations that can interconvert between each other in different solutions. These features impose challenges for ensemble‐average techniques, such as X‐ray crystallography, NMR spectroscopy, and circular dichroism (CD), but leave room for single‐molecular approaches to illustrate the structure, stability, and transition kinetics of individual non‐B DNA species in a solution mixture. Deconvolution of the mixture can be further facilitated by statistical data treatment, such as iPoDNano (i ntegrated po pulation d econvolution with nano meter resolution), which resolves populations with subnanometer size differences. This Personal Account summarizes current mechanical unfolding and refolding methods to interrogate single non‐B DNA species, with an emphasis on DNA G‐quadruplexes and i‐motifs. These single‐molecule studies start to demonstrate that structures and transitions in non‐B DNA species can approach the complexity of those in RNA or proteins, which provides solid justification for the biological functions carried out by non‐B DNA species.     

Structure of DNA-cationic surfactant complexes at hydrophobically modified and hydrophilic silica surfaces as revealed by neutron reflectometry

In this article, we discuss the structure and composition of mixed DNA-cationic surfactant adsorption layers on both hydrophobic and hydrophilic solid surfaces. We have focused on the effects of the bulk concentrations, the surfactant chain length, and the type of solid surface on the interfacial layer structure (the location, coverage, and conformation of the DNA and surfactant molecules). Neutron reflectometry is the technique of choice for revealing the surface layer structure by means of selective deuteration. We start by studying the interfacial complexation of DNA with dodecyltrimethylammonium bromide (DTAB) and hexadecyltrimethylammonium bromide (CTAB) on hydrophobic surfaces, where we show that DNA molecules are located on top of a self-assembled surfactant monolayer, with the thickness of the DNA layer and the surfactant-DNA ratio determined by the surface coverage of the underlying cationic layer. The surface coverages of surfactant and DNA are determined by the bulk concentration of the surfactant relative to its critical micelle concentration (cmc). The structure of the interfacial layer is not affected by the choice of cationic surfactant studied. However, to obtain similar interfacial structures, a higher concentration in relation to its cmc is required for the more soluble DTAB surfactant with a shorter alkyl chain than for CTAB. Our results suggest that the DNA molecules will spontaneously form a relatively dense, thin layer on top of a surfactant monolayer (hydrophobic surface) or a layer of admicelles (hydrophilic surface) as long as the surface concentration of surfactant is great enough to ensure a high interfacial charge density. These findings have implications for bioanalytical and nanotechnology applications, which require the deposition of DNA layers with well-controlled structure and composition.     

Bioreactive surfaces prepared via the self-assembly of dendron thiols and subsequent dendrimer bridging reactions

Here, we report a novel route to prepare bioreactive surfaces on gold by the self-assembly of generation-three hydroxyl-terminated dendron thiols (G3-OH) and subsequent bridging reactions using generation-two amine-terminated dendrimers (G2-NH(2)). It has been shown that G3-OH dendron thiols form a stable and uniform self-assembled monolayer on gold, which can be activated by the homobifunctional cross-linker N,N-disuccinimidyl carbonate (DSC). Subsequent derivatization of the activated monolayer via dendrimer bridging reactions with G2-NH(2) enhances the stability, reactivity, and versatility of the prepared surface. Each step of the surface formation reaction has been monitored, and the resulting surface has been characterized by wetting, electrochemistry, scanning tunneling microscopy (STM), and infrared (IR) spectroscopy measurements. The reactivity of this surface was demonstrated by a Schiff base coupling reaction with 4-cyanobenzaldehyde, by immobilizing biotin molecules onto the peripheral amine groups using one of the conjugation methods, and by further binding avidin onto the biotinylated surface. We believe that the prepared bioreactive surface with a high density of amine groups will be useful for the immobilization of biological macromolecules for various biosensor applications, such as the fabrication of DNA microarrays and protein chips.     

In situ scanning tunneling microscopy of DNA-modified gold surfaces: bias and mismatch dependence

In situ scanning tunneling microscopy has been performed on DNA-modified gold surfaces under physiological conditions. The STM images of DNA-modified gold surfaces are strongly dependent on the applied potential and percentage of DNA duplexes containing a single base mismatch. At negative surface potentials we observe reproducible features that are attributed to DNA agglomerates where the DNA duplexes are in the upright orientation; at positive potentials, when DNA molecules lie down on the surface, the film is transparent, and only the gold surface is distinguishable. These observations indicate that DNA possesses a non-negligible local density of states which can be probed when the DNA duplex is in the upright orientation. By varying the percentage of DNA duplexes containing a single base mismatch, we have observed a dramatic change in the image contrast as a result of the perturbation induced by the mismatch on the electronic pathway inside the DNA. These results emphasize the central role of the integrity of the pi-stack for DNA charge transport. Duplex DNA is a promising candidate in molecular electronics, but only in arrangements where the orbitals can efficiently overlap with the electronic states of the electrodes and the environment does not constrain the DNA in non-native, poorly stacked conformations.     

Self-assembled multilayer of gold nanoparticles for amplified electrochemical detection of cytochrome c

Although different kinds of film materials and some modification techniques are applied for the development of protein-film electrochemistry, the design of a more ordered adsorption platform with improved sensitivity is still required. Here we employ single-strand DNA (ssDNA)-functionalized gold nanoparticles as scaffolds for the construction of a multilayered uniform self-assembled structure via the hybridization of complementary ssDNA. After adsorbing with native conformation onto the uniformly built electrode, cytochrome c responded very well in voltammetry experiments. The peak currents increase with the addition of the number of gold nanoparticle layers, which indicates that the multilayer gold nanoparticles not only provide a compatible microenvironment for the protein to undergo direct electron transfer reactions but also amplify the electrochemical signals by increasing the binding sites for the protein immobilization. Furthermore, ultra-sensitive detection of cytochrome c by using this multilayer gold nanoparticle-modified electrode is carried out. The linear range is from 2 x 10(-9) to 1 x 10(-7) M with a detection limit of 6.7 x 10(-10) M.     

Selective enzymatic labeling to detect packing-induced denaturation of double-stranded DNA at interfaces

The adsorption of DNA on surfaces is a widespread procedure and is a common way for fabrication of biosensors, DNA chips, and nanoelectronic devices. Although the biologically relevant and prevailing in vivo structure of DNA is its double-stranded (dsDNA) conformation, the characterization of DNA on surfaces has mainly focused on single-stranded DNA (ssDNA). Studying the structure of dsDNA on surfaces is of invaluable importance to microarray performance since their effectiveness relies on the ability of two DNA molecules to hybridize and remain stable. In addition, many of the enzymatic transactions performed on DNA require dsDNA, rather than ssDNA, as a substrate. However, it is not established that adsorbed dsDNA remains in its structure and does not denature. Here, two methodologies have been developed for distinguishing between surface-adsorbed single- and double-stranded DNA. We demonstrate that, upon formation of a dense monolayer, the nonthiolated strand comprising the dsDNA is released and the monolayer consists of mostly ssDNA. The fraction of dsDNA within the ssDNA monolayer depends on the length of the oligomers. A likely mechanism leading to this rearrangement is discussed.     

Enzyme-modified nanoparticles using biomimetically synthesized silica

The entrapment of enzymes within biomimetic silica nanoparticles offers unique and simple immobilization protocols that merge the stability of proteins confined in solid phases with the high loading and reduced diffusion limitations inherent to nano-sized structures. Herein, we report on the biomimetic silica entrapment of chemically derivatized horseradish peroxidase for amperometric sensing applications. Scanning electron microscopy shows evidence of the formation of enzyme-modified nanospheres using poly(ethylenimine) as a template for silicic acid condensation. When these nanospheres are directly deposited on graphite electrodes, chemically modified anionic peroxidase shows direct electron transfer at 0 mV vs Ag|AgCl. Microgravimetric measurements as well as SEM images demonstrate that negatively charged peroxidase is also entrapped when silica precipitates at gold electrodes are modified with a self-assembled monolayer of poly(ethylenimine). Electrostatic interactions may play a crucial role for efficient enzyme entrapment and silica condensation at the PEI template monolayer. The in-situ biomimetically synthesized peroxidase nanospheres are catalytically active, enabling direct bioelectrocatalysis at 0 mV vs Ag|AgCl with long-term stability.     

Hierarchical positioning of gold nanoparticles into periodic arrays using block copolymer nanoring templates

We report a simple and versatile self-assembly method for controlling the placement of functional gold nanoparticles on silicon substrates using micellar templates. The hierarchical positioning of gold nanoparticles is achieved in one-step during the spontaneous phase inversion of spherical poly(styrene)-block-poly(2-vinylpyridine) copolymer micelles into nanoring structures. The placement is mainly driven by the establishment of electrostatic interactions between the nanoparticle ligands and the pyridine groups exposed at the interface. In particular, we show the formation of ordered arrangements of single gold nanoparticles or nanoparticle clusters and demonstrate that their morphologies, densities and periodicities can be tuned by simply varying the initial block copolymer molecular weight or the deposition conditions. Besides gold nanoparticles, the method can be used for controlling the assembly of a large variety of nanoscale building blocks, thus opening an attractive pathway for generating functional hybrid surfaces with periodic nanopatterns.     

Two-dimensional self-organization of polystyrene-capped gold nanoparticles

Thiol end-functionalized polystyrene chains have been introduced onto the surface of gold nanoparticles via a two-step grafting-to method. This simple grafting procedure is demonstrated to be efficient for gold nanoparticles of different sizes and for particles initially dispersed in either aqueous or organic media. The method has been applied successfully for a relatively large range of polystyrene chain lengths. Grafting densities, as determined by thermogravimetric analysis, are found to decrease with increasing chain length. In all cases, the grafting density indicates a dense brush conformation for the tethered chains. The resulting functionalized nanoparticles self-organize into hexagonally ordered monolayers when cast onto solid substrates from chloroform solution. Furthermore, the distance between the gold cores in the dried monolayer is controlled by the molecular weight of the grafted polystyrene. Optical absorption spectra recorded for the organized monolayers show the characteristic plasmon absorption of the gold particles. Importantly, the plasmon resonance frequency exhibits a distinct dependence on interparticle separation that can be attributed to plasmon coupling between neighboring gold cores.     

Development of a biologically relevant calcium phosphate substrate for sum frequency generation vibrational spectroscopy

A novel biologically relevant composite substrate has been prepared consisting of a calcium phosphate (CaP) layer formed by magnetron sputter-coating from a hydroxyapatite (HA) target onto a gold-coated silicon substrate. The CaP layer is intended to mimic tooth and bone surfaces and allows polymers used in oral care to be deposited in a procedure analogous to that used for dental surfaces. The polymer cetyl dimethicone copolyol (CDC) was deposited onto the CaP surface of the substrate by Langmuir Blodgett deposition, and the structure of the adsorbed layer was investigated by the surface specific technique of sum frequency generation (SFG) vibrational spectroscopy. The gold sublayer provides enhancement of the SFG signal arising from the polymer but plays no part in the adsorption of the polymer. The surface morphology of the substrate was investigated using SEM and AFM. The surface roughness was commensurate with that of the thermally evaporated gold sublayer and uniform over areas of at least 36 mum(2). The chemical composition of the CaP-coated surface was determined by FTIR and TOF-SIMS. It was concluded that the surface is primarily calcium phosphate present as a mixture of amorphous, non-hydroxylated phases rather than solely stoichiometric hydroxyapatite. The SFG spectra from CDC on CaP were closely similar, both in resonance wavenumbers and in their relative intensities, with spectra of thin films of CDC recorded directly on gold. Application of previous analysis of the spectra of CDC on gold therefore enabled interpretation of the polymer orientation and conformation on the CaP substrate.     

Probing the interaction of a glycoprotein IIb/IIIa receptor antagonist with bound platelets using electrochemical impedance

A label-free assay is described to monitor the interaction of abciximab, a glycoprotein IIb/IIIa receptor antagonist (ReoPro), with platelets bound to a fibrinogen-functionalised electrode surface. Firstly, fibrinogen is deposited in a defined pattern onto a gold electrode using microcontact printing, and then platelets from whole blood are captured on the patterned surface. Patterning influences the spreading of platelets, which is strikingly different to that observed on homogeneously coated surfaces. The drug–platelet interaction has been investigated using AC impedance on uniform and patterned fibrinogen-modified surfaces. The results demonstrate that patterned fibrinogen surfaces can provide deep insights into the interaction of abciximab with different platelet sub-populations. The key advantages of this approach are that it is rapid, label free and does not require pre-processing of patient blood samples.