Label free electrochemical DNA hybridization discrimination effects at the binary and ternary mixed monolayers of single stranded DNA/diluent/s in presence of cationic intercalators

Electrochemical label free DNA hybridization discrimination of the brain tumor sequence CK20 has been made at the gold-thiol and thiol diluent binary and ternary mixed monolayer interfaces in presence of the [Fe(CN)6](3-) and double stranded DNA (dsDNA) specific cationic intercalators, proflavine (PF) and methylene blue (MB), respectively. Thiol hexane labeled single stranded DNA (HS-ssDNA) and thiol diluents such as 6-mercapto-1-hexanol (MCH) and 3-mercaptopropionic acid (MPA) are used to construct the mixed monolayers. Change in the peak-to-peak separation (Delta Ep) for the [Fe(CN)6](3-) redox reaction indicates the efficiency of the diluents in removing the randomly oriented HS-ssDNA. Smaller Delta Ep 248 mV noticed for the HS-ssDNA/MPA compared to the HS-ssDNA/MCH mixed monolayers (812 mV) indicates the less influence of the MCH diluent on the arrangement of HS-ssDNA layer. However, the hybridization discrimination effect negotiated in presence of both the [Fe(CN)6](3-) and PF intercalator showed zero effect for the HS-ssDNA/MPA interface, and approximately 20-30% effect for the HS-ssDNA/MCH interface. The discrimination effect at the HS-ssDNA/MPA interface further increased to 80% by inserting the MCH at the local defects to form a multicomponent ternary HS-ssDNA/MPA/MCH layer interface. These differential discrimination effects are attributed to the formation of compact and/or defective layer structures, evidenced from their reductive desorption voltammetry in 0.5M KOH. The presence of single base (C-A) mismatch in the hybrid is diagnosed by a decrease in coulometric charge compared to the perfect dsDNA. The target concentration of 10 pM is detected selectively and sensitively.     

Electrochemical DNA biosensor based on silver nanoparticles/poly(3-(3-pyridyl) acrylic acid)/carbon nanotubes modified electrode

In this work, we present an electrochemical DNA sensor based on silver nanoparticles/poly(trans-3-(3-pyridyl) acrylic acid) (PPAA)/multiwalled carbon nanotubes with carboxyl groups (MWCNTs-COOH) modified glassy carbon electrode (GCE). The polymer film was electropolymerized onto MWCNTs-COOH modified electrode by cyclic voltammetry (CV), and then silver nanoparticles were electrodeposited on the surface of PPAA/MWCNTs-COOH composite film. Thiol group end single-stranded DNA (HS-ssDNA) probe was easily covalently linked onto the surface of silver nanoparticles through a 5′ thiol linker. The DNA hybridization events were monitored based on the signal of the intercalated adriamycin by differential pulse voltammetry (DPV). Based on the response of adriamycin, only the complementary oligonucleotides gave an obvious current signal compared with the three-base mismatched and noncomplementary oligonucleotides. Under the optimal conditions, the increase of reduction peak current of adriamycin was linear with the logarithm of the concentration of the complementary oligonucleotides from 9.0 × 10⁻¹² to 9.0 × 10⁻⁹ M with a detection limit of 3.2 × 10⁻¹² M. In addition, this DNA sensor exhibited an excellent reproducibility and stability during DNA hybridization assay.     

Application of impedance spectroscopy for monitoring colloid Au-enhanced antibody immobilization and antibody-antigen reactions

We used colloidal Au to enhance the amount of antibody immobilized on a gold electrode and ultimately monitored the interaction of antigen-antibody by impedance measurement. Self-assembly of 6 nm (diameter) colloidal Au onto the self-assembled monolayers (SAMs) of 4-aminothiophenol modified gold electrode resulted in an easier attachment of antibody. The redox reactions of [Fe(CN)6](4-)/[Fe(CN)6](3-) on the gold surface were blocked due to the procedures of self-assembly of 4-aminothiophenol and antibody immobilization, which were investigated by cyclic voltammetry and impedance spectroscopy. The interaction of antigen with grafted antibody recognition layers was carried out by soaking the modified electrode into a phosphate buffer at pH 7.4 with various concentrations of antigen at 37 degrees C for 30 min. The antibody recognition layers and their interactions with various concentrations of antigen could be detected by measurements of the impedance change. The results show that this method has good correlation for detection of Hepatitis B virus surface antigen in the range of 0.5-200 microg/l and a detection limit of about 50 ng/l.     

Surface plamon resonance imaging of DNA based biosensors for potential applications in food analysis

The adsorption processes of oligonucleotides immobilised onto suitable photolithographic patterned gold substrates have been investigated in aqueous buffer solution by using a home made surface plasmon resonance (SPR) imaging equipment. A rapid self-assembled method for the construction of DNA chips to be used in SPR imaging experiments have been followed. The immobilised DNA molecules (probes) adopted in our SPR experiments anchored to a gold surface via thiol group were 5'thiol-modified containing a (CH(2))(15) tail. The hybridisation processes taking place with its complementary sequence have been observed and characterized by monitoring phenomena by a SPR imaging system. The two analysed oligonucleotides (probes and target) are of interest in plant gene biotechnological application and differing for the presence at the 5'-end of a poly T16 spacer. Dynamic investigation of smallest changes in SPR imaging pictures performed in liquid phase in the presence of DNA complementary probes have been performed. Quantitative information in terms of threshold of sensitivity has been extracted by using a specific images treatment.     

A DNA biosensor based on peptide nucleic acids on gold surfaces

We present a DNA biosensor based on self-assembled monolayers (SAMs) of thiol-derivatized peptide nucleic acid (PNA) molecules adsorbed on gold surfaces. Previous works have shown that PNA molecules at an optimal concentration can be self-assembled with their molecular axes normal to the surface. In such structural configuration BioSAMs of PNAs maintain their capability for recognizing complementary DNA. We describe the combined use of PM-RAIRS and synchrotron radiation XPS for the detection and spectroscopic characterization of PNA-DNA hybridization process on gold surfaces. RAIRS and XPS are powerful techniques for surface characterization and molecular detection, which do not require a fluorescence labeling of the target. We present a characterization of the spectroscopic IR and XPS features, some of them associated to the phosphate groups of the DNA backbone, as an unambiguous signature of the PNA-DNA heteroduplex formation. The N(1s) XPS core level peak after DNA hybridization is decomposed in curves components, and every component assigned to different chemical species. Therefore, the results obtained by means of two complementary structural characterization techniques encourage the use of PNA-based biosensors for the detection of DNA molecules on natural samples.     

microAg particle-based molecular sensing/recognition via surface-enhanced Raman spectroscopy

In this study, we demonstrate that powders of commercially available 2-microm-sized Ag (microAg) can be used as a core material for constructing molecular sensing/recognition units operating via surface-enhanced Raman scattering (SERS). This is possible because microAg powders are very efficient substrates for both the infrared and Raman-spectroscopic characterization of molecular adsorbates prepared in a similar manner on silver surfaces. The Raman spectrum of organic monolayers on powdered silver is a SERS spectrum. The agglomeration of microAg particles in a highly concentrated buffer solution could be prevented by the deposition of polar molecules like 1,4-phenylenediisocyanide (1,4-PDI), and mixed self-assembled monolayers of 1,4-PDI and N-(+)-biotinyl-6-aminocaproic acid on microAg particles were then confirmed via the SERS of 1,4-PDI to selectively recognize the avidin arrays formed on a separate biotinylated substrate. According to a dose response curve, avidin at >10(-6)g/mL could be easily identified by the present method. In addition, the non-specific adsorption of microAg particles was found to be negligibly small, probably because the Ag particles were too heavy to be retained on organic substrates solely by non-specific interaction.     

Electrochemical sensor for guanine using a self-assembled monolayer of 1,8,15,22-tetraaminophthalocyanatonickel(II) on glassy carbon electrode

This article describes the selective determination of guanine (G) using the self-assembled monolayer (SAM) of 1,8,15,22-tetraaminophthalocyanatonickel(II) (4α-Ni(II)TAPc) modified glassy carbon electrode (GCE) in 0.2 M acetate buffer solution (pH 4.0). The SAM of 4α-Ni(II)TAPc was formed on GCE by spontaneous adsorption of 1 mM 4α-Ni(II)TAPc in dimethylformamide (DMF). It shows two pairs of redox waves corresponding to Ni(III)/Ni(II) and Ni(III)Pc(-1)/Ni(III)Pc(-2) in 0.2 M acetate buffer solution. The SAM modified electrode exhibits excellent electrocatalytic activity toward the oxidation of G by enhancing its oxidation current with 150 mV less positive potential shift in contrast to bare GCE. Furthermore, the SAM modified electrode selectively determines G in the presence of high concentration of adenine (A). In differential pulse voltammetry measurements, the oxidation current response of G was increased linearly in the concentration range of 10 to 100 μM, and a detection limit was found to be 3×10(-8)M (signal/noise=3).     

Electrochemical studies of DNA immobilization onto the azide-terminated monolayers and its interaction with taxol

A surface modification procedure for the creation of self-assembled monolayers (SAMs) that can be used as a scaffold for double-stranded DNA (dsDNA) incorporation onto the gold surfaces is described. The SAMs of an azidohexane thiol derivative were prepared on the Au electrode and then used for the immobilization of dsDNA. The electrochemical characteristics of dsDNA onto the SAM-modified gold electrode were investigated by cyclic voltammetry and electrochemical impedance spectroscopy, and the surface concentration of dsDNA onto the SAMs surface was estimated. The interaction of dsDNA with the anticancer drug, taxol (paclitaxel), was also studied on the surface of DNA/SAM/Au electrode. The observed decrease in the guanine oxidation peak current was used to monitor the interaction of taxol with DNA. The resulting Langmuir isotherm for taxol binding to DNA at the modified electrode was used to evaluate the binding constant of taxol-DNA. The results obtained supported the groove binding interaction of taxol with DNA. The modified electrode was used as a sensitive sensor for quantification of taxol in human serum sample.     

Micropatterned, self-assembled monolayers for fabrication of transfected cell microarrays

The aim of this study was to develop the cell microarray that allows efficient transfer of multiple genes into mammalian cells cultured on the microarray in a high-throughput fashion. A microarray was fabricated using a gold-coated glass plate having a micropatterned, self-assembled monolayer of alkanethiols carrying ionic and nonionic terminal groups. Plasmid DNA and a cationic lipid were loaded by alternate electrostatic adsorption to the microspots to obtain a plasmid DNA microarray. The loading and the release of lipid-DNA complex were studied by, respectively, the fluorescence staining of DNA and the imaging of the microarray with a surface plasmon resonance (SPR) apparatus. The transfection efficiency was evaluated by directly plating and culturing human embryonic kidney cells onto the microarray. The results demonstrated that cells which adhered to the DNA-loaded spots were transfected to express the encoded model proteins for several days. The chemistry of the monolayers and the number of alternate adsorption cycles had large effects on the efficiency of transfection. This may be explained from the availability of the lipid-DNA complex to the cells directly contacted. We conclude that the micropatterned, self-assembled monolayers greatly facilitate regionally defined loading of DNAs and expression of the encoded protein in mammalian cells.     

Determination of thalidomide in transport buffer for Caco-2 cell monolayers by high-performance liquid chromatography with ultraviolet detection

We report simple validated HPLC methods for the determination of thalidomide in the transport buffer for the human colonic cell line (Caco-2) cell monolayers. An aliquot of 50 microl of the mixture was injected onto a Spherex C(18) column (150 x 4.6 mm; 5 microm) at a flow-rate of 0.5 ml/min of mobile phase consisting of acetonitrile-10 mM ammonium acetate buffer (24:76, v/v, pH 5.5), and thalidomide was detected by ultraviolet detector at a wavelength of 220 nm. Calibration curves for thalidomide were constructed at the concentration range of 0.025-1.0 and 1.0-50 microM in transport buffer. The validated methods were used to determine the transport of thalidomide by Caco-2 monolayers. The transport across the monolayers from the apical (A) to basolateral (B) side was similar to that from B to A side. The apparent permeability coefficient (P(app)) values of thalidomide at 10-300 microM from the A to B and from B to A side was 2-6 x 10(-5) cm/s, with a marked decrease in P(app) values from A to B side at increased thalidomide concentration. The A to B transport appears to be dependent on temperature and sodium ion. Sodium azide, 2,4-dinitrophenol (both ATP inhibitors), 5-fluorouracil, cytidine and glutamic acid significantly inhibited the transport of thalidomide. These results indicate that the transport of thalidomide by Caco-2 monolayers was rapid, which might involve an energy-dependent mechanism.     

Sensing with electro-switchable biosurfaces

The conformation of charged molecules tethered to conducting substrates can be controlled efficiently through the application of external voltages. Biomolecules like DNA or oligopeptides can be forced to stretch away from??or fold onto??surfaces biased at moderate potentials of merely hundreds of millivolts. These externally controlled conformation changes can be used to switch the biological function of molecular monolayers on and off, by revealing or concealing molecular recognition sites at will. Moreover, the electrical actuation of biomolecular surface probes bears great potential as a novel, label-free, yet highly sensitive measurement modality for the analysis of molecular interactions. The binding of target molecules to an oscillating probe layer significantly alters the layer??s switching behavior in terms of the conformation switching amplitude and, most remarkably, with respect to the molecular switching dynamics. Analyzing the switching response of target?Cprobe complexes from the low- to the high-frequency regime reveals a wealth of previously inaccessible information. Besides ??classical?? interaction parameters like binding affinities and kinetic rate constants, information on the size, shape, bending flexibility, and elasticity of the target molecule may be obtained in a single assay. This review describes the advent of electrically switchable biosurfaces, focusing on DNA monolayers. The preparation of self-assembled switchable oligonucleotide monolayers and their electrical interactions with charged substrates are highlighted. Special attention is paid to the merits of evaluating the dynamic response of charged biolayers which are operated at high driving frequencies. Several applications of biosensors based on electrically manipulated molecules are exemplified. It is emphasized that the electrical actuation of biomolecules bears many advantages over passive sensor surfaces.     

Nucleic acid sensor for insecticide detection

Nucleic acid sensor based on polyaniline (PANI) has been fabricated by covalently immobilizing double stranded calf thymus (dsCT) DNA onto perchlorate (ClO(-) (4))-doped PANI film deposited onto indium-tin-oxide (ITO) glass plate using 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride (EDC)/N-hydroxysuccinimide (NHS) chemistry. These dsCT-DNA-PANI-ClO(4)/ITO and PANI-ClO(4)/ITO electrodes have been characterized using square wave voltammetry, electrochemical impedance, scanning electron microscopy (SEM) and Fourier-transform-infrared (FTIR) measurements. This disposable dsCT-DNA-PANI-ClO(4)/ITO bioelectrode, stable for about 4 months, can be used to detect cypermethrin (0.005 ppm) and trichlorfon (0.01 ppm) in 30 and 60 s, respectively.     

A novel spectroscopic probe for molecular chirality

Recent advances in developing sum frequency generation (SFG) as a novel spectroscopic probe for molecular chirality are reviewed. The basic principle underlying the technique is briefly described, in comparison with circular dichroism (CD). The significantly better sensitivity of the technique than CD is pointed out, and the reason is discussed. Bi-naphthol (BN) and amino acids are used as representatives for two different types of chiral molecules; the measured chirality in their electronic transitions can be understood by two different molecular models, respectively, that are extensions of models developed earlier for CD. Optically active or chiral SFG from vibrational transitions are weaker, but with the help of electronic-vibrational double resonance, the vibrational spectrum of a monolayer of BN has been obtained. Generally, optically active SFG is sufficiently sensitive to be employed to probe in-situ chirality of chiral monolayers and thin films.     

Direct characterization of the physicochemical properties of fungal spores using functionalized AFM probes

A new method is described for characterizing the physicochemical properties of native microbial cells by using atomic force microscopy (AFM) with chemically functionalized probes. Adhesion forces were measured, under deionized water, between probes and model substrata functionalized with alkanethiol self-assembled monolayers terminated with OH and CH(3) groups. These were found to be 6 +/- 2 nN (n = 1024), 0.9 +/- 0.4 nN, and approximately 0 nN, for CH(3)/CH(3), CH(3)/OH, and OH/OH surfaces, respectively, and were not significantly influenced by changes of ionic strength (0.1 M NaCl versus deionized water). This shows that functionalized probes are very sensitive to changes of surface hydrophobicity. Using OH- and CH(3)-terminated probes, patterns of rodlets, approximately 10 nm in diameter, were visualized, under physiological conditions, at the surface of spores of Phanerochaete chrysosporium. Multiple (1024) force-distance curves recorded over 500 x 500-nm areas at the spore surface, either in deionized water or in 0.1 M NaCl solutions, always showed no adhesion for both OH- and CH(3)-terminated probes. Control experiments indicated that the lack of adhesion is not due to transfer of cellular material onto the probe, but to the hydrophilic nature of the spore surface.     

Comparison of a carboxylated terthiophene surface with carboxymethylated dextran layer for surface plasmon resonance detection of progesterone

Functionalization of a gold surface is usually accomplished by covalent binding via self-assembled monolayers (SAMs) on the gold surface, followed by attachment of flexible polymeric linker layers such as dextran hydrogels. However, these techniques require multiple steps and also have nonspecific interactions and steric problems. In this study, a self-assembled carboxylated terthiophene monolayer was formed onto a gold surface to create a sensitive and stable surface plasmon resonance (SPR) biosensing system. Compared with a commercial carboxymethyl dextran chip (CM5), the terthiophene SAM surface provided more than six times more antibody-binding signals and nearly three times the SPR assay sensitivity for progesterone (P₄).     

Kinetics of the processes of desorption from fatty acid monolayers

The surface area, A, of contracting fatty acid monolayers was measured as a function of time, t, at constant surface pressure. In the initial temporal phase, ln A was linear with radical t. In a subsequent steady-state phase, ln A was linear with t. The initial desorption coefficient for sodium palmitate, K(i), and the steady-state desorption coefficient, K(s), varied directly with surface pressure and subphase pH, and these desorption coefficients also varied with the composition of the subphase buffer. However, the K(s)/K(i) ratio was independent of these variables. The diffusion coefficient, D(25), for sodium palmitate calculated from desorption coefficient ratios was 4.8 +/- 0.6 x 10(-6) cm(2)/sec. This value was in reasonable agreement with D(25) for sodium palmitate measured by time-lag diffusion, 3.7 +/- 0.6 x 10(-6) cm(2)/sec. D(25) values obtained for a series of fatty acids suggested that higher members of the series diffused as small aggregates averaging two to four molecules in size. Kinetic and diffusion data both supported a model for the desorption process described by Ter Minassian-Saraga.     

In situ molecular level studies on membrane related peptides and proteins in real time using sum frequency generation vibrational spectroscopy

Sum frequency generation (SFG) vibrational spectroscopy has been demonstrated to be a powerful technique to study the molecular structures of surfaces and interfaces in different chemical environments. This review summarizes recent SFG studies on hybrid bilayer membranes and substrate-supported lipid monolayers and bilayers, the interaction between peptides/proteins and lipid monolayers/bilayers, and bilayer perturbation induced by peptides/proteins. To demonstrate the ability of SFG to determine the orientations of various secondary structures, studies on the interactions between different peptides/proteins (melittin, G proteins, alamethicin, and tachyplesin I) and lipid bilayers are discussed. Molecular level details revealed by SFG in these studies show that SFG can provide a unique understanding on the interactions between a lipid monolayer/bilayer and peptides/proteins in real time, in situ and without any exogenous labeling.     

Molecular dynamics imaging in micropatterned living cells

Micropatterning approaches using self-assembled monolayers of alkyl thiols on gold are not optimal for important imaging modalities in cell biology because of absorption of light and scattering of electrons by the gold layer. We report here an anisotropic solid microetching (ASOMIC) procedure that overcomes these limitations. The method allows molecular dynamics imaging by wide-field and total internal reflection fluorescence (TIRF) microscopy of living mammalian cells and correlative platinum replica electron microscopy.     

A simple and effective sample preparation method for atomic force microscopy visualization of individual DNA molecules in situ

A simple, controllable and effective sample preparation method was established for atomic force microscopy (AFM) imaging of individual DNA molecules in aqueous solution. Firstly, magnesium ion (Mg²⁺) at a concentration of 5.0–10.0 mM as a positively charged bridge was transferred onto mica to immobilize DNA molecules. Then Mg²⁺-modified mica was used to investigate DNA molecules in any buffer without magnesium ion by AFM. AFM images demonstrated that DNA molecules can be successfully observed in solution with good resolution, reproducibility, and stability. Further, this DNA sample preparation method makes AFM successful to investigate DNA molecular interaction in situ and DNA/chitosan complex in gene delivery.     

Controlled immobilization of DNA molecules using chemical modification of mica surfaces for atomic force microscopy: characterization in air

Immobilization of biomolecules on surfaces while keeping the maximum conformational flexibility of the molecules is one of the most important techniques for atomic force microscopy imaging. We have developed two methods of controlling adsorption of DNA molecules on mica surfaces. The first method is the use of a mica surface modified with diluted 3-aminopropyltriethoxysilane (APS). Here we named this a "diluted APS-treated mica (AP-mica)" technique. The second method is the use of a mica surface modified with mixed self-assembled monolayers of organosilanes. In both of the techniques, the number of DNA molecules immobilized on a mica surface was controlled. Further, a conformational change of circular DNA, from a supercoiled to a relaxed form was observed for the molecules immobilized on a diluted AP-mica surface, when 254-nm UV light was irradiated. This observation demonstrated that flexibility of circular DNA molecules was kept on a diluted AP-mica surface.