Base-dependent competitive adsorption of single-stranded DNA on gold

We characterize the room-temperature adsorption of single-stranded DNA homo-oligonucleotides from solution onto polycrystalline Au films, including competitive adsorption between all possible pairs of unmodified oligomers. Fourier transform infrared (FTIR) and X-ray photoelectron (XPS) spectroscopy analysis of the resulting films shows that oligonucleotides adsorb with a strongly base-dependent affinity, adenine (A) > cytosine (C) >/= guanine (G) > thymine (T). In competitive adsorption experiments on Au, oligo(dA) strongly dominates over the other oligonucleotides. The relative adsorption affinity of oligo(dA) is so great that it competes effectively against adsorption of thiolated oligomers and even causes hybridized oligo(dA).oligo(dT) duplexes to denature in the presence of Au.     

Dissociative and non-dissociative adsorption of selenophene on Au(1 1 1) depending on the preparation method

Selenophene (C₄H₄Se) monolayers on Au(1 1 1) were prepared by two different methods: ultrahigh vacuum (UHV) and atmospheric vapor adsorption method. Near-edge X-ray absorption fine structure (NEXAFS) and X-ray photoelectron spectroscopy (XPS) results clearly indicate that the two monolayers are in different chemical forms; selenophene is molecularly adsorbed under UHV condition, while it is dissociatively chemisorbed via the C–Se bond cleavage under atmospheric condition. The dissociative chemisorption under atmospheric condition is interpreted in terms of the trapping mediated adsorption in the presence of a high-pressure ambient gas phase.     

Self-assembly and molecular recognition of adenine- and thymine-functionalized nucleolipids in the mixed monolayers and thymine-functionalized nucleolipids on aqueous melamine at the air-water interface

Self-assembly and molecular recognition of the monolayers composed of an equimolar mixture of adenine- and thymine-functionalized nucleolipids at the air-water interface have been investigated in detail using surface pressure-molecular area isotherms and in situ infrared reflection absorption spectroscopy (IRRAS). Prior to molecular recognition, the adenine moieties in the monolayer were almost oriented on an end-on mode through π-stacking and hydrogen bonding interactions, and the C-C-C planes of the alkyl chains were preferentially oriented perpendicular to the water surface, while the thymine moieties in the monolayer were involved in hydrogen bonding almost with a flat-on orientation. On aqueous subphases containing complementary bases, no significant molecular recognition was observed for the monolayers of individual nucleolipids. In the monolayer of equimolar mixture, molecular recognition occurred between the adenine and thymine moieties through hydrogen bonding probably with the development of cyclic structures of adenine-thymine-adenine-thymine quartets. Although molecular recognition between the monolayer of thymine-functionalized nucleolipids and aqueous melamine took place through triple hydrogen bonds, no melamine binding to the monolayer of equimolar mixture was observed, which reflects the formation of the quartets in the mixed monolayers at the air-water interface. FTIR and small-angle X-ray diffraction (XRD) results of the corresponding Langmuir-Blodgett films support the hydrogen bonding recognition and molecular orientation.     

Recognition of thymine and related nucleosides by a Zn(II)-cyclen complex bearing a ferrocenyl pendant

A cyclen derivative bearing a ferrocenyl arm (L) and a series of its ZnII complexes [ZnL(OH2)][ClO4]2 (C1), [ZnL(OH)][ClO4] (C2), and [ZnL(Cl)][ClO4].CH3CN (C3) (cyclen = 1,4,7,10-tetraazacyclododecane, L = 1-(ferrocenemethyl)-1,4,7,10-tetraazacyclododecane) have been prepared and characterized spectroscopically. An X-ray structure determination confirmed the formation of complex C1 and revealed that the coordinated water participates in hydrogen bonding with the perchlorate counter ions. The pKa value for deprotonation of the water molecule determined by potentiometric titration was found to be 7.36 +/- 0.09 at 25 degrees C and I = 0.1 (KNO3). The possibility of using complex C1 as a potential sensor for thymine derivatives in aqueous solution has been examined. Shifts in the 1H and 13C NMR resonances showed the binding occurred with thymine (T) and two thymine derivatives, thymidine (dT) and thymidine 5'-monophosphate (TMP2-). Significant shifts of the nuC=O and nuC=C vibrations of the thymine derivatives were also observed via IR spectroscopy upon complexation with the receptor. The thymine adduct, [ZnL(thymine anion)][ClO4].2H2O (C4), has been crystallized and characterized. The X-ray structure of C4 confirmed the thymine binding to the receptor, and the short Zn-N(thymine) distance of 1.975(5) A indicated clearly that the ferrocenyl arm does not affect the complexation of the DNA base. In contrast to the large spectral changes, electrochemical studies showed a small shift of the reversible potential of the redox couple Fc+/Fc (Fc = ferrocene) and subtle changes in voltammetry upon the addition of an excess of dT, TMP2-, and guanine (dG) at physiological pH, indicating the level of interaction is similar in both Fc and Fc+ forms.     

Functional monolayers for improved resistance to protein adsorption: oligo(ethylene glycol)-modified silicon and diamond surfaces

The interaction of proteins with semiconductors such as silicon and diamond is of great interest for applications such as electronic biosensing. We have investigated the use of covalently bound oligo(ethylene glycol), EG, monolayers on diamond and silicon to minimize nonspecific protein adsorption. Protein adsorption was monitored by fluorescence scanning as a function of the length of the ethylene glycol chain (EG3 through EG6) and the terminal functional group (methyl- versus hydroxyl-terminated EG3 monolayer). More quantitative measurements were made by eluting adsorbed avidin from the surface and measuring the intensity of fluorescence in the solution. The attachment chemistry of the tri(ethylene glycol) molecules and monolayer orientation was studied by X-ray photoelectron spectroscopy. Improvement in the selectivity of surfaces modified with EG functionality was demonstrated in two model biosensing assays. We find that high-quality EG monolayers are formed on silicon and diamond and that these EG3 monolayers are as effective as EG3 self-assembled monolayers on gold at resisting nonspecific avidin adsorption. These results show promise for use of silicon and diamond materials in many potential applications such as biosensing and medical implants.     

Brownian dynamics simulations of the reactions of hydrated electrons with components of DNAs and a DNA double-helix

As a first step toward developing simulation models for studying the indirect mechanism of radiation damage to DNAs, we have carried out Brownian dynamics simulations to study the reactions of hydrated electrons with a 12-base-pair B-DNA, (dA)₁₂(dT)₁₂, and with bases, monodeoxynucleotides, and polydeoxynucleotides. We first studied in detail the sensitivity of diffusion reaction rate constants to different model and simulation parameters. Based on the sensitivity studies, a set of model and simulation parameters was obtained for the final production runs. The use of this set of parameters reduced the computational costs but delivered reasonably reliable results. The calculated reaction rate constants were in qualitative agreement with experiments. For the DNA double-helix, (dA)₁₂(dT)₁₂, the simulations demonstrated that hydrated electrons preferred to attack the two ends of the double-helix. Electrostatic interactions between the DNA and the hydrated electrons make the T strand more susceptible to attack than the A strand. The increased reactivity of the T strand due to electrostatic interactions results from the increased reactivity of the C6 sites of the thymine bases, at the expense of the reactivity of the C8 sites of the adenine bases. The reactivity of the relatively buried reactive sites of the adenine and thymine bases are less affected by electrostatic interactions. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 888–901, 1997     

Clustering of nucleobases with alkali metals studied by electrospray ionization tandem mass spectrometry: implications for mechanisms of multistrand DNA stabilization

Self-clustering of the five common nucleobases was investigated by electrospray ionization tandem mass spectrometry and shown to provide insight into the non-covalent interactions between identical bases. Alkali and ammonium cations significantly increase self-aggregation of the nucleobases and lead to the formation of uniquely stable magic number clusters. Sodium adducts of guanine, thymine and uracil preferentially take the form of tetrameric (quartet) clusters. This gas-phase result correlates with previously reported solution-phase data on sodium cation stabilized guanosine, thymine and uracil quartet structures believed to be responsible for telomere stabilization. In the presence of potassium, cesium or ammonium cations, pentameric magic number clusters are formed from thymine and uracil, while in solution the nucleoside isoguanosine yields clusters of this favored size. The formation of magic number metaclusters occurs for thymine and uracil in the presence of ammonium cations. These doubly charged 10- and 15-mers are tentatively attributed to the formation of pentamer/ammonium cation/ pentamer sandwich structures.     

Quantitative analysis and characterization of DNA immobilized on gold

We describe the complementary use of X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy to quantitatively characterize the immobilization of thiolated (dT)(25) single-stranded DNA (ssDNA) on gold. When electron attenuation effects are accurately accounted for in the XPS analysis, the relative coverage values obtained by the two methods are in excellent agreement, and the absolute coverage can be calculated on the basis of the XPS data. The evolution of chemically specific spectral signatures during immobilization indicates that at lower coverages much of the DNA lies flat on the surface, with a substantial fraction of the thymine bases chemisorbed. At higher immobilization densities, the (dT)(25) film consists of randomly coiled ssDNA molecules each anchored via the thiol group and at possibly one or two other bases. We use two examples to demonstrate how the quantitative analysis can be applied to practical problems: the effects of different buffer salts on the immobilization efficiency; the immobilization kinetics. Buffers with divalent salts dramatically increase the efficiency of immobilization and result in very high surface densities (>5 x 10(13)/ cm(2)), densities that may only be possible if the divalent counterions induce strong attractive intermolecular interactions. In contrast with previous reports of alkanethiol adsorption kinetics on gold, ssDNA immobilization in 1 M phosphate buffer does not occur with Langmuir kinetics, a result attributable to rearrangement within the film that follows the initial adsorption.     

The Formation of DNA Photodamage: The Role of Exciton Localization

The electronic structure during the formation of a cyclobutane pyrimidine dimer (CPD) between two thymine bases is investigated using semi‐empirical and first‐principles approaches. The dimerization of two isolated thymine bases is found to have no barrier or a very small barrier in agreement with previous studies suggesting low photostability of DNA. The well‐known high photostability of DNA can only be explained taking other factors into account. We investigate the role of the exciton location in the particular environment. Different model systems, from isolated thymine bases to an oligonucleotide in aqueous solution, are discussed. Analysis of the frontier orbitals allows one to understand the connection between the location of the exciton, the relative orientation of the thymine bases, and the observed reactivity.     

Effects of DNA Probe Length on the Performance of a Dynamics‐based Electrochemical Hg(II) Sensor

We investigated the effects of DNA probe length on the performance of a dynamics‐based electrochemical metal ion (E‐ION) Hg(II) sensor. A systematic comparison of three versions of the Hg(II) sensor fabricated using oligothymine (oligo‐T) probes of different lengths (6, 12, and 18 bases) is presented here. Independent of the probe length, the sensing mechanism of the sensor remains the same. It is based on the specific interactions between Hg(II) and thymine (T), formation of the T‐Hg(II)‐T complexes rigidifies the methylene blue (MB)‐modified oligo‐T probes, resulting in a concentration‐dependent reduction in the MB signal. Although there are noted differences in sensor characteristics such as the limit of detection and dynamic range, all three sensors have demonstrated to be specific and selective. Thus, depending on the specific sensor properties that are required for the analysis, a shorter or longer oligo‐T probe should be employed. With further optimization, this sensor could find applications in real time detection of Hg(II) in environmental samples.     

Nanoscale water condensation on click-functionalized self-assembled monolayers

We have examined the nanoscale adsorption of molecular water under ambient conditions onto a series of well-characterized functionalized surfaces produced by Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC or "click") reactions on alkyne-terminated self-assembled monolayers on silicon. Water contact angle (CA) measurements reveal a range of macroscopic hydrophilicity that does not correlate with the tendency of these surfaces to adsorb water at the molecular level. X-ray reflectometry has been used to follow the kinetics of water adsorption on these "click"-functionalized surfaces, and also shows that dense continuous molecular water layers are formed over 30 h. For example, a highly hydrophilic surface, functionalized by an oligo(ethylene glycol) moiety (with a CA = 34°) showed 2.9 ? of adsorbed water after 30 h, while the almost hydrophobic underlying alkyne-terminated monolayer (CA = 84°) showed 5.6 ? of adsorbed water over the same period. While this study highlights the capacity of X-ray reflectometry to study the structure of adsorbed water on these surfaces, it should also serve as a warning for those intending to characterize self-assembled monolayers and functionalized surfaces to avoid contamination by even trace amounts of water vapor. Moreover, contact angle measurements alone cannot be relied upon to predict the likely degree of moisture uptake on such surfaces.     

Experiments on convective in-plane orientation of monolayers

Flow-compressed monolayers of stiff rod-like polymers (poly-glutamates) mixed with oleophilic tracer dyes showed significant in-plane dichroism of dye absorption at the water surface, indicating lateral ordering of polyglutamate-rods more or less “perpendicular” to flow direction. During LB-deposition the lateral orientation of dye- and polymer-molecules was maintained, in-plane orientation of the LB-film was thus depending on substrate-orientation relative to flow-direction. Identical monolayers compressed in a regular Langmuir-trough (with moving barrier) showed no large-scale ordering at the water surface, but during film-transfer polymer matrix and dye were oriented in dipping direction, irrespective of substrate orientation relative to compression direction.     

Adsorption of oligonucleotides on PMMA/PNIPAM core-shell latexes: polarity of the PNIPAM shell probed by fluorescence

The adsorption of a rhodamine X labeled oligonucleotide composed of 25-mers of thymine (dT(25)-ROX) onto the thermosensitive shell of PMMA/PNIPAM core-shell latex particles was studied at 22 and 40 degrees C, below and above the T(VPT) (volume phase transition temperature) of the PNIPAM shell, respectively. The experimental binding isotherms were well fitted with the cooperative Hill model. The Hill coefficient is lower than 1 at both temperatures showing that the adsorption is anticooperative. The polarity of the shell was probed by both the lifetimes and solvatochromic shifts of the zwitterionic form of rhodamine X. For temperatures below the shell T(VPT) has a polarity similar to that of water, while for temperatures above the transition the polarity is equivalent to that of a water/dioxane mixture with 30% (v/v) water.     

Specific and nonspecific metal ion-nucleotide interactions at aqueous/solid interfaces functionalized with adenine, thymine, guanine, and cytosine oligomers

This article reports nonlinear optical measurements that quantify, for the first time directly and without labels, how many Mg(2+) cations are bound to DNA 21-mers covalently linked to fused silica/water interfaces maintained at pH 7 and 10 mM NaCl, and what the thermodynamics are of these interactions. The overall interaction of Mg(2+) with adenine, thymine, guanine, and cytosine is found to involve -10.0 ± 0.3, -11.2 ± 0.3, -14.0 ± 0.4, and -14.9 ± 0.4 kJ/mol, and nonspecific interactions with the phosphate and sugar backbone are found to contribute -21.0 ± 0.6 kJ/mol for each Mg(2+) ion bound. The specific and nonspecific contributions to the interaction energy of Mg(2+) with oligonucleotide single strands is found to be additive, which suggests that within the uncertainty of these surface-specific experiments, the Mg(2+) ions are evenly distributed over the oligomers and not isolated to the most strongly binding nucleobase. The nucleobases adenine and thymine are found to bind only three Mg(2+) ions per 21-mer oligonucleotide, while the bases cytosine and guanine are found to bind eleven Mg(2+) ions per 21-mer oligonucleotide.     

Factors that determine the protein resistance of oligoether self-assembled monolayers --internal hydrophilicity,terminal hydrophilicity,and lateral packing density

Protein resistance of oligoether self-assembled monolayers (SAMs) on gold and silver surfaces has been investigated systematically to elucidate structural factors that determine whether a SAM will be able to resist protein adsorption. Oligo(ethylene glycol) (OEG)-, oligo(propylene glycol)-, and oligo(trimethylene glycol)-terminated alkanethiols with different chain lengths and alkyl termination were synthesized as monolayer constituents. The packing density and chemical composition of the SAMs were examined by XPS spectroscopy; the terminal hydrophilicity was characterized by contact angle measurements. IRRAS spectroscopy gave information about the chain conformation of specific monolayers; the amount of adsorbed protein as compared to alkanethiol monolayers was determined by ellipsometry. We found several factors that in combination or by themselves suppress the protein resistance of oligoether monolayers. Monolayers with a hydrophobic interior, such as those containing oligo(propylene glycol), show no protein resistance. The lateral compression of oligo(ethylene glycol) monolayers on silver generates more highly ordered monolayers and may cause decreased protein resistance, but does not necessarily lead to an all-trans chain conformation of the OEG moieties. Water contact angles higher than 70 degrees on gold or 65 degrees on silver reduce full protein resistance. We conclude that both internal and terminal hydrophilicity favor the protein resistance of an oligoether monolayer. It is suggested that the penetration of water molecules in the interior of the SAM is a necessary prerequisite for protein resistance. We discuss and summarize the various factors which are critical for the functionality of "inert" organic films.     

Molecular electrotatic potential of a triple stranded helix: Poly(dT)·poly(dA)·poly(dT)

The molecular electrostatic potential of the triple helix poly(dT)·tpoly(dA)·poly(dT) is calculated, and the results are examined in relation to those obtained for its component double and single helical parts. For the double helix presenting the standard Watson–Crick hydrogen bonds, the deepest potentials are formed on the side of the major groove, a situation similar to that observed in the A-DNA duplex. For the double helix presenting Hoogsteen-type hydrogen bonds the deepest potentials lie in the major groove, on the side of the pyrimidine strand. In the triple helix the deepest potentials are located in the major groove in a narrow zone over the thymine bases of the Watson–Crick pair.     

In situ characterization of functional purple membrane monolayers at the air-water interface

The purple membrane (PM) of Halobacterium salinarum contains a single type of protein, bacterio-rhodopsin (bR), which is a member of the seven alpha-helices transmembrane protein family. This protein is a photoactive proton pump, translocating one proton from the cytoplasmic to the extracellular side of the PM per photon absorbed. bR is found in trimers in PM, where they are assembled in a two-dimensional hexagonal lattice. We show herein that stable and functional films can be built in monolayers at the air-water interface by spreading aqueous suspensions of purified and native PM patches. In situ spectroscopic measurements at the air-water interface indicate that bR remains photoactive in this environment. Physical parameters of these PM films, such as protein molecular area, irreversible in-plane aggregation, z-axis orientation, film thickness, and surface roughness, were determined from surface pressure and surface potential-area isotherms, fluorescence spectroscopy, and X-ray reflectivity at the air-water interface. We find that PM do form organized monolayers of membranes, with an optimal packing density at a surface pressure of approximately 20 mN/m, although no preferential vectorial alignment, with respect to the plane normal to the membrane, can be detected from fluorescence quenching experiments.     

Polymer ultrathin films with immobilized photosynthetic reaction center proteins

Properties of mixed monolayers of lipid-photosynthetic reaction center proteins (RC) were studied and the optimum conditions for stable films fabrication were determined. The following synthetic: N-acryloylphosphatidylethanolamine (ACPE), tetracosa-11, 13-diinoic acid (TDA), pentacosa-10, 12-diinoic acid (PDA), dioctadecyldienoylphosphatidylcholine (DODL) and natural lipids: L-α-phosphatidylethanolamine (PE), L-α-phosphatidylcholine (PC) were used. The rate of polymerization of the mixed ACPE-RC and TDA-RC monolayers is lower in comparison with corresponding values for pure lipid-like monomers on air/water interface. The optical and photoelectrical measurements provide evidence for an orientation of RCs on interface. Hydrophilic H-subunit in monomeric and polymeric ACPE-RCs, and monomeric DODL-RCs monolayers is preferentially oriented towards water as in the pure RC monolayers. Opposite orientation was found with TDA-RCs and PDA-RCs films. No preferential orientation for lipid-RCs from C. aurantiacus monolayers was found because of the RCs having low assymmetry of hydrophobic subunits (M and L).     

Theoretical investigation on the structural and electronic properties of complexes formed by thymine and 2′-deoxythymidine with different anions

Hydrogen bonding interactions between thymine nucleobase and 2′-deoxythymidine nucleoside (dT) with some biological anions such as F⁻ (fluoride), Cl⁻ (chloride), OH⁻ (hydroxide), and NO₃ ⁻ (nitrate) have been explored theoretically. In this study, complexes have been studied by density functional theory (B3LYP method and 6-311++G (d,p) basis set). The relevant geometries, energies, and characteristics of hydrogen bonds (H-bonds) have been systematically investigated. There is a correlation between interaction energy and proton affinity for complexes of thymine nucleobase. The nature of all the interactions has been analyzed by means of the natural bonding orbital (NBO) and quantum theory atoms in molecules (QTAIM) approaches. Donors, acceptors, and orbital interaction energies were also calculated for the hydrogen bonds. Excellent correlations between structural parameter (δR) and electron density topological parameter (ρ _b) as well as between E(2) and ρ _b have been found. It is interesting that hydrogen bonds with anions can affect the geometry of thymine and 2′-deoxythymidine molecules. For example, these interactions can change the bond lengths in thymine nucleobase, the orientation of base unit with respect to sugar ring, the furanose ring puckering, and the C1′–N1 glycosidic linkage in dT nucleoside. Thus, it is necessary to obtain a fundamental understanding of chemical behavior of nucleobases and nucleosides in presence of anions.     

Structural development of mercaptophenol self-assembled monolayers and the overlying mineral phase during templated CaCO3 crystallization from a transient amorphous film

Formation of biomineral structures is increasingly attributed to directed growth of a mineral phase from an amorphous precursor on an organic matrix. While many in vitro studies have used calcite formation on organothiol self-assembled monolayers (SAMs) as a model system to investigate this process, they have generally focused on the stability of amorphous calcium carbonate (ACC) or maximizing control over the order of the final mineral phase. Little is known about the early stages of mineral formation, particularly the structural evolution of the SAM and mineral. Here we use near-edge X-ray absorption spectroscopy (NEXAFS), photoemission spectroscopy (PES), X-ray diffraction (XRD), and scanning electron microscopy (SEM) to address this gap in knowledge by examining the changes in order and bonding of mercaptophenol (MP) SAMs on Au(111) during the initial stages of mineral formation as well as the mechanism of ACC to calcite transformation during template-directed crystallization. We demonstrate that formation of ACC on the MP SAMs brings about a profound change in the morphology of the monolayers: although the as-prepared MP SAMs are composed of monomers with well-defined orientations, precipitation of the amorphous mineral phase results in substantial structural disorder within the monolayers. Significantly, a preferential face of nucleation is observed for crystallization of calcite from ACC on the SAM surfaces despite this static disorder.