ssDNA Films Research Articles

A unified model for mechanical deformations of single stranded DNA-microbeam biosensors considering surface charge effects

A unified energy model for mechanical deformation of the microbeam included by single stranded DNA (ssDNA) adsorption considering the surface charge density on substrate is investigated. First, a free energy model is established to quantify the deflection and axial displacement of the microbeam, the ion concentration in the solution, as well as the electric potential distribution inside and outside the ssDNA film with a uniform surface charge density. Then, the governing equations and corresponding boundary conditions are obtained by minimizing the free energy with three types of variational variables. And, the relationship of the electric potential difference between the two sides of the ssDNA film and the deformation of microcantilever and simply support beam are determined in different solutions (1: 1, 1: 2, 1: 3). Moreover, the numerical solutions of the electric potential distribution inside and outside the ssDNA film are investigated by using the finite difference method and Newton's iteration method. The results suggest that the nonlinear model for electric potential distribution should be used under higher surface charge density. By fitting and comparing the present predictions with Arroyo-Hernandez's experimental data, the effectiveness of the model is verified. The study shows that the surface charge density can modulate the magnitude and direction of ssDNA-microbeam deformation, which also indicates that there exists a critical surface charge density, causing the failure of ssDNA-microbeam detection. These conclusions are helpful for designing the efficient biosensors based on DNA-microbeam.

Morphological and Mechanical Characterization of DNA SAMs Combining Nanolithography with AFM and Optical Methods.

The morphological and mechanical properties of thiolated ssDNA films self-assembled at different ionic strength on flat gold surfaces have been investigated using Atomic Force Microscopy (AFM). AFM nanoshaving experiments, performed in hard tapping mode, allowed selectively removing molecules from micro-sized regions. To image the shaved areas, in addition to the soft contact mode, we explored the use of the Quantitative Imaging (QI) mode. QI is a less perturbative imaging mode that allows obtaining quantitative information on both sample topography and mechanical properties. AFM analysis showed that DNA SAMs assembled at high ionic strength are thicker and less deformable than films prepared at low ionic strength. In the case of thicker films, the difference between film and substrate Young’s moduli could be assessed from the analysis of QI data. The AFM finding of thicker and denser films was confirmed by X-Ray Photoelectron Spectroscopy (XPS) and Spectroscopic Ellipsometry (SE) analysis. SE data allowed detecting the DNA UV absorption on dense monomolecular films. Moreover, feeding the SE analysis with the thickness data obtained by AFM, we could estimate the refractive index of dense DNA films.

Influence of intra-molecular flexibility on the elastic property of double-stranded DNA film on a substrate

DNA film self-assembled or nanografted on a substrate, as a kind of soft matter, consists of fixed DNA chains endowed with negative charges and an aqueous solution full of cations, anions and water molecules. Their thermal/electrical/mechanical properties are closely related to the complex biodetection signals in nano-/micro-scale biosensors and other new genome technologies. This makes it important to properly characterize these properties. In this paper, the effect of flexible micro-scale configurations on the elastic moduli of DNA films is investigated. First, illuminated by Qiu’s sphere model, an alternative bead-chain model in terms of the Yukawa potential is presented for flexible intra-DNA configurations to describe interactions between DNA fragments. The effective charges of coarse-grained DNA beads could be derived, in which the empirical parameters are identified by curve fitting with Qiu’s experimental data. Second, the updated mesoscopic bead-chain model and the thought experiment of a continuum compression bar are used to compare the elastic moduli of double-stranded DNA (dsDNA) films prepared by self-assembling and nanografting techniques. Configurational sampling is achieved via Monte Carlo simulation. Our predictions quantitatively or qualitatively agree well with the relevant experiments on the effective charge of dsDNA from low to moderate monovalent counterion concentration, immobilization deflection of single-stranded DNA (ssDNA) or dsDNA microcantilever with the variation of salt concentration, and elastic modulus of ssDNA film in the air. The results reveal that different solution environment stimulates the diverse mechanical properties of dsDNA film on a substrate, and the end effect (i.e. terminal group effect) makes self-assembling dsDNA film stiffer in the sense of the same average packing density.

Inverse piezoelectricity of single-stranded DNA film on microcantilever

The paper aims to reveal the relation between the inverse piezoelectricity of singlestranded DNA (ssDNA) film and the origin and sign of the deflection of microcantilever produced by the DNA immobilization. By using Zhang’s two-variable method for strain field of laminated beam and the linearized Poisson-Boltzmann equation for bioelectric potential of polyelectrolyte brush, an approximate model is presented to confirm the previous conjecture that the sign of the piezoelectric constant of ssDNA film might decide the sign of the surface stress. There is only one fitting parameter (piezoelectric stress constant) needed in the simplified model, which greatly reduces the difficulty of identifying the nanoscale electrical/mechanical properties of DNA film. Numerical fitting curves based-on the analytical models agree well with the pertinent experimental dada. The difference between the previous four-layered model and the present two-layered approximate model is also compared.

Influence of disordered packing pattern on elastic modulus of single-stranded DNA film on substrate.

Determining mechanical properties of single-stranded DNA film grafted on gold surface is critical for analysis and design of DNA-microcantilever biosensors. However, it remains an open issue to quantify the relations among the disordered packing patterns of DNA chains, the mechanical properties of DNA film and the resultant biodetection signals. In this paper, first, the bending experiment of microcantilever is carried out to provide the basic data for a refined multi-scale model of microcantilever deflection induced by ssDNA immobilization. In the model, the complicated interactions in DNA film (consisting of DNA, water molecules and salt ions) are simplified as effective interactions among coarse-grained soft cylinders, which can reveal the varieties of DNA structure in the circumstances of different lengths and salt concentrations; Ohshima's distribution of net charge density is employed to incorporate compositional variations of salt ions along the thickness direction into the Strey's mesoscopic empirical potential on molecular interactions in DNA solutions, and the related model parameters for ssDNA film on substrate are obtained from the curve fitting with our microcantilever bending experiment. Second, the effect of nanoscopic distribution of DNA chains on elastic modulus of ssDNA film is studied by a thought experiment of uniaxial compression, and the disordered patterns of DNA chains are generated by Monte Carlo method. Simulation results point out that nanoscale ssDNA film shows size effect, gradient and diversity in elastic modulus and can achieve maximum stiffness by preferring a disordered and energetically favorable packing pattern collectively induced by electrostatic force, hydration force and configurational entropy.

Cetyltrimethylammonium micelles enhance the sensitivity of ssDNA-based electrochemical sensor for the determination of pyridoxol

CTAB surfactant was assembled on ssDNA film electrode by electrostatic attraction between CTAB and ssDNA. The self-assembly of CTAB on ssDNA formed the micellar bilayer. Pyridoxol anions adsorbed on the micellar bilayer resulted in a markedly enhanced sensitivity. Practical applicability can be realized by the direct assay of pharmaceutical samples.

An electrochemical sensor based on single-stranded DNA–poly(sulfosalicylic acid) composite film for simultaneous determination of adenine, guanine, and thymine

Poly(sulfosalicylic acid) and single-stranded DNA composite (PSSA–ssDNA)-modified glassy carbon electrode (GCE) was prepared by electropolymerization and then successfully used to simultaneously determine adenine (A), guanine (G), and thymine (T). The characterization of electrochemically synthesized PSSA–ssDNA film was investigated by scanning electron microscopy (SEM) and electrochemical impedance spectroscopy (EIS). The modified electrode exhibited enhanced electrocatalytic behavior and good stability for the simultaneous determination of A, G, and T in 0.1 M phosphate buffer solution (PBS, pH 7.0). Well-separated voltammetric peaks were obtained among A, G, and T presented in the analyte mixture. Under the optimal conditions, the peak currents for A, G, and T increased linearly with the increase of analyte mixture concentration in the ranges of 6.5 × 10 −8 to 1.1 × 10 −6, 6.5 × 10 −8 to 1.1 × 10 −6, and 4.1 × 10 −6 to 2.7 × 10 −5 M, respectively. The detection limits (signal/noise = 3) for A, G, and T were 2.2 × 10 –8, 2.2 × 10 –8, and 1.4 × 10 –6 M, respectively.

Hybridization in ssDNA films—a multi-technique spectroscopy study

A combination of X-ray photoelectron spectroscopy (XPS), high-resolution XPS, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and sum-frequency-generation (SFG) spectroscopy was used to monitor two types of ssDNA films on Au(111) before and after hybridization. As probe systems, films of thiolated and block-oligonucleotides were used, taking thiolated thymine d(T) homo-oligonucleotides and thymine-adenine d(A-T) diblock-oligonucleotides as representative examples. In accordance with previous work, hybridization of the shorter and more densely packed thiolated ssDNA films produced fewer (if any) hybrids, whereas the longer and less densely packed layers exhibited a larger hybridization yield. The above effects were less pronounced in the case of the d(A-T) films where the hybridization yield of the less densely packed monolayers was significantly lower. This was presumably due to the formation of internal dimeric hybrids in the immobilization step of the probe molecules, resulting in the generation of fewer probe-target hybrids upon exposure to the target molecules. In all ssDNA films displaying a reasonable number of hybrids present, significant orientational changes were observed and could be monitored in detail. These results suggest that the given combination of spectroscopic techniques can be a valuable tool to gain molecular-level information about hybrids at interfaces.

Orientation and Ordering in Monomolecular Films of Sulfur-Modified Homo-oligonucleotides on Gold

The chemical integrity, packing density, orientation, and ordering in monomolecular films of sulfur-modified single-stranded DNA (ssDNA) on Au{111} were probed by a combination of X-ray photoelectron spectroscopy, angle-resolved near-edge absorption fine structure spectroscopy (at all relevant absorption edges), and infrared reflection absorption spectroscopy. As model systems, short chain (five nucleotides) thymine- and adenine-based homo-oligonucleotides were used. All ssDNA moieties were found to be bound to the substrate by the thiolate anchor, with no physisorbed ssDNA species but some contamination present. The density of the ssDNA moieties in the thymine- and adenine-based films was estimated at ∼4.8 × 1013 and ∼5.9 × 1013 mol/cm−2, respectively. At the same time, the former films exhibited a higher degree of the orientational order as compared to the latter ones. The lack of correlation between the packing density and orientational order is noteworthy and is assumed to be a specific property of sulfur-modified ssDNA films. Such behavior can be related to a special character of inter- and intramolecular interaction in these systems along with the influence of direct interaction between the nucleobases and substrate.

Electrochemical detection of lateral charge transport in metal complex-DNA monolayers synthesized on Si(111) electrodes

The lateral charge transport in films comprising metal complexes bound to DNA monolayers on Si electrodes was measured by scanning electrochemical microscopy (SECM) in the steady-state feedback mode. Single-stranded (ss) DNA monolayers covalently bonded to the Si surface were prepared by automated solid-phase synthesis on hydroxyl-terminated n-alkyl monolayers at atomically flat Si(1 1 1)–H surfaces. Duplex (ds) DNA films were produced by hybridisation to the ssDNA monolayers. Our previous STM imaging investigations showed these dsDNA films exhibit considerable alignment, but the ssDNA films were observed by AFM to be rather disordered. Using solutions of Fe(CN)64-, IrCl63-, Ru(bipy)32+, Co(bipy)33+ and Ru(NH3)63+ as redox mediators, we compared the rate of charge transport in dsDNA films to that in ssDNA films. Lateral charge transport on the substrate – the source of the SECM feedback – depends on the self-exchange rate between the surface and solution as well as the rate of diffusion of charged, surface-bound species. Several mechanisms of lateral charge transfer (physical surface diffusion, electron hopping between DNA-bound redox species, charge injection into Si and DNA-mediated long-range electron transfer) were explored as possible explanations for the positive feedback observed in Ru(bipy)32+ and Ru(NH3)63+ solutions. While Ru(bipy)33+ was found to inject holes into the silicon valence band across the organic monolayer, the fast charge transport in Ru(NH3)63+/dsDNA films (effective diffusion coefficient, (2.2 ± 0.3) × 10−5 cm2 s−1) was attributed to a combination of physical diffusion of the ruthenium centres on the surface and charge injection into the Si electrode. For analysis of the SECM feedback experiments with lateral charge transport coupled to electron transfer to dissolved mediators, an analytical approximation was developed and validated by comparison with the results of finite difference simulations. This model successfully accounts for the variation in the SECM feedback with the concentration of the mediator in the solution.

Quantitative Characterization of DNA Films by X-ray Photoelectron Spectroscopy

We describe the use of self-assembled films of thiolated (dT)25 single-stranded DNA (ssDNA) on gold as a model system for quantitative characterization of DNA films by X-ray photoelectron spectroscopy (XPS). We evaluate the applicability of a uniform and homogeneous overlayer-substrate model for data analysis, examine model parameters used to describe DNA films (e.g., density and electron attenuation length), and validate the results. The model is used to obtain quantitative composition and coverage information as a function of immobilization time. We find that when the electron attenuation effects are properly included in the XPS data analysis, excellent agreement is obtained with Fourier transform infrared (FTIR) measurements for relative values of the DNA coverage, and the calculated absolute coverage is consistent with a previous radiolabeling study. Based on the effectiveness of the analysis procedure for model (dT)25 ssDNA films, it should be generally valid for direct quantitative comparison of DNA films prepared under widely varying conditions.

Integrity and redox properties of homogeneous and heterogeneous DNA films on gold surface probed by cyclic voltammetry

5′-thiol-labeled single-stranded DNA (22 mer ssDNA) adsorbed onto the gold surface by both non-specific binding and Au–S linkage, whereas 5′-thiol-labeled double-stranded DNA (22-bp dsDNA) formed a packed layer mainly through the Au–S linkage. The coating of homogeneous ssDNA or dsDNA films or heterogeneous DNA films mixed with n-hexadecyl mercaptan (HDM) on gold surface facilitated the redox reaction of methylene blue (MB). MB binds with ssDNA through electrostatic interaction with the charged backbone and adsorbed through the ssDNA film. MB binds with dsDNA through both electrostatic interaction and intercalation into the dsDNA base pairs and undergoes redox reaction by diffusing through the dsDNA film to the gold surface and/or electron transfer through the DNA helix. The addition of HDM enhanced the integrity and stability upon NaOH treatment for both ssDNA and dsDNA films.