Electrical conduction through poly(dA)-poly(dT) and poly(dG)-poly(dC) DNA molecules

Synthesis of steroid-oligonucleotide conjugates for a DNA site-encoded SPR immunosensor

The excellent self-assembling properties of DNA and the excellent specificity of the antibodies to detect analytes of small molecular weight under competitive conditions have been combined in this study. Three oligonucleotide sequences (N(1)up, N(2)up, and N(3)up) have been covalently attached to three steroidal haptens (8, hG, and 13) of three anabolic-androgenic steroids (AAS), stanozolol (ST), tetrahydrogestrinone (THG), and boldenone (B), respectively. The synthesis of steroid-oligonucleotide conjugates has been performed by the reaction of oligonucleotides carrying amino groups with carboxyl acid derivatives of steroidal haptens. Due to the chemical nature of the steroid derivatives, two methods for coupling the haptens and the ssDNA have been studied: a solid-phase coupling strategy and a solution-phase coupling strategy. Specific antibodies against ST, THG, and B have been used in this study to asses the possibility of using the self-assembling properties of the DNA to prepare biofunctional SPR gold chips based on the immobilization of haptens, by hybridization with the complementary oligonucleotide strands possessing SH groups previously immobilized. The capture of the steroid-oligonucleotide conjugates and subsequent binding of the specific antibodies can be monitored on the sensogram due to variations produced on the refractive index on top of the gold chip. The resulting steroid-oligonucleotide conjugates retain the hybridization and specific binding properties of oligonucleotides and haptens as demonstrated by thermal denaturation experiments and surface plasmon resonance (SPR).

Polaron transport mechanism in DNA

A theory of polaron-hopping transport is studied in DNA in the presence of an electric field. The helix structure of DNA consists of a molecule of phosphoric acid, a molecule of sugar and a molecule of a nitrogen compound called a nitrogen base. The charge carriers are localized near the bases. Phonons are created due to internal motions such as changes in winding or the inclination angle of the helix. It is considered that, due to the interaction between a charge carrier and a phonon, a localized polaron is formed in the helix near a base. These internal motions also promote hopping of the localized polarons. By interacting with a phonon, the polaron undergoes a hopping process in the helix structure. We consider that the localized polaron sites are distributed randomly in both space and energy coordinates. A polaron hops from one site to another site in this space. Conduction is a result of many series of hops through this hopping space. This approach differs from the percolation method and others in the calculation of the conductivity. The present theory is used to explain the electric-field- and temperature-dependent conductivity experiments of DNA. A good agreement is found between theory and experiments.

Electrical characterization of gold-DNA-gold structures in presence of an external magnetic field by means of I-V curve analysis

This work presents an experimental study of gold-DNA-gold structures in the presence and absence of external magnetic fields with strengths less than 1,200.00 mT. The DNA strands, extracted by standard method were used to fabricate a Metal-DNA-Metal (MDM) structure. Its electric behavior when subjected to a magnetic field was studied through its current-voltage (I-V) curve. Acquisition of the I-V curve demonstrated that DNA as a semiconductor exhibits diode behavior in the MDM structure. The current versus magnetic field strength followed a decreasing trend because of a diminished mobility in the presence of a low magnetic field. This made clear that an externally imposed magnetic field would boost resistance of the MDM structure up to 1,000.00 mT and for higher magnetic field strengths we can observe an increase in potential barrier in MDM junction. The magnetic sensitivity indicates the promise of using MDM structures as potential magnetic sensors.

Charge transport in DNA: dependence of diffusion coefficient on temperature and electron-phonon coupling constant

The diffusion coefficient is calculated for a charge propagating along a double-stranded DNA, while it interacts with the nonlinear fluctuational openings of base pairs. The latter structural dynamics of DNA is described by the Peyrard-Bishop-Dauxois model [T. Dauxois, M. Peyrard, and A. R. Bishop, Phys Rev. E 47 R44 (1993)], which represents essential anharmonicities of base-pair stretchings. The dependence of the diffusion coefficient on the temperature and the electron-phonon coupling constant is presented. The diffusion coefficient decreases when either the temperature or the electron-phonon coupling increases. Analytical expressions are provided that describe the temperature dependence of the diffusion coefficient. The variation of the parameters of these expressions with the electron-phonon coupling constant is also discussed. These results quantitatively demonstrate how DNA structural nonlinear dynamics affects macroscopic charge transport properties.

Self-aligned sub-10-nm nanogap electrode array for large-scale integration

A novel approach to creating a gap on the nanometer scale between two adjacent electrodes of the same or different metals is described. The gap size can be well controlled through sidewall coverage in a self-aligned manner and it can be tuned from 60 nm down to 5 nm with high reproducibility. This technique is fully compatible with traditional microfabrication technology and it is easily implemented to fabricate a nanogap electrode array for integration purposes. An array of short-channel single-walled carbon nanotube field-effect transistors is demonstrated.

Plasmonic nanofabrication by long-range excitation transfer via DNA nanowire

Driven by the demand for ongoing integration and increased complexity of today's microelectronic circuits, smaller and smaller structures need to be fabricated with a high throughput. In contrast to serial nanofabrication techniques, based, e.g., on electron beam or scanning probe methods, optical methods allow a parallel approach and thus a high throughput. However, they rarely reach the desired resolution. One example is plasmon lithography, which is limited by the utilized plasmonic metal structures. Here we show a new approach extending plasmonic lithography with the potential for a highly parallel nanofabrication with a higher level of complexity based on nanoantenna effects combined with molecular nanowires. Thereby femtosecond laser pulse light is converted by Ag nanoparticles into a high plasmonic excitation guided along attached DNA structures. An underlying poly(methyl methacrylate) (PMMA) layer acting as an electron-sensitive resist is so structured along the former DNA position. This apparently DNA-guided effect leads to nanometer grooves reaching even micrometers away from the excited nanoparticle, representing a novel effect of long-range excitation transfer along DNA nanowires.

Ni2+-enhanced charge transport via π-π stacking corridor in metallic DNA

The mechanism underlying DNA charge transport is intriguing. However, poor conductivity of DNA makes it difficult to detect DNA charge transport. Metallic DNA (M-DNA) has better conducting properties than native DNA. Ni(2+) may chelate in DNA and thus enhance DNA conductivity. On the basis of this finding, it is possible to reveal the mechanisms underlying DNA charge transport. The conductivity of various Ni-DNA species such as single-stranded, full complement, or mismatched sequence molecules was systematically tested with ultraviolet absorption and electrical or chemical methods. The results showed that the conductivity of single-stranded Ni-DNA (Ni-ssDNA) was similar to that of a native DNA duplex. Moreover, the resistance of Ni-DNA with a single basepair mismatch was significantly higher than that of fully complementary Ni-DNA duplexes. The resistance also increased exponentially as the number of mismatched basepairs increased linearly after the tunneling current behavior predicted by the Simmons model. In conclusion, the charges in Ni(2+)-doped DNA are transported through the Ni(2+)-mediated π-π stacking corridor. Furthermore, Ni-DNA acts as a conducting wire and exhibits a tunneling barrier when basepair mismatches occur. This property may be useful in detecting single basepair mismatches.

Synthesis of long DNA-based nanowires

Here we describe novel procedures for production of DNA-based nanowires. This include synthesis and characterization of the one-to-one double-helical complex of poly(dG)-poly(dC), triple-helical poly(dG)-poly(dG)-poly(dC) and G4-DNA, which is a quadruple-helical form of DNA. All these types of DNA-based molecules were synthesized enzymatically using Klenow exo(-) fragment of DNA Polymerase I. All the above types of nanowires are characterized by a narrow-size distribution of molecules. The contour length of the molecules can be varied from tens to hundreds of nanometers. These structures possess improved conductive and mechanical properties with respect to a canonical random-sequenced DNA and can possibly be used as wire-like conducting or semiconducting nanostructures in the field of nanoelectronics.

Selective formation of a latticed nanostructure with the precise alignment of DNA-templated gold nanowires

A very efficient method is introduced to selectively align and uniformly separate λ-DNA molecules and thus DNA-templated gold nanowires (AuNW's) using a combination of molecular combing and surface-patterning techniques. By the method presented in this work, it is possible to obtain parallel and latticed nanostructures consisting of DNA molecules and thus DNA-templated AuNW's aligned at 400 nm intervals. DNA-templated AuNW's are uniformly formed with an average height of 2.5 nm. This method is expected to hold potential for the integration of nanosized building blocks applicable to nanodevice construction.

Electronic structure of genomic DNA: a photoemission and X-ray absorption study

The electronic structure of genomic DNA has been comprehensively characterized by synchrotron-based X-ray absorption and X-ray photoelectron spectroscopy. Both unoccupied and occupied states close to the Fermi level have been unveiled and attributed to particular sites within the DNA structure. A semiconductor-like electronic structure with a band gap of approximately 2.6 eV has been found at which the pi and pi* orbitals of the nucleobase stack make major contributions to the highest occupied and lowest unoccupied molecular orbitals, respectively, in agreement with previous theoretical predictions.

Electronic parameters for charge transfer along DNA

We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The pi molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wave functions and energies of DNA bases are discussed and then used for calculating the corresponding wave functions of the two B-DNA base-pairs (adenine-thymine and guanine-cytosine). The obtained HOMO and LUMO energies of the bases are in good agreement with available experimental values. Our results are then used for estimating the complete set of charge transfer parameters between neighboring bases and also between successive base-pairs, considering all possible combinations between them, for both electrons and holes. The calculated microscopic quantities can be used in mesoscopic theoretical models of electron or hole transfer along the DNA double helix, as they provide the necessary parameters for a tight-binding phenomenological description based on the pi molecular overlap. We find that usually the hopping parameters for holes are higher in magnitude compared to the ones for electrons. Our findings are also compared with existing calculations from first principles.

Polaron Hopping in Nano-scale Poly(dA)-Poly(dT) DNA

We investigate the current-voltage relationship and the temperature-dependent conductance of nano-scale samples of poly(dA)-poly(dT) DNA molecules. A polaron hopping model has been used to calculate the I-V characteristic of nano-scale samples of DNA. This model agrees with the data for current versus voltage at temperatures greater than 100 K. The quantities G(0), i(0), and T(1d) are determined empirically, and the conductivity is estimated for samples of poly(dA)-poly(dT).

Nanogap electrodes

Nanogap electrodes (namely, a pair of electrodes with a nanometer gap) are fundamental building blocks for the fabrication of nanometer-sized devices and circuits. They are also important tools for the examination of material properties at the nanometer scale, even at the molecular scale. In this review, the techniques for the fabrication of nanogap electrodes, the preparation of assembled devices based on the nanogap electrodes, and the potential application of these nanodevices for analysis of material properties are introduced. The history, the research status, and the prospects of nanogap electrodes are also discussed.

Nanogap biosensors for electrical and label-free detection of biomolecular interactions

We demonstrate nanogap biosensors for electrical and label-free detection of biomolecular interactions. Parallel fabrication of nanometer distance gaps has been achieved using a silicon anisotropic wet etching technique on a silicon-on-insulator (SOI) wafer with a finely controllable silicon device layer. Since silicon anisotropic wet etching resulted in a trapezoid-shaped structure whose end became narrower during the etching, the nanogap structure was simply fabricated on the device layer of a SOI wafer. The nanogap devices were individually addressable and a gap size of less than 60 nm was obtained. We demonstrate that the nanogap biosensors can electrically detect biomolecular interactions such as biotin/streptavidin and antigen/antibody pairs. The nanogap devices show a current increase when the proteins are bound to the surface. The current increases proportionally depending upon the concentrations of the molecules in the range of 100 fg ml(-1)-100 ng ml(-1) at 1 V bias. It is expected that the nanogap developed here could be a highly sensitive biosensor platform for label-free detection of biomolecular interactions.

Field and temperature dependence of the small polaron hopping electrical conductivity in 1D disordered systems

We investigate the effect of the electric field and the temperature on the electrical conductivity of one-dimensional disordered systems due to phonon assisted hopping of small polarons. The microscopic transport mechanism is treated within the framework of the generalized molecular crystal model and the Kubo formula, while percolation theoretical arguments lead to analytical expressions for the macroscopic behavior of the electrical conductivity at high (multi-phonon assisted hopping) and low (few-phonon assisted hopping) temperatures under the influence of moderate electric fields. The theoretical results are successfully applied to recent experimental findings for a wide temperature range and from low up to moderate electric fields. Comparison is made with other theories.

Effects of the environment on the electric conductivity of double-stranded DNA molecules

We present a theoretical analysis of the effects of the environment on charge transport in double-stranded synthetic poly(G)-poly(C) DNA molecules attached to two ideal leads. Coupling of the DNA to the environment results in two effects: (i) localization of carrier functions due to static disorder and (ii) phonon-induced scattering of the carriers between the localized states, resulting in hopping conductivity. A nonlinear Pauli master equation for populations of localized states is used to describe the hopping transport and calculate the electric current as a function of the applied bias. We demonstrate that, although the electronic gap in the density of states shrinks as the disorder increases, the voltage gap in the I-V characteristics becomes wider. A simple physical explanation of this effect is provided.

Modulational instability of charge transport in the Peyrard-Bishop-Holstein model

We report on modulational instability (MI) on a DNA charge transfer model known as the Peyrard-Bishop-Holstein (PBH) model. In the continuum approximation, the system reduces to a modified Klein-Gordon-Schrödinger (mKGS) system through which linear stability analysis is performed. This model shows some possibilities for the MI region and the study is carried out for some values of the nearest-neighbor transfer integral. Numerical simulations are then performed, which confirm analytical predictions and give rise to localized structure formation. We show how the spreading of charge deeply depends on the value of the charge-lattice-vibrational coupling.

Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories

We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics (MD) simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD trajectories and thus encodes the influence of dynamical disorder arising from the environment (water, backbone, counterions) and from the internal base dynamics. We show that the correlated fluctuations of the base pair dynamics are crucial in determining the transport properties of the wire and that the effect of fluctuations can be quite different for sequences with low and high static disorders (differences in base ionization potentials). As a result, in structures with high static disorder as is the case of the studied Dickerson dodecamer, the weight of high-transmissive structures increases due to dynamical fluctuations and so does the calculated average transmission. Our analysis further supports the basic intuition of charge-transfer active conformations as proposed by Barton et al. [J. Am. Chem. Soc. 126, 11471 (2004)]. However, not DNA conformations with good stacking contacts leading to large interbase hopping values are necessarily the most important, but rather those where the average fluctuation of ionization potentials along the base stack is small. The reason behind this is that the ensemble of conformations leads to average electronic couplings, which are large enough for sufficient transmission. On the other hand, the alignment of onsite energies is the critical parameter which gates the charge transport.

Trapping and motion of polarons in weakly disordered DNA molecules

Polaron effects for charge migration in DNA molecules have been previously considered within the Peyrard-Bishop-Holstein model. When a uniform electric field is applied, the polaron moves asymptotically at a constant velocity, provided dissipative effects are taken into account, and then current flows through DNA. Disorder originating from interactions with a random environment of solute molecules and ions surrounding the DNA molecule could prevent charge migration due to the localization of the carrier wavefunction. We studied numerically the Peyrard-Bishop-Holstein model when the disordered DNA molecule is subjected to a uniform electric field. We found the threshold value of the electric field to observe polaron motion when disorder is present. We also calculated the fluctuations of the electric current and found that they provide valuable information about the polaron dynamics.

Charge transport through biomolecular wires in a solvent: bridging molecular dynamics and model Hamiltonian approaches

We present a hybrid method based on a combination of classical molecular dynamics simulations, quantum-chemical calculations, and a model Hamiltonian approach to describe charge transport through biomolecular wires with variable lengths in presence of a solvent. The core of our approach consists in a mapping of the biomolecular electronic structure, as obtained from density-functional based tight-binding calculations of molecular structures along molecular dynamics trajectories, onto a low-dimensional model Hamiltonian including the coupling to a dissipative bosonic environment. The latter encodes fluctuation effects arising from the solvent and from the molecular conformational dynamics. We apply this approach to the case of pG-pC and pA-pT DNA oligomers as paradigmatic cases and show that the DNA conformational fluctuations are essential in determining and supporting charge transport.

Heat conduction through a DNA-gold composite

This paper reports results from electrical and thermal conduction measurements carried out on the DNA-gold composite for which the overall conduction is shown to be dominated by the DNA rather than the discontinuous gold coatings. The electrical and thermal conductivities of the composite were about 14 S/cm and 150 W/(m K) at room temperature, respectively. The resulting value of 3.6 x 10(-4) W ohms/K(2) for the Lorentz number indicates that thermal transport in the DNA is phonon-dominated and that the molecular vibrations play a key role in both electrical and thermal conduction processes of DNA molecules.

Current-voltage-temperature characteristics of DNA origami

The temperature dependences of the current-voltage characteristics of a sample of triangular DNA origami deposited in a 100 nm gap between platinum electrodes are measured using a probe station. Below 240 K, the sample shows high impedance, similar to that of the substrate. Near room temperature the current shows exponential behavior with respect to the inverse of temperature. Sweep times of 1 s do not yield a steady state; however sweep times of 450 s for the bias voltage secure a steady state. The thermionic emission and hopping conduction models yield similar barriers of approximately 0.7 eV at low voltages. For high voltages, the hopping conduction mechanism yields a barrier of 0.9 eV and the thermionic emission yields 1.1 eV. The experimental data set suggests that the dominant conduction mechanism is hopping in the range 280-320 K. The results are consistent with theoretical and experimental estimates of the barrier for related molecules.

Direct simulation of electron transfer reactions in DNA radical cations

The electron transfer properties of DNA radical cations are important in DNA damage and repair processes. Fast long-range charge transfer has been demonstrated experimentally, but the subtle influences that experimental conditions as well as DNA sequences and geometries have on the details of electron transfer parameters are still poorly understood. In this work, we employ an atomistic QM/MM approach, based on a one-electron tight binding Hamiltonian and a classical molecular mechanics forcefield, to conduct nanosecond length MD simulations of electron holes in DNA oligomers. Multiple spontaneous electron transfer events were observed in 100 ns simulations with neighboring adenine or guanine bases. Marcus parameters of charge transfer could be extracted directly from the simulations. The reorganization energy lambda for hopping between neighboring bases was found to be ca. 25 kcal/mol and charge transfer rates of 4.1 x 10(9) s(-1) for AA hopping and 1.3 x 10(9) s(-1) for GG hopping were obtained.

Correlated small polaron hopping transport in 1D disordered systems at high temperatures: a possible charge transport mechanism in DNA

Based on the generalized molecular crystal model (GMCM) and theoretical percolation arguments we investigate small polaron hopping transport in 1D disordered systems at high temperatures. Correlation (cr) effects are taken into account. An analytical expression for the temperature dependence of the electrical conductivity, lnσ(h,cr)∼T(-1/2), is obtained. This result reproduces satisfactorily the experimental data reported for λ-DNA and for poly(dA)-poly(dT) DNA, considering DNA as a one-dimensional disordered molecular wire in which small polarons are the charge carriers. lnσ(h,cr) versus T(-1/2) plots permit the evaluation of the maximum hopping distance. The results indicate that correlation effects are probably responsible for large hopping distances in DNA samples.

Sequence dependent electron transport in wet DNA: ab initio and molecular dynamics studies

We combine molecular dynamics simulations and density functional theory to analyze the electrical structure and transmission probability in four different DNA sequences under physiological conditions. The conductance in these sequences is primarily controlled by interstrand and intrastrand coupling between low-energy guanine orbitals. Insertion of adenine-thymine base pairs between the guanine-cytosine rich domains acts as a tunneling barrier. Our theory explains recent length dependent conductance data for individual DNA molecules in water.

Modelling the effect of structure and base sequence on DNA molecular electronics

DNA is a material that has the potential to be used in nanoelectronic devices as an active component. However, the electronic properties of DNA responsible for its conducting behaviour remain controversial. Here we use a self-consistent quantum molecular dynamics method to study the effect of DNA structure and base sequence on the energy involved when electrons are added or removed from isolated molecules and the transfer of the injected charge along the molecular axis when an electric field is applied. Our results show that the addition or removal of an electron from DNA molecules is most exothermic for poly(dC)-poly(dG) in its B-form and poly(dA)-poly(dT) in its A-form, and least exothermic in its Z-form. Additionally, when an electric field is applied to a charged DNA molecule along its axis, there is electron transfer through the molecule, regardless of the number and sign of the injected charge, the molecular structure and the base sequence. Results from these simulations provide useful information that is hard to obtain from experiments and needs to be considered for further modelling aiming to improve charge transport efficiency in nanoelectronic devices based on DNA.

Water induced weakly bound electrons in DNA

We have studied the effect of humidity on the electronic properties of DNA base pairs. We found that the hydrogen links of the nucleobases with water molecules lead to a shift of the pi electron density from carbon atoms to nitrogen atoms and can change the symmetry of the wave function for some nucleobases. As a result, the orbital energies are shifted which leads to a decrease in the potential barrier for the hole transfer between the G-C and A-T pairs from 0.7 eV for the dehydrated case to 0.123 eV for the hydrated. More importantly, the pi electron density redistribution activated by hydration is enhanced by the intrastrand interactions. This leads to a modification of the nucleobase chemical structures from the covalent type to a resonance structure with separated charges, where some pi electrons are not locked up into the covalent bonds. Within the (G-C)(2) sequences, there is overlapping of the electronic clouds of such unlocked electrons belonging to the stacked guanines, that significantly increases the electron coupling between them to V(DA)=0.095 eV against the V(DA)=0.025 eV for the dehydrated case. Consequently, the charge transfer between two guanines within the (G-C)(2) sequences is increased by 250 times due to hydration. The presence of nonbonded electrons suppress the band gap up to approximately 3.0 eV, that allows us to consider DNA as a narrow band gap semiconductor.