Colloidal interactions and self-assembly using DNA hybridization

The specific binding of complementary DNA strands has been suggested as an ideal method for directing the controlled self-assembly of microscopic objects. We report the first direct measurements of such DNA-induced interactions between colloidal microspheres, as well as the first colloidal crystals assembled using them. The interactions measured with our optical tweezer method can be modeled in detail by well-known statistical physics and chemistry, boding well for their application to directed self-assembly. The microspheres' binding dynamics, however, have a surprising power-law scaling that can significantly slow annealing and crystallization.     

Stacking interactions in denaturation of DNA fragments

A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time-dependent paths contributing to the partition function. The size of the paths ensemble, which measures the degree of cooperativity of the system, is computed versus temperature consistently with the model potential physical requirements. It is shown that the ensemble size strongly varies with the molecule backbone stiffness providing a quantitative relation between stacking and features of the melting transition. The latter is an overall smooth crossover which begins from the adenine-thymine-rich portions of the fragment. The harmonic stacking coupling shifts, along the T -axis, the occurrence of the multistep denaturation but it does not change the character of the crossover. The methods to compute the fractions of open base pairs versus temperature are discussed: by averaging the base pair displacements over the path ensemble, we find that such fractions signal the multisteps of the transition in good agreement with the indications provided by the specific heat plots.     

Wormlike chain theory and bending of short DNA

The probability distributions for bending angles in double helical DNA obtained in all-atom molecular dynamics simulations are compared with theoretical predictions. The computed distributions remarkably agree with the wormlike chain theory and qualitatively differ from predictions of the subelastic chain model. The computed data exhibit only small anomalies in the apparent flexibility of short DNA and cannot account for the recently reported AFM data. It is possible that the current atomistic DNA models miss some essential mechanisms of DNA bending on intermediate length scales. Analysis of bent DNA structures reveal, however, that the bending motion is structurally heterogeneous and directionally anisotropic on the length scales where the experimental anomalies were detected. These effects are essential for interpretation of the experimental data and they also can be responsible for the apparent discrepancy.     

The kinetics of vacancy annihilation and short range order formation in Ni 11.4 at % Cr

In Ni-Cr alloys annealing after quenching from high temperatures leads to an increase of electrical resistivity which is attributed to a short range order state often denoted as K-state. Here the kinetics of the formation of the K-state in a Ni 10% Cr alloy is investigated by resistivity measurements for different quenching and annealing temperatures. The measurements are analyzed by an extended Schulze-Lücke method [22] which assumes that the rate of resistivity change is proportional to the vacancy concentration and that this rate as well as the rate of vacancy annihilation is described by a chemical rate equation.This analysis allowed a quantitative determination of the parameters determining the kinetics of short range order formation under different vacancy concentrations as well as the kinetics of annealing out of the quenched-in surplus vacancies. Among other quantities this treatment yielded the activation energies for vacancy formation H_F = 1.16 eV, for vacancy migration H_M = 1.56 eV and, as an independent cross check, for self diffusion H_D = 2.73 eV in good agreement with H_F + H_M = 2.72 eV.     

Anisotropic Brownian motion in ordered phases of DNA fragments

Using Fluorescence Recovery After Photobleaching, we investigate the Brownian motion of DNA rod-like fragments in two distinct anisotropic phases with a local nematic symmetry. The height of the measurement volume ensures the averaging of the anisotropy of the in-plane diffusive motion parallel or perpendicular to the local nematic director in aligned domains. Still, as shown in using a model specifically designed to handle such a situation and predicting a non-Gaussian shape for the bleached spot as fluorescence recovery proceeds, the two distinct diffusion coefficients of the DNA particles can be retrieved from data analysis. In the first system investigated (a ternary DNA-lipid lamellar complex), the magnitude and anisotropy of the diffusion coefficient of the DNA fragments confined by the lipid bilayers are obtained for the first time. In the second, binary DNA-solvent system, the magnitude of the diffusion coefficient is found to decrease markedly as DNA concentration is increased from isotropic to cholesteric phase. In addition, the diffusion coefficient anisotropy measured within cholesteric domains in the phase coexistence region increases with concentration, and eventually reaches a high value in the cholesteric phase.     

Direct immobilization and hybridization of DNA on group III nitride semiconductors

A key concern for group III-nitride high electron mobility transistor (HEMT) biosensors is the anchoring of specific capture molecules onto the gate surface. To this end, a direct immobilization strategy was developed to attach single-stranded DNA (ssDNA) to AlGaN surfaces using simple printing techniques without the need for cross-linking agents or complex surface pre-functionalization procedures. Immobilized DNA molecules were stably attached to the AlGaN surfaces and were able to withstand a range of pH and ionic strength conditions. The biological activity of surface-immobilized probe DNA was also retained, as demonstrated by sequence-specific hybridization experiments. Probe hybridization with target ssDNA could be detected by PicoGreen fluorescent dye labeling with a minimum detection limit of 2 nM. These experiments demonstrate a simple and effective immobilization approach for attaching nucleic acids to AlGaN surfaces which can further be used for the development of HEMT-based DNA biosensors.     

Low cost optical detection of DNA hybridization on biochips

The detection of DNA hybridization can be either complicated or require expensive devices. Some methods use a fluorescence signal to investigate hybridization. Here, we present an optical probe based on optical fibers both for illumination and for fluorescence collection. The detection is made with a microspectrophotometer and the signal is then treated with a PC. We also developed the DNA biochips (glass plate with a gold layer functionalized with target DNA) as well as a dedicated microtank which maintains a constant flow of probe DNA over the target one. Finally, the detection of hybridization with this simple and versatile system is presented.     

Unzipping kinetics of double-stranded DNA in a nanopore

We studied the unzipping of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. Polymerase chain reaction analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip each molecule was inferred from the ionic current signature of DNA traversal. The distribution of times to unzip under various experimental conditions fit a simple kinetic model. Using this model, we estimated the enthalpy barriers to unzipping and the effective charge of a nucleotide in the pore, which was considerably smaller than previously assumed.     

Equilibrium establishment kinetics for a heavy component in short thermionic discharges

The effect of the heavy component balance in a short Knudsen-type thermionic discharge initiated in cesium vapor is studied. Detailed measurements of the plasma parameters at the instant of discharge initiation and at switching from one quasi-stationary regime to another make it possible to elucidate the temporal hierarchy of processes responsible for the heavy component balance: ionization of atoms in the discharge gap up to an ultimate degree of plasma ionization, establishment of heavy particle-electrode equilibrium, and establishment of heavy particle-buffer volume equilibrium in the discharge gap (the last process is the slowest).     

Immobilization/hybridization of amino-modified DNA on plasma-polymerized allyl chloride

The present work describes the fabrication and characterization of chloride-derivatized polymer coatings prepared by continuous wave (cw) plasma polymerization as adhesion layers in DNA immobilization/hybridization. The stability of plasma-polymerized allyl chloride (ppAC) in H₂O was characterized by variation of the thickness of polymer films and its wettability was examined by water contact angle technique. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) were used to study polymer matrix properties and oligonucleotide/DNA binding interaction. With the same carrier gas rate and process pressure, plasma polymers deposited at different input powers show various comparable immobilization properties; nevertheless, low input power plasma-polymerized films gives a lower sensitivity toward DNA binding than that from high input power plasma-deposited films. The following DNA immobilization on chloride-functionalized surfaces was found dependence on the macromolecular architecture of the plasma films. The hybridization between probe DNA and total mismatch target DNA shows no non-specific adsorption between target and ppAC.     

Thermodynamics of RNA/DNA hybridization in high-density oligonucleotide microarrays

We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high-density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity vs. the hybridization free energy of RNA/DNA duplexes in solution, for perfect matching and mismatching probes. Both values tend to align on a single master curve in good agreement with Langmuir adsorption theory, provided one takes into account the decrease of the effective target concentration due to target–target hybridization in solution. We give an example of a deviation from the expected thermodynamical behavior for the probe set 1091_at due to annotation problems, i.e., the surface-bound probe is not the exact complement of the target RNA sequence, because of errors present in public databases at the time when the array was designed. We show that the parametrization of the experimental data with RNA/DNA free energy improves the quality of the fits and enhances the stability of the fitting parameters compared to previous studies.     

Fluorescence quenching kinetics in short polymer chains: Dependence on chain length

Monte Carlo simulations of chain conformations and the diffusion equation were used to analyze the fluorescence kinetics of short polymer chains labeled with a probe and a quencher at opposite ends. In simulations, three chain models were considered: an ideal chain (without volume interactions); a self-avoiding chain taking into account the exclusive volume effect; and a self-avoiding chain with limited flexibility between nearest segments. For each model, end-to-end distance distribution functions were obtained, which were different from Gaussian ones. The distribution functions were used in a diffusion equation to simulate the fluorescence kinetics of the probe affected by intramolecular end-to-end collisions of short chains. The kinetics has been numerically calculated for a representative experimental system in a nonviscous solution. The simulated time-resolved fluorescence decays were monoexponential except at very short times (<2 ns). Diffusion coefficients were calculated for different chain models and different chain lengths. The experimental data could be reproduced by assuming systematically smaller end-to-end diffusion coefficients for the shorter chains.     

Temperature dependence of transport behavior of a short DNA molecule

DNA molecules may work as novel devices due to their interesting electronic transport properties. We here propose a theoretical method to deal with the temperature dependence of the transport behavior of a short DNA molecule, taking into account Coulomb interaction of electrons and the coupling between electrons and the two-level system in the DNA molecule. The nonlinear current-voltage curves are derived by using the Landauer formulae. We find that the voltage gap of the current-voltage curves is sensitive to the parameters of the two-level system. We also find that Coulomb blockade peaks can be controlled by varying the temperature, which relates to particular features of the DNA molecule.     

The kinetic energy of fission fragments

The Coulomb energy is calculated for the nucleus in the process of fission (in the general case asymmetrical) into two spherical fragments and for ellipsoidal deformations. In the first case the calculation has been done on an M-20 electronic computer. Conclusions are drawn on the form of the nucleus in symmetrical fission at the moment of fragmentation and its effect on the kinetic energy of the fragments.We wish to express our thanks to Yu. Volkov for making the numerical calculations.     

Dorsal horn-enriched genes identified by DNA microarray, in situ hybridization and immunohistochemistry

Background  

Neurons in the dorsal spinal cord play important roles in nociception and pain. These neurons receive input from peripheral sensory neurons and then transmit the signals to the brain, as well as receive and integrate descending control signals from the brain. Many molecules important for pain transmission have been demonstrated to be localized to the dorsal horn of the spinal cord. Further understanding of the molecular interactions and signaling pathways in the dorsal horn neurons will require a better knowledge of the molecular neuroanatomy in the dorsal spinal cord.     

Localized single-stranded bubble mechanism for cyclization of short double helix DNA

Recent experiments indicate that double-stranded DNA molecules of approximately 100 base pairs in length have a probability of cyclization which is up to 10(5) times larger than that expected based on the known bending modulus of the double-helix. We argue that for short molecules, the formation of a few base pairs of single-stranded DNA can provide a "flexible hinge" that facilitates loop formation. A detailed calculation shows that this mechanism explains the experimental data.