Structure and Function Analysis of DNA Monolayers Created from Self-Assembling DNA-Dendron Conjugates.

Short sequences of DNA immobilized on gold surfaces can be used to capture an array of target molecules because of their high level of specificity. Depending on the nature of the target molecules, the proper density and distribution of the immobilized DNA molecules are fundamental to the quality of the sensor. With the aim to control the packing density and minimize the heterogeneity of the surfaces, DNA-dendron conjugate molecules were synthesized in solution and used to make self-assembled monolayers of single-stranded DNA surfaces on gold. The headgroups used were polyamido amine dendrons (cleaved cystamine core dendrimers) of generations two through five. The structural composition of these self-assembled monolayers was characterized using grazing angle Fourier-transform infrared and X-ray photoelectron spectroscopies. Surface plasmon resonance was used to measure surface densities of the probe monolayers and each monolayer's ability to capture fully complementary DNA strands from solution. The surface density of the probe monolayers was found to decrease with increasing dendron generation number, while the hybridization efficiency increased with increasing dendron generation number.

Origami Arrays as Substrates for the Determination of Reaction Kinetics Using High-Speed Atomic Force Microscopy.

DNA nanostructures (DN) are powerful platforms for the programmable assembly of nanomaterials. As applications for DN both as a structural material and as a support for functional biomolecular sensing systems develop, methods enabling the determination of reaction kinetics in real time become increasingly important. In this report, we present a study of the kinetics of streptavidin binding onto biotinylated DN constructs enabled by these planar structures. High-speed AFM was employed at a 2.5 frame/s rate to evaluate the kinetics and indicates that the binding fully saturates in less than 60 s. When the the data was fitted with an adsorption-limited kinetic model, a forward rate constant of 5.03 × 105 s-1 was found.

Thiolated dendrimers as multi-point binding headgroups for DNA immobilization on gold.

The synthesis of multithiolated DNA molecules that can be used to produce self-assembled monolayers of single-stranded DNA oligonucleotides on gold substrates is described. Generation 3 polyamidoamine (PAMAM) dendrimers were conjugated to DNA oligomers and functionalized with ~30 protected thiol groups. The protected thiol groups-thioacetate groups-allowed the dendrimer-DNA constructs to be stored in a buffer solution for at least 2 months before deprotection without any observable decrease in their ability to assemble into functional layers. The monolayers formed using these multithiolated DNA probe strands demonstrate target capture efficiencies comparable to those of analogous monolayers assembled with DNA functionalized with single thiol groups. A functional advantage of using dendrimer headgroups is the resistance to probe strand loss in prolonged exposure to buffer solutions at a high temperature (95 °C).

Utilization of myosin and actin bundles for the transport of molecular cargo.

The utilization of motor proteins for the movement and assembly of synthetic components is currently a goal of nanoengineering research. Application of the myosin actin motor system for nanotechnological uses has been hampered due to the low flexural rigidity of individual F-actin filaments. Here it is demonstrated how actin bundling can be used to affect the translational behavior of myosin-propelled filaments, transport molecules across a motor-patterned surface, and that the movement of bundled actin can be regulated photonically. These data suggest that actin bundling may significantly improve the applicability of the myosin motor for future nanotechnological applications.

Application of poly(amidoamine) dendrimers for use in bionanomotor systems.

The study and utilization of bionanomotors represents a rapid and progressing field of nanobiotechnology. Here, we demonstrate that poly(amidoamine) (PAMAM) dendrimers are capable of supporting heavy meromyosin dependent actin motility of similar quality to that observed using nitrocellulose, and that microcontact printing of PAMAM dendrimers can be exploited to produce tracks of active myosin motors leading to the restricted motion of actin filaments across a patterned surface. These data suggest that the use of dendrimer surfaces will increase the applicability of using protein biomolecular motors for nanotechnological applications.

Impedance measurements on a DNA junction.

1 microm double-stranded DNA molecules are immobilized between pairs of gold and pairs of platinum microelectrodes with gaps of 0.4 and 1 microm, respectively, and their electrical characteristics are determined under the application of constant and sinusoidal bias voltages. Due to their extremely high impedance for constant voltage bias, the samples of DNA are excellent insulators; however, their impedances show strong frequency dependence in the range of 10 Hz-7.5 MHz. Favorable response in the gold electrodes is attributed to the higher ability of DNA molecules to bridge the narrower gold electrode gaps in contrast to that in the wider platinum junctions.

Scattering, accommodation, and trapping of HCl in collisions with a hydroxylated self-assembled monolayer.

Time-of-flight molecular beam scattering techniques are used to explore the energy exchange, thermal accommodation, and residence time of HCl in collisions with an OH-terminated self-assembled monolayer. The monolayer, consisting of 16-mercapto-1-hexadecanol (HS(CH(2))(16)OH) self-assembled on gold, provides a well-characterized surface containing hydroxyl groups located at the gas-solid interface. Upon colliding with the hydroxylated surface, the gas-phase HCl is found to follow one of three pathways: direct impulsive scattering, thermal accommodation followed by prompt desorption, and temporary trapping through HO--- HCl hydrogen bond formation. For an incident energy of 85 kJ/mol, the HCl transfers the majority, >80%, of its translational energy to the surface. The extensive energy exchange facilitates thermalization, leading to very large accommodation probabilities on the surface. Under the experimental conditions used in this work, over 75% of the HCl approaches thermal equilibrium with the surface before desorption and, for a 6 kJ/mol HCl beam, nearly 100% of the molecules that recoil from the surface can be described by a thermal distribution at the temperature of the surface. For the molecules that reach thermal equilibrium with the surface prior to desorption, a significant fraction appear to form hydrogen bonds with surface hydroxyl groups. The adsorption energy, determined by measuring the HCl residence time as a function of surface temperature, is 24 +/- 2 kJ/mol.

Homologous, long-chain alkyl dendrons form homologous thin films on silver oxide surfaces.

As suggested by X-ray crystal structures, homologous, long-chain alkyl dendrons with three carboxyl groups form thin films on silver oxide surfaces, which give reflection-absorption infrared spectra that show a linear increase in intensities of methylene C-H stretching absorptions.

Plasma treatment of PDMS for applications of in vitro motility assays.

In vitro motility assays are readily used to simplify the complex environments within the cell and in muscle tissue. These assays have afforded considerable insight into the fundamentals of their underlying biophysics, interactions with cargo, intracellular regulation, and motor cooperation/competition. Extension of the standard in vitro motility assay into a more automated and cost-effective fluidic design while providing availability to the scientific community without expertise in lithographic fabrication is critical for the continued advancement of the field. In this work, we utilized a standard plasma cleaner to oxidize the widely prevalent material polydimethylsiloxane (PDMS) to create flow cells that could be used for in vitro motility assays. Our analysis indicated that a 40 min pre-treatment of the PDMS with plasma exposure resulted in optimal bundle motility. This finding was attributed to the condition at which the least amount of oxygen permeates the PDMS slab, enters the motility buffer, and oxidizes the motor proteins. Based on these findings, we developed a method for constructing microfluidic devices from glass and plasma-treated PDMS molds in which motility could be observed.

Experimental and theoretical studies of the effect of mass on the dynamics of gas/organic-surface energy transfer.

The effect of mass on gas/organic-surface energy transfer is explored via investigation of the scattering dynamics of rare gases (Ne, Ar, and Kr) from regular (CH3-terminated) and omega-fluorinated (CF3-terminated) alkanethiol self-assembled monolayers (SAMs) at 60 kJmol collision energy. Molecular-beam scattering experiments carried out in ultrahigh vacuum and molecular-dynamics simulations based on high-accuracy potentials are used to obtain the rare-gases' translational-energy distributions after collision with the SAMs. Simulations indicate that mass is the most important factor in determining the changes in the energy exchange dynamics for Ne, Ar, and Kr collisions on CH3- and CF3-terminated SAMs at 60 kJmol collision energy. Other factors, such as changes in the gas-surface potential and intrasurface interactions, play only a minor role in determining the differential dynamics behavior for the systems studied.

Dynamics of HCl collisions with hydroxyl- and methyl-terminated self-assembled monolayers.

Molecular beam scattering techniques are used to explore the energy exchange and thermal accommodation efficiencies of HCl in collisions with long-chain OH- and CH(3)-terminated self-assembled monolayers (SAMs) on gold. Upon colliding with the nonpolar methyl-terminated SAM, HCl (E(i) = 85 kJ/mol) is found to transfer the majority, 83%, of its translational energy to the surface. The extensive energy loss for HCl helps to bring the molecules into thermal equilibrium with the monolayer. Specifically, 72% of the HCl approaches thermal equilibrium prior to desorption. For the molecules that do not thermally accommodate, but scatter after an impulsive collision with the surface, the final translational energy is observed to be directly proportional to the surface temperature as the thermal surface energy and gas translational energy exchange during the collision. For the OH-terminated SAM, the impulsively scattered HCl escapes from the surface with slightly more average energy. The rigid nature of the OH-terminated SAM is due to the extended intra-monolayer hydrogen-bonding network that restricts some of the low-energy modes of the surface. However, despite the rigid nature of this system, the extent of thermal accommodation for HCl on these two surfaces is remarkably similar. It appears that the potential energy well between the impinging HCl and the polar surface groups is sufficient enough to trap HCl molecules that would otherwise scatter impulsively from this rigid SAM.

Theoretical study of the effect of surface density on the dynamics of Ar + alkanethiolate self-assembled monolayer collisions.

We present a classical-trajectory study of energy transfer in collisions of Ar atoms with alkanethiolate self-assembled monolayers (SAMs) of different densities. The density of the SAMs is varied by changing the distance between the alkanethiolate chains in the organic monolayers. Our calculations indicate that SAMs with smaller packing densities absorb more energy from the impinging Ar atoms, in agreement with recent molecular-beam scattering experiments. We find that energy transfer is enhanced by a decrease in the SAM density because (1) less dense SAMs increase the probability of multiple encounters between Ar and the SAM, (2) the vibrational frequencies of large-amplitude motions of the SAM chains decrease for less dense SAMs, which makes energy transfer more efficient in single-encounter collisions, and (3) increases in the distance between chains promote surface penetration of the Ar atom. Analysis of angular distributions reveals that the polar-angle distributions do not have a cosine shape in trapping-desorption processes involving penetration of the Ar atom into the alkanethiolate self-assembled monolayers. Instead, there is a preference for Ar atoms that penetrate the surface to desorb along the chain-tilt direction.

Packing density and structure effects on energy-transfer dynamics in argon collisions with organic monolayers.

A combined experimental and molecular-dynamics simulation study has been used to investigate energy-transfer dynamics of argon atoms when they collide with n-alkanethiols adsorbed to gold and silver substrates. These surfaces provide the opportunity to explore how surface structure and packing density of alkane chains affect energy transfer in gas-surface collisions while maintaining the chemical nature of the surface. The chains pack standing up with 12 degrees and 30 degrees tilt angles relative to the surface normal and number densities of 18.9 and 21.5 A(2)molecule on the silver and gold substrates, respectively. For 7-kJmol argon scattering, the two surfaces behave equivalently, fully thermalizing all impinging argon atoms. In contrast, these self-assembled monolayers (SAMs) are not equally efficient at absorbing the excess translational energy from high-energy, 35 and 80 kJmol, argon collisions. When high-energy argon atoms are scattered from a SAM on silver, the fraction of atoms that reach thermal equilibrium with the surface and the average energy transferred to the surface are lower than for analogous SAMs on gold. In the case of argon atoms with 80 kJmol of translational energy scattering from long-chain SAMs, 60% and 45% of the atoms detected have reached thermal equilibrium with the monolayers on gold and silver surfaces, respectively. The differences in the scattering characteristics are attributed to excitation efficiencies of different types of surface modes. The high packing density of alkyl chains on silver restricts certain low-energy degrees of freedom from absorbing energy as efficiently as the lower-density monolayers. In addition, molecular-dynamics simulations reveal that the extent to which argon penetrates into the monolayer is related to packing density. For argon atoms with 80-kJmol incident energy, we find 16% and 7% of the atoms penetrate below the terminal methyl groups of C(10) SAMs on gold and silver, respectively.