Light-induced surface wettability of a tethered DNA base

We show that the DNA base thymine and other uracil derivatives, when alkylated with a hydrocarbon chain and assembled at a gold interface, dimerize when subjected to UV irradiation. The process is robust and reversible and is accompanied by a substantial decrease in wettability as well as a marked decrease in acidity constant when the dimer is formed. There is a concerted molecular reorientation that accompanies photodimerization, with the dimer displaying a marked affinity for the gold surface. The spatial requirements for this reorganization are satisfied during dimerization by the reduction in intermolecular distance that occurs when the cyclobutane ring is formed between adjacent bases. The structural changes observed here for a tethered DNA base provide a direct route for exploring reactions, in two dimensions, that are of central interest in biology.     

Hydrothermal syntheses and single crystal structural characterization of M(H2O)6(OPTA)2 [M = Co(II), Ni(II), Zn(II); OPTA = 1-oxopyridinium-2-thioacetato]

A new class of compounds of the family M(H₂O)₆(OPTA)₂ (where M = Co(II), Ni(II), and Zn(II); OPTA = 1-oxopyridinium-2-thioacetato) was prepared from the appropriate metal acetates, 1-oxo-pyridinium-2-thioacetic acid (OPTAH), and potassium hydroxide in hydrothermal media and structurally characterized. The structure is constructed from M(H₂O)₆ ²⁺ and two anions of OPTAH (C₇H₆NO₃S) linked through hydrogen bonding into an extended network.     

Mechanistic Insights into the Oxidative Coupling of N‐Heterocyclic Carbenes within the Coordination Sphere of Copper Complexes

The behavior of N‐heterocyclic carbene (NHC) ligands in organometallic chemistry is hugely important for catalysis, due to the effect of these ligands on catalytic pathways and their involvement in catalyst decomposition. In this report, a combined experimental and computational study is presented, which provides mechanistic understanding of the unprecedented oxidative coupling of NHCs at Cu. The presence of Cu^I–, Cu^II–, and Cu^III–NHC complexes during the process is postulated, with the unusual C_carbene–C_carbene oxidative coupling reaction occurring under extremely mild reaction conditions. This process may represent a novel pathway for the decomposition of Cu–NHC complexes.     

DNAzyme‐Mediated Genetically Encoded Sensors for Ratiometric Imaging of Metal Ions in Living Cells

Genetically encoded fluorescent proteins (FPs) have been used for metal ion detection. However, their applications are restricted to a limited number of metal ions owing to the lack of available metal‐binding proteins or peptides that can be fused to FPs and the difficulty in transforming the binding of metal ions into a change of fluorescent signal. We report herein the use of Mg²⁺‐specific 10–23 or Zn²⁺‐specific 8–17 RNA‐cleaving DNAzymes to regulate the expression of FPs as a new class of ratiometric fluorescent sensors for metal ions. Specifically, we demonstrate the use of DNAzymes to suppress the expression of Clover2, a variant of the green FP (GFP), by cleaving the mRNA of Clover2, while the expression of Ruby2, a mutant of the red FP (RFP), is not affected. The Mg²⁺ or Zn²⁺ in HeLa cells can be detected using both confocal imaging and flow cytometry. Since a wide variety of metal‐specific DNAzymes can be obtained, this method can likely be applied to imaging many other metal ions, expanding the range of the current genetically encoded fluorescent protein‐based sensors.     

Proton-detected solid-state NMR reveals intramembrane polar networks in a seven-helical transmembrane protein proteorhodopsin

We used high-resolution proton-detected multidimensional NMR to study the solvent-exposed parts of a seven-helical integral membrane proton pump, proteorhodopsin (PR). PR samples were prepared by growing the apoprotein on fully deuterated medium and reintroducing protons to solvent-accessible sites through exchange with protonated buffer. This preparation leads to NMR spectra with proton resolution down to ca. 0.2 ppm at fast spinning (28 kHz) in a protein back-exchanged at a level of 40%. Novel three-dimensional proton-detected chemical shift correlation spectroscopy allowed for the identification and resonance assignment of the solvent-exposed parts of the protein. Most of the observed residues are located at the membrane interface, but there are notable exceptions, particularly in helix G, where most of the residues are susceptible to H/D exchange. This helix contains Schiff base-forming Lys231, and many conserved polar residues in the extracellular half, such as Asn220, Tyr223, Asn224, Asp227, and Asn230. We proposed earlier that high mobility of the F-G loop may transiently expose a hydrophilic cavity in the extracellular half of the protein, similar to the one found in xanthorhodopsin. Solvent accessibility of helix G is in line with this hypothesis, implying that such a cavity may be a part of the proton-conducting pathway lined by this helix.     

Conductance switching in diarylethenes bridging carbon nanotubes

The recently reported photoswitching of diarylethene derivative molecules bridging carbon nanotube (CNT) contacts is theoretically analyzed. The short lifetime of the lowest unoccupied molecular orbital (LUMO) indicates that neither the open nor closed form of the molecule can be photoexcited into a charge-neutral excited state for any appreciable length of time preventing photochromic ring opening. Analysis of the highest occupied molecular orbital (HOMO) and LUMO lifetimes also suggests that photoexcitation results in oxidation of the molecules. This either reduces the quantum yield of photochromic ring closing, or it gives rise to the possibility of oxidative ring closing. Analysis of the resistance values and energy levels indicates that the HOMO energy levels of the closed isomers relevant for transport must lie within a few k(B)T of the CNT Fermi level. For armchair contacts, the change in resistance with isomer or substituent group is the result of shifts in the energy level of the molecular HOMO. The coupling of the molecular HOMO to the CNT contacts is insensitive to the isomer type or substituent group. For zigzag CNTs, the conductance is dominated by surface states at the Fermi level on the cut ends of the CNTs so that the conductance is relatively insensitive to the isomer type, and the conductance switching ratio is low. Multiple bridging molecules can interact coherently, resulting in energy splitting, shifting, and interference that cause a nonlinear change in conductance with increasing numbers of molecules. Instead of a factor of 3 increase in conductance expected for three independent channels, a factor of 10(3) increase in conductance is obtained for three bridging molecules.     

Charge state dependent energy deposition by ion impact

We report on a measurement of craters in thin dielectric films formed by Xe(Q+) (26 ≤ Q ≤ 44) projectiles. Tunnel junction devices with ion-irradiated barriers were used to amplify the effect of charge-dependent cratering through the exponential dependence of tunneling conductance on barrier thickness. Electrical conductance of a crater σ(c)(Q) increased by 4 orders of magnitude (7.9 × 10(-4) μS to 6.1 μS) as Q increased, corresponding to crater depths ranging from 2 to 11 ?. By employing a heated spike model, we determine that the energy required to produce the craters spans from 8 to 25 keV over the investigated charge states. Considering energy from preequilibrium nuclear and electronic stopping as well as neutralization, we find that at least (27 ± 2)% of available projectile neutralization energy is deposited into the thin film during impact.     

Robust analysis of multiplexed SERS microscopy of Ag nanocubes using an alternating minimization algorithm

To drive the application of surface‐enhanced Raman spectroscopy (SERS) mapping in ex vivo diagnostic imaging and non‐biological material characterization, we have designed a robust and accurate multiplex spectral fitting method using an alternating minimization algorithm to extract individual constituent Raman spectra with very small overall fitting error (as low as 2%). For each mixed Raman signal, constituent spectra and mixture coefficients were estimated jointly based on reference spectra that were measured in the lab. Our method is based on a Poisson model to reflect the photon counting nature of Raman signals and includes the nonlinear noise in the measured data, making our method robust against data containing relatively large random noise. In our method, we minimized a cost function consisting of two terms: (1) the overall fitting error between the measured and modeled spectra and (2) the sum of the individual error between each reference spectrum and its corresponding constituent. This method inherently guarantees that the estimates will approach the global minimum with monotonic convergence. The accuracy of our method was validated by applying it to a SERS spectral fitting problem and comparing our results to those from existing methods. Copyright © 2013 John Wiley & Sons, Ltd.     

Interface Stability of Compressible Fluid Displacements in Porous Media

Transport in Porous Media - We use linear stability theory to investigate the effect of fluid compressibility on interface stability during a dissipative displacement (Darcy flow). We find that...     

Fabrication Process Comparison and Dynamics Evaluation of Electrothermal Actuators for a Prototype MEMS Safe and Arming Devices

Electrothermal actuators fabricated using the Polysilicon Multi-User MEMS Process (PolyMUMPs) and the Sandia Ultra-Planar, Multi-Level MEMS Technology 5 (SUMMiT V) have been investigated for use in integrated microelectromechanical systems (MEMS) safe and arming devices. The fabricated electrothermal actuators have been dynamically tested to determine and compare the responses of devices from both processes. Furthermore, the integration of these devices into a safe and arming device were tested and investigated for each process. Initial results indicate that the SUMMiT devices provide the most optimum results based on consistency of operation and reliability.