PNA-DNA duplexes, triplexes, and quadruplexes are stabilized with trans-cyclopentane units

Peptide nucleic acids (PNAs) are non-natural nucleic acid mimics that bind to complementary DNA and RNA with high affinity and selectivity. PNA can bind to nucleic acids in a number of different ways. Currently, the formation of PNA-oligonucleotide duplex, triplex, and quadruplex structures have been reported. PNAs have been used in numerous biomedicial applications, but there are few strategies to predictably improve the binding properties of PNAs by backbone modification. We have been studying the benefits of incorporating (S,S)-trans-cyclopentane diamine units (tcyp) into the PNA backbone. In this Communication, we report the improvement in stability associated with tcyp incorporation into PNA-DNA duplexes, triplexes, and quadruplexes. The broad utility of this modification across multiple types of PNA structures is unique and should prove useful in the development of applications that rely on PNA.     

An asymptotic finite-deformation analysis of the elastostatic field near the tip of a crack

Summary This paper contains an asymptotic treatment, consistent with the fully nonlinear equilibrium theory of compressible elastic solids, of the stresses and deformations near the tip of a traction-free crack in a slab of all-around infinite extent under conditions of plane strain. The loading applied at infinity is taken to be one of uniform uniaxial tension at right angles to the faces of the crack. For the particular class of elastic materials considered the tensile stress in large homogeneous uni-axial extension is asymptotic to a continuously adjustable power of the corresponding principal stretch. The asymptotic analysis of the foregoing crack problem is reduced to a nonlinear eigenvalue problem, the solution of which is established in closed form, in terms of elementary functions and a transcendental integral of such functions. This solution involves two arbitrary constants, one of which governs the amplitude of the ensuing elastostatic field near the tip of the crack. A precise estimate of the amplitude parameter, valid at sufficiently small load intensities, is deduced with the aid of a known conservation law. The remaining arbitrary constant, which is left indeterminate by the present lowest-order asymptotic analysis, does not affect the dominant behavior of the field quantities of primary physical interest. II-lustrative numerical results, appropriate to both hardening and softening materials, are presented.

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Zusammenfassung Diese Arbeit betrifft die asymptotische Ermittelung, im Rahmen der nichtlinearen Elastizitätstheorie ebener Verformungen, von den Spannungen und Verschiebungen am Ende eines Schlitzes in einer allseitig unendlich ausgedehnten Scheibe. Die Scheibe ist im Unendlichen durch einen gleichförmigen Zug senkrecht zur Schlitzachse belastet. Die asymptotische Behandlung dieses Problems wird auf ein Eigenwertproblem zurückgeführt, dessen Lösung in geschlossener Form durch elementare Funktionen dargestellt wird. Die gefundene Lösung enthält zwei unbestimmte Konstanten von welchen eine die Amplitude der lokalen Feldsingularitäten bestimmt. Diese Konstante wird für kleine Belastungen streng abgeschätzt auf Grund eines Erhaltungssatzes und mit Hilfe der bekannten Lösung des linearisierten Schlitzproblems.

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The results communicated in this paper were obtained in the course of an investigation supported under Contract N00014-67-A-0094-0020 of the California Institute of Technology with the Office of Naval Research in Washington, D.C.     

Cellular responses to patterned poly(acrylic acid) brushes

We use patterned poly(acrylic acid) (PAA) polymer brushes to explore the effects of surface chemistry and topography on cell-surface interactions. Most past studies of surface topography effects on cell adhesion have focused on patterned feature sizes that are larger than the dimensions of a cell, and PAA brushes have been characterized as cell repellent. Here we report cell adhesion studies for RBL mast cells incubated on PAA brush surfaces patterned with a variety of different feature sizes. We find that when patterned at subcellular dimensions on silicon surfaces, PAA brushes that are 30 or 15 nm thick facilitate cell adhesion. This appears to be mediated by fibronectin, which is secreted by the cells, adsorbing to the brushes and then engaging cell-surface integrins. The result is detectable accumulation of plasma membrane within the brushes, and this involves cytoskeletal remodeling at the cell-surface interface. By decreasing brush thickness, we find that PAA can be 'tuned' to promote cell adhesion with down-modulated membrane accumulation. We exemplify the utility of patterned PAA brush arrays for spatially controlling the activation of cells by modifying brushes with ligands that specifically engage IgE bound to high-affinity receptors on mast cells.     

Topological conjugacy to given constant length substitution minimal systems

We find necessary and sufficient conditions for a symbolic dynamical system to be topologically conjugate to any given constant length substitution minimal system, thus extending the results in Coven et al. (2008) for the Morse and Toeplitz substitutions.     

Length/voltage phase diagram for a thin superconducting wire subjected to an applied voltage

A thin superconducting wire (bridge) subjected to a voltage gradient is studied via the time-dependent Ginzburg-Landau system under bridge geometry boundary conditions. Our numerical experiments reveal a rich array of phase slip center behavior, period-doubling, period-tripling and quasi-periodic solutions. We show that the parameter plane (L, V), where 2L =  wire length, V =  voltage, is partitioned into regimes, where the solutions exhibit different periodicity. In particular we find that when L is below a certain critical value, the system always evolves to a state that has the basic Josephson period P = 2π/V.     

Dark forces at the Tevatron

A simple explanation of the W+dijet excess recently reported by the CDF collaboration involves the introduction of a new gauge boson with sizable couplings to quarks, but with no or highly suppressed couplings to leptons. Anomaly-free theories which include such a leptophobic gauge boson must also include additional particle content, which may include a stable and otherwise viable candidate for dark matter. Based on the couplings and mass of the Z^′ required to generate the CDF excess, we predict such a dark matter candidate to possess an elastic scattering cross section with nucleons on the order of σ∼¹⁰−40 cm², providing a natural explanation for the signals reported by the CoGeNT and DAMA/LIBRA collaborations. In this light, CDF may be observing the gauge boson responsible for the force which mediates the interactions between the dark and visible matter of our universe.     

Quantum chemical study of mechanisms for oxidative dehydrogenation of propane on vanadium oxide

We have carried out a hybrid density functional study of mechanisms for oxidative dehydrogenation of propane on the (010) surface of V2O5. The surface was modeled using both vanadium oxide clusters and a periodic slab. We have investigated a Mars-van Krevelen mechanism that involves stepwise adsorption of the propane at an oxygen site followed by desorption of a water molecule and propene, and subsequent adsorption of an oxygen molecule to complete the catalytic cycle. The potential energy surface is found to have large barriers, which are lowered somewhat when the possibility of a triplet state is considered. The barriers for propane adsorption and propene elimination are 45-60 kcal/mol. The highest energy on the potential energy surface at the B3LYP/6-31G* level of theory is about 80 kcal/mol above the energy of the reactants and corresponds to formation of an oxygen vacancy after water elimination. Subsequent addition of an oxygen molecule to fill the vacancy is predicted to be energetically downhill. The reactions of propane at a bridging oxygen site and at a vanadyl site have similar energetics. The key results of the cluster calculations are confirmed by periodic calculations. Factors that may lower the barriers on the potential energy surface, including the interaction of vanadium oxide clusters with a support material and a concerted reaction with O2, are discussed.     

A linear ion trap mass spectrometer with versatile control and data acquisition for ion/ion reactions

A linear ion trap (LIT) with electrospray ionization (ESI) for top-down protein analysis has been constructed. An independent atmospheric sampling glow discharge ionization (ASGDI) source produces reagent ions for ion/ion reactions. The device is also meant to enable a wide variety of ion/ion reaction studies. To reduce the instrument's complexity and make it available for wide dissemination, only a few simple electronics components were custom built. The instrument functions as both a reaction vessel for gas-phase ion/ion reactions and a mass spectrometer using mass-selective axial ejection. Initial results demonstrate trapping efficiency of 70% to 90% and the ability to perform proton transfer reactions on intact protein ions, including dual polarity storage reactions, transmission mode reactions, and ion parking.     

Probing dynamic generation of hot-spots in self-assembled chains of gold nanorods by surface-enhanced Raman scattering

Further progress in the applications of self-assembled nanostructures critically depends on developing a fundamental understanding of the relation between the properties of nanoparticle ensembles and their time-dependent structural characteristics. Following dynamic generation of hot-spots in the self-assembled chains of gold nanorods, we established a direct correlation between ensemble-averaged surface-enhanced Raman scattering and extinction properties of the chains. Experimental results were supported with comprehensive finite-difference time-domain simulations. The established relationship between the structure of nanorod ensembles and their optical properties provides the basis for creating dynamic, solution-based, plasmonic platforms that can be utilized in applications ranging from sensing to nanoelectronics.     

Dissociation of different conformations of ubiquitin ions

The fragmentation pathways of different conformations of three charge states of ubiquitin ions are examined using ion mobility/collisional activation/time-of-flight techniques. Mass spectra for fragments for different conformers of a single charge state appear to be identical (within the experimental reproducibility). These results are consistent with a mechanism in which different conformers of each charge state rearrange to similar dissociation transition states prior to fragment formation.